Science.gov

Sample records for coarse aggregates

  1. Chemical-mineralogical characterisation of coarse recycled concrete aggregate

    SciTech Connect

    Limbachiya, M.C. . E-mail: m.limbachiya@kingston.ac.uk; Marrocchino, E.; Koulouris, A.

    2007-07-01

    The construction industry is now putting greater emphasis than ever before on increasing recycling and promoting more sustainable waste management practices. In keeping with this approach, many sectors of the industry have actively sought to encourage the use of recycled concrete aggregate (RCA) as an alternative to primary aggregates in concrete production. The results of a laboratory experimental programme aimed at establishing chemical and mineralogical characteristics of coarse RCA and its likely influence on concrete performance are reported in this paper. Commercially produced coarse RCA and natural aggregates (16-4 mm size fraction) were tested. Results of X-ray fluorescence (XRF) analyses showed that original source of RCA had a negligible effect on the major elements and a comparable chemical composition between recycled and natural aggregates. X-ray diffraction (XRD) analyses results indicated the presence of calcite, portlandite and minor peaks of muscovite/illite in recycled aggregates, although they were directly proportioned to their original composition. The influence of 30%, 50%, and 100% coarse RCA on the chemical composition of equal design strength concrete has been established, and its suitability for use in a concrete application has been assessed. In this work, coarse RCA was used as a direct replacement for natural gravel in concrete production. Test results indicated that up to 30% coarse RCA had no effect on the main three oxides (SiO{sub 2}, Al{sub 2}O{sub 3} and CaO) of concrete, but thereafter there was a marginal decrease in SiO{sub 2} and increase in Al{sub 2}O{sub 3} and CaO contents with increase in RCA content in the mix, reflecting the original constituent's composition.

  2. Ceramic ware waste as coarse aggregate for structural concrete production.

    PubMed

    García-González, Julia; Rodríguez-Robles, Desirée; Juan-Valdés, Andrés; Morán-Del Pozo, Julia M; Guerra-Romero, M Ignacio

    2015-01-01

    The manufacture of any kind of product inevitably entails the production of waste. The quantity of waste generated by the ceramic industry, a very important sector in Spain, is between 5% and 8% of the final output and it is therefore necessary to find an effective waste recovery method. The aim of the study reported in the present article was to seek a sustainable means of managing waste from the ceramic industry through the incorporation of this type of waste in the total replacement of conventional aggregate (gravel) used in structural concrete. Having verified that the recycled ceramic aggregates met all the technical requirements imposed by current Spanish legislation, established in the Code on Structural Concrete (EHE-08), then it is prepared a control concrete mix and the recycled concrete mix using 100% recycled ceramic aggregate instead of coarse natural aggregate. The concretes obtained were subjected to the appropriate tests in order to conduct a comparison of their mechanical properties. The results show that the concretes made using ceramic sanitary ware aggregate possessed the same mechanical properties as those made with conventional aggregate. It is therefore possible to conclude that the reuse of recycled ceramic aggregate to produce recycled concrete is a feasible alternative for the sustainable management of this waste. PMID:25188783

  3. Properties of Concrete with Tire Derived Aggregate Partially Replacing Coarse Aggregates

    PubMed Central

    Siringi, Gideon; Abolmaali, Ali; Aswath, Pranesh B.

    2015-01-01

    Tire derived aggregate (TDA) has been proposed as a possible lightweight replacement for mineral aggregate in concrete. The role played by the amount of TDA replacing coarse aggregate as well as different treatment and additives in concrete on its properties is examined. Conventional concrete (without TDA) and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, splitting tensile strength based on ASTM C496, modulus of rupture (flexural strength) based on ASTM C78, and bond stress based on ASTM C234. Results indicate that while replacement of coarse aggregates with TDA results in reduction in strength, it may be mitigated with addition of silica fume to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product while utilizing recycled TDA. PMID:26161440

  4. Properties of Concrete with Tire Derived Aggregate Partially Replacing Coarse Aggregates.

    PubMed

    Siringi, Gideon; Abolmaali, Ali; Aswath, Pranesh B

    2015-01-01

    Tire derived aggregate (TDA) has been proposed as a possible lightweight replacement for mineral aggregate in concrete. The role played by the amount of TDA replacing coarse aggregate as well as different treatment and additives in concrete on its properties is examined. Conventional concrete (without TDA) and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, splitting tensile strength based on ASTM C496, modulus of rupture (flexural strength) based on ASTM C78, and bond stress based on ASTM C234. Results indicate that while replacement of coarse aggregates with TDA results in reduction in strength, it may be mitigated with addition of silica fume to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product while utilizing recycled TDA. PMID:26161440

  5. Effects of Elevated Temperature on Concrete with Recycled Coarse Aggregates

    NASA Astrophysics Data System (ADS)

    Salau, M. A.; Oseafiana, O. J.; Oyegoke, T. O.

    2015-11-01

    This paper discusses the effects of heating temperatures of 200°C, 400°C and 600°C each for 2 hours at a heating rate of 2.5°C/min on concrete with the content of Natural Coarse Aggregates (NCA) partially replaced with Recycled Coarse Aggregates (RCA), obtained from demolished building in the ratio of 0%, 15% and 30%.There was an initial drop in strength from 100°C to 200°C which is suspected to be due to the relatively weak interfacial bond between the RCA and the hardened paste within the concrete matrix;a gradual increase in strength continued from 200°C to 450°C and steady drop occurred again as it approached 600°C.With replacement proportion of 0%, 15% and 30% of NCA and exposure to peak temperature of 600°C, a relative concrete strength of 23.6MPa, 25.3MPa and 22.2MPa respectively can be achieved for 28 days curing age. Furthermore, RAC with 15% NCA replacement when exposed to optimum temperature of 450°C yielded high compressive strength comparable to that of control specimen (normal concrete). In addition, for all concrete samples only slight surface hairline cracks were noticed as the temperature approached 400°C. Thus, the RAC demonstrated behavior just like normal concrete and may be considered fit for structural use.

  6. Behaviour of Recycled Coarse Aggregate Concrete: Age and Successive Recycling

    NASA Astrophysics Data System (ADS)

    Sahoo, Kirtikanta; Pathappilly, Robin Davis; Sarkar, Pradip

    2016-05-01

    Recycled Coarse Aggregate (RCA) concrete construction technique can be called as `green concrete', as it minimizes the environmental hazard of the concrete waste disposal. Indian standard recommends target mean compressive strength of the conventional concrete in terms of water cement ratio (w/c). The present work is an attempt to study the behaviour of RCA concrete from two samples of parent concrete having different age group with regard to the relationship of compressive strength with water cement ratios. Number of recycling may influence the mechanical properties of RCA concrete. The influence of age and successive recycling on the properties such as capillary water absorption, drying shrinkage strain, air content, flexural strength and tensile splitting strength of the RCA concrete are examined. The relationship between compressive strength at different w/c ratios obtained experimentally is investigated for the two parameters such as age of parent concrete and successive recycling. The recycled concrete using older recycled aggregate shows poor quality. While the compressive strength reduces with successive recycling gradually, the capillary water absorption increases abruptly, which leads to the conclusion that further recycling may not be advisable.

  7. Behaviour of Recycled Coarse Aggregate Concrete: Age and Successive Recycling

    NASA Astrophysics Data System (ADS)

    Sahoo, Kirtikanta; Pathappilly, Robin Davis; Sarkar, Pradip

    2016-06-01

    Recycled Coarse Aggregate (RCA) concrete construction technique can be called as `green concrete', as it minimizes the environmental hazard of the concrete waste disposal. Indian standard recommends target mean compressive strength of the conventional concrete in terms of water cement ratio ( w/ c). The present work is an attempt to study the behaviour of RCA concrete from two samples of parent concrete having different age group with regard to the relationship of compressive strength with water cement ratios. Number of recycling may influence the mechanical properties of RCA concrete. The influence of age and successive recycling on the properties such as capillary water absorption, drying shrinkage strain, air content, flexural strength and tensile splitting strength of the RCA concrete are examined. The relationship between compressive strength at different w/ c ratios obtained experimentally is investigated for the two parameters such as age of parent concrete and successive recycling. The recycled concrete using older recycled aggregate shows poor quality. While the compressive strength reduces with successive recycling gradually, the capillary water absorption increases abruptly, which leads to the conclusion that further recycling may not be advisable.

  8. STUDY ON THE EVALUATION FOR DRYING SHRINKAGE PROPERTIES OF COARSE AGGREGATE

    NASA Astrophysics Data System (ADS)

    Yamada, Hiroshi; Katahira, Hiroshi; Watanabe, Hiroshi

    Drying shrinkage of coarse aggregate is one of principal indexes to evaluate drying shrinkage of concrete. However, testing of drying shrinkage of a coarse aggregate particle has not been commonly conducted. We carried out measurement of drying shrinkage of a coarse aggregate particle using wire strain gauges and discussed the variation in the measurement. We found that variation among particles in drying shrinkage strain of coarse aggregate is intrinsic and much bigger than test result due to the simplified unidirectional strain measurement under the assumption of ignoring multi-axial strain field. Strong relationship between the mean value of drying shrinkage strain of coarse aggregate and drying shrinkage strain of concrete prism specimens was observed, which indicates that measured drying shrinkage strain of aggregate particles intrinsically contains large variation, however the mean value is an effective index to estimate drying shrinkage of concrete.

  9. Generic Coarse-Grained Model for Protein Folding and Aggregation

    NASA Astrophysics Data System (ADS)

    Bereau, Tristan; Deserno, Markus

    2009-03-01

    The complexity involved in protein structure is not only due to the rich variety of amino acids, but also the inherent weak interactions, comparable to thermal energy, and important cooperative phenomena. This presents a challenge in atomistic simulations, as it is associated with high-dimensionality and ruggedness of the energy landscape as well as long equilibration times. We have recently developed a coarse-grained (CG) implicit solvent peptide model which has been designed to reproduce key consequences of the abovementioned weak interactions. Its intermediate level of resolution, four beads per amino acid, allows for accurate sampling of local conformations by designing a force field that relies on simple interactions. A realistic ratio of α-helix to β-sheet content is achieved by mimicking a nearest-neighbor dipole interaction. We tune the model in order to fold helical proteins while systematically comparing the structure with NMR data. Very good agreement is achieved for proteins that have simple tertiary structures. We further probe the effects of cooperativity between amino acids by looking at peptide aggregation, where hydrophobic peptide fragments cooperatively form large-scale β-sheet structures. The model is able to reproduce features from atomistic simulations on a qualitative basis.

  10. Three-dimensional shape analysis of coarse aggregates: New techniques for and preliminary results on several different coarse aggregates and reference rocks

    SciTech Connect

    Erdogan, S.T.; Quiroga, P.N.; Fowler, D.W.; Saleh, H.A.; Livingston, R.A.; Garboczi, E.J. . E-mail: edward.garboczi@nist.gov; Ketcham, P.M.; Hagedorn, J.G.; Satterfield, S.G.

    2006-09-15

    The shape of aggregates used in concrete is an important parameter that helps determine many concrete properties, especially the rheology of fresh concrete and early-age mechanical properties. This paper discusses the sample preparation and image analysis techniques necessary for obtaining an aggregate particle image in 3-D, using X-ray computed tomography, which is then suitable for spherical harmonic analysis. The shapes of three reference rocks are analyzed for uncertainty determination via direct comparison to the geometry of their reconstructed images. A Virtual Reality Modeling Language technique is demonstrated that can give quick and accurate 3-D views of aggregates. Shape data on several different kinds of coarse aggregates are compared and used to illustrate potential mathematical shape analyses made possible by the spherical harmonic information.

  11. Effect of Different Coarse Aggregate Sizes on the Strength Characteristics of Laterized Concrete

    NASA Astrophysics Data System (ADS)

    Salau, M. A.; Busari, A. O.

    2015-11-01

    The high cost of conventional concrete materials is a major factor affecting housing delivery in developing countries such as Nigeria. Since Nigeria is blessed with abundant locally available materials like laterite, researchers have conducted comprehensive studies on the use of laterite to replace river sand partially or fully in the concrete. However, the works did not consider the optimum use of coarse aggregate to possibly improve the strength of the laterized concrete, since it is normally lower than that of normal concrete. The results of the tests showed that workability, density and compressive strength at constant water-cement ratio increase with the increase in the coarse aggregate particle size and also with curing age. As the percentage of laterite increases, there was a reduction in all these characteristics even with the particle size of coarse aggregate reduction due to loss from the aggregate-paste interface zone. Also, when sand was replaced by 25% of laterite, the 19.5mm and 12.5mm coarse aggregate particle sizes gave satisfactory results in terms of workability and compressive strength respectively at 28 days of curing age, compared to normal concrete. However, in case of 50% up to 100% laterite contents, the workability and compressive strength values were very low.

  12. Time-dependent behaviour of high performance concrete: influence of coarse aggregate characteristics

    NASA Astrophysics Data System (ADS)

    Makani, A.; Vidal, T.; Pons, G.; Escadeillas, G.

    2010-06-01

    This paper examines the influence of coarse aggregate characteristics on the time-dependent deformations of High Performances Concretes (HPC). Four concretes made using the same cement paste but incorporating different types of aggregate (rolled siliceous gravel, crushed granite, crushed limestone and crushed siliceous gravels) were studied in order to investigate the effect of aggregate properties on the compressive strength, modulus of elasticity, shrinkage and creep. The results indicate that the aggregate type has a significant effect on creep and shrinkage deformations of HPC. An influence of the shape of aggregate on time-dependent deformations has also been observed. On the basis of these results, long-term behaviour seems to be correlated to the characteristics of the Interfacial Transition Zone (ITZ) strongly depending on the mineralogical nature and properties of aggregates. The experimental results are compared with the values calculated using the current Eurocode 2 model in order to assess the accuracy of the predictions.

  13. Effects of oil palm shell coarse aggregate species on high strength lightweight concrete.

    PubMed

    Yew, Ming Kun; Bin Mahmud, Hilmi; Ang, Bee Chin; Yew, Ming Chian

    2014-01-01

    The objective of this study was to investigate the effects of different species of oil palm shell (OPS) coarse aggregates on the properties of high strength lightweight concrete (HSLWC). Original and crushed OPS coarse aggregates of different species and age categories were investigated in this study. The research focused on two OPS species (dura and tenera), in which the coarse aggregates were taken from oil palm trees of the following age categories (3-5, 6-9, and 10-15 years old). The results showed that the workability and dry density of the oil palm shell concrete (OPSC) increase with an increase in age category of OPS species. The compressive strength of specimen CD3 increases significantly compared to specimen CT3 by 21.8%. The maximum achievable 28-day and 90-day compressive strength is 54 and 56 MPa, respectively, which is within the range for 10-15-year-old crushed dura OPS. The water absorption was determined to be within the range for good concrete for the different species of OPSC. In addition, the ultrasonic pulse velocity (UPV) results showed that the OPS HSLWC attain good condition at the age of 3 days. PMID:24982946

  14. Effects of Oil Palm Shell Coarse Aggregate Species on High Strength Lightweight Concrete

    PubMed Central

    Yew, Ming Kun; Bin Mahmud, Hilmi; Ang, Bee Chin; Yew, Ming Chian

    2014-01-01

    The objective of this study was to investigate the effects of different species of oil palm shell (OPS) coarse aggregates on the properties of high strength lightweight concrete (HSLWC). Original and crushed OPS coarse aggregates of different species and age categories were investigated in this study. The research focused on two OPS species (dura and tenera), in which the coarse aggregates were taken from oil palm trees of the following age categories (3–5, 6–9, and 10–15 years old). The results showed that the workability and dry density of the oil palm shell concrete (OPSC) increase with an increase in age category of OPS species. The compressive strength of specimen CD3 increases significantly compared to specimen CT3 by 21.8%. The maximum achievable 28-day and 90-day compressive strength is 54 and 56 MPa, respectively, which is within the range for 10–15-year-old crushed dura OPS. The water absorption was determined to be within the range for good concrete for the different species of OPSC. In addition, the ultrasonic pulse velocity (UPV) results showed that the OPS HSLWC attain good condition at the age of 3 days. PMID:24982946

  15. A Coarse-Grained Model for Polyglutamine Aggregation Modulated by Amphipathic Flanking Sequences

    PubMed Central

    Ruff, Kiersten M.; Khan, Siddique J.; Pappu, Rohit V.

    2014-01-01

    The aggregation of proteins with expanded polyglutamine (polyQ) tracts is directly relevant to the formation of neuronal intranuclear inclusions in Huntington’s disease. In vitro studies have uncovered the effects of flanking sequences as modulators of the driving forces and mechanisms of polyQ aggregation in sequence segments associated with HD. Specifically, a seventeen-residue amphipathic stretch (N17) that is directly N-terminal to the polyQ tract in huntingtin decreases the overall solubility, destabilizes nonfibrillar aggregates, and accelerates fibril formation. Published results from atomistic simulations showed that the N17 module reduces the frequency of intermolecular association. Our reanalysis of these simulation results demonstrates that the N17 module also reduces interchain entanglements between polyQ domains. These two effects, which are observed on the smallest lengthscales, are incorporated into phenomenological pair potentials and used in coarse-grained Brownian dynamics simulations to investigate their impact on large-scale aggregation. We analyze the results from Brownian dynamics simulations using the framework of diffusion-limited cluster aggregation. When entanglements prevail, which is true in the absence of N17, small spherical clusters and large linear aggregates form on distinct timescales, in accord with in vitro experiments. Conversely, when entanglements are quenched and a barrier to intermolecular associations is introduced, both of which are attributable to N17, the timescales for forming small species and large linear aggregates become similar. Therefore, the combination of a reduction of interchain entanglements through homopolymeric polyQ and barriers to intermolecular associations appears to be sufficient for providing a minimalist phenomenological rationalization of in vitro observations regarding the effects of N17 on polyQ aggregation. PMID:25185558

  16. Leaching assessment of concrete made of recycled coarse aggregate: physical and environmental characterisation of aggregates and hardened concrete.

    PubMed

    Galvín, A P; Agrela, F; Ayuso, J; Beltrán, M G; Barbudo, A

    2014-09-01

    Each year, millions of tonnes of waste are generated worldwide, partially through the construction and demolition of buildings. Recycling the resulting waste could reduce the amount of materials that need to be manufactured. Accordingly, the present work has analysed the potential reuse of construction waste in concrete manufacturing by replacing the natural aggregate with recycled concrete coarse aggregate. However, incorporating alternative materials in concrete manufacturing may increase the pollutant potential of the product, presenting an environmental risk via ground water contamination. The present work has tested two types of concrete batches that were manufactured with different replacement percentages. The experimental procedure analyses not only the effect of the portion of recycled aggregate on the physical properties of concrete but also on the leaching behaviour as indicative of the contamination degree. Thus, parameters such as slump, density, porosity and absorption of hardened concrete, were studied. Leaching behaviour was evaluated based on the availability test performed to three aggregates (raw materials of the concrete batches) and on the diffusion test performed to all concrete. From an environmental point of view, the question of whether the cumulative amount of heavy metals that are released by diffusion reaches the availability threshold was answered. The analysis of concentration levels allowed the establishment of different groups of metals according to the observed behaviour, the analysis of the role of pH and the identification of the main release mechanisms. Finally, through a statistical analysis, physical parameters and diffusion data were interrelated. It allowed estimating the relevance of porosity, density and absorption of hardened concrete on diffusion release of the metals in study. PMID:24889792

  17. A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation

    NASA Astrophysics Data System (ADS)

    Ilie, Ioana M.; den Otter, Wouter K.; Briels, Wim J.

    2016-02-01

    Particles in simulations are traditionally endowed with fixed interactions. While this is appropriate for particles representing atoms or molecules, objects with significant internal dynamics—like sequences of amino acids or even an entire protein—are poorly modelled by invariable particles. We develop a highly coarse grained polymorph patchy particle with the ultimate aim of simulating proteins as chains of particles at the secondary structure level. Conformational changes, e.g., a transition between disordered and β-sheet states, are accommodated by internal coordinates that determine the shape and interaction characteristics of the particles. The internal coordinates, as well as the particle positions and orientations, are propagated by Brownian Dynamics in response to their local environment. As an example of the potential offered by polymorph particles, we model the amyloidogenic intrinsically disordered protein α-synuclein, involved in Parkinson's disease, as a single particle with two internal states. The simulations yield oligomers of particles in the disordered state and fibrils of particles in the "misfolded" cross-β-sheet state. The aggregation dynamics is complex, as aggregates can form by a direct nucleation-and-growth mechanism and by two-step-nucleation through conversions between the two cluster types. The aggregation dynamics is complex, with fibrils formed by direct nucleation-and-growth, by two-step-nucleation through the conversion of an oligomer and by auto-catalysis of this conversion.

  18. Aggregation of alpha-synuclein by a coarse-grained Monte Carlo simulation

    NASA Astrophysics Data System (ADS)

    Farmer, Barry; Pandey, Ras

    Alpha-synuclein, an intrinsic protein abundant in neurons, is believed to be a major cause of neurodegenerative diseases (e.g. Alzheimer, Parkinson's disease). Abnormal aggregation of ASN leads to Lewy bodies with specific morphologies. We investigate the self-organizing structures in a crowded environment of ASN proteins by a coarse-grained Monte Carlo simulation. ASN is a chain of 140 residues. Structure detail of residues is neglected but its specificity is captured via unique knowledge-based residue-residue interactions. Large-scale simulations are performed to analyze a number local and global physical quantities (e.g. mobility profile, contact map, radius of gyration, structure factor) as a function of temperature and protein concentration. Trend in multi-scale structural variations of the protein in a crowded environment is compared with that of a free protein chain.

  19. CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

    NASA Astrophysics Data System (ADS)

    Ruff, Kiersten M.; Harmon, Tyler S.; Pappu, Rohit V.

    2015-12-01

    We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.

  20. CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

    SciTech Connect

    Ruff, Kiersten M.; Harmon, Tyler S.; Pappu, Rohit V.

    2015-12-28

    We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.

  1. The prediction of the freeze/thaw durability of coarse aggregate in concrete by mercury intrusion porosimetry

    NASA Astrophysics Data System (ADS)

    Lindgren, M. N.

    1980-10-01

    Aggregates from fifty-two Indiana highway cores were tested as were five rock samples supplied by the Portland Cement Association. The Expected Durability Factor values were determined from the pore size distributions, and an average value was assigned to each pavement associated with the cores. These values were then compared with the field performance of the pavement to ascertain the borderline between EDF values for durable and for nondurable aggregates. A good correlation between the field performance and the average EDF values was found. A pavement will be durable if its coarse aggregate has an EDF value greater than 50 for 90% or more of the aggregate. This criterion applies to stone and gravel aggregates with a maximum size of 1-1/2 to 2-1/2 inches. The pavement will be durable for at lest thirty years.

  2. Osmolyte Induced Changes in Peptide Conformational Ensemble Correlate with Slower Amyloid Aggregation: A Coarse-Grained Simulation Study.

    PubMed

    Sukenik, Shahar; Sapir, Liel; Harries, Daniel

    2015-12-01

    Stabilizing osmolytes are known to impact the process of amyloid aggregation, often altering aggregation kinetics. Recent evidence further suggests that osmolytes modify the peptide conformational dynamics, as well as change the physical characteristics of assembling amyloid fibrils. To resolve how these variations emerge on the molecular level, we simulated the initial aggregation steps of an amyloid-forming peptide in the presence and absence of the osmolyte sorbitol, a naturally occurring polyol. To this end, a coarse-grained force field was extended and implemented to access larger aggregate sizes and longer time scales. The force field optimization procedure placed emphasis on calibrating the solution thermodynamics of sorbitol, the aggregating peptide in its monomeric form, and the interaction of both of these components with each other and with water. Our simulations show a difference in aggregation kinetics and structural parameters in the presence of sorbitol compared to water, which qualitatively agree well with our experimentally resolved aggregation kinetics of the same peptide. The kinetic changes induced by sorbitol can be traced in our simulations to changes in monomer conformations resulting from osmolyte presence. These translate into changes in peptide conformations within the aggregated clusters and into differences in rates of monomer nucleation and of association to formed fibrils. We find that, compared to pure water as solvent, the presence of sorbitol induces formation of more aggregates each containing fewer peptides, with an increased tendency toward parallel interpeptide contacts. PMID:26587669

  3. Properties of concrete made with north carolina recycled coarse and fine aggregates. Final report, 1 July 1994-30 June 1996

    SciTech Connect

    Ahmad, S.H.; Fisher, D.G.; Sackett, K.W.

    1996-06-30

    Reconstruction of roadways generates large quantities of waste material and requires considerable amounts of aggregate. The recycling of concrete from old deteriorated pavements into aggregates for construction of new pavements reduces disposal costs as well as providing a source of aggregates to replace natural supplies. In this study, recycled coarse and fine aggregates were obtained from a portion of concrete pavement which was removed from Interstate 40 in North Carolina. Various amounts of recycled coarse and fine aggregates were volumerically substituted for natural coarse and fine aggregates of a control mixture. A relatively higher cement factor was used for the control mix, compared to NCDOT standard. The effects on plastic and hardened concrete properties were investigated.

  4. Molecular dynamics simulations of ionic aggregates in a coarse%3CU%2B2010%3Egrained ionomer melt.

    SciTech Connect

    Hall, Lisa Michelle; Frischknecht, Amalie Lucile; Stevens, Mark Jackson

    2010-11-01

    Ionomers--polymers containing a small fraction of covalently bound ionic groups--have potential application as solid electrolytes in batteries. Understanding ion transport in ionomers is essential for such applications. Due to strong electrostatic interactions in these materials, the ions form aggregates, tending to slow counterion diffusion. A key question is how ionomer properties affect ionic aggregation and counterion dynamics on a molecular level. Recent experimental advances have allowed synthesis and extensive characterization of ionomers with a precise, constant spacing of charged groups, making them ideal for controlled measurement and more direct comparison with molecular simulation. We have used coarse-grained molecular dynamics to simulate such ionomers with regularly spaced charged beads. The charged beads are placed either in the polymer backbone or as pendants on the backbone. The polymers, along with the counterions, are simulated at melt densities. The ionic aggregate structure was determined as a function of the dielectric constant, spacing of the charged beads on the polymer, and the sizes of the charged beads and counterions. The pendant ion architecture can yield qualitatively different aggregate structures from those of the linear polymers. For small pendant ions, roughly spherical aggregates have been found above the glass transition temperature. The implications of these aggregates for ion diffusion will be discussed.

  5. The influence of coarse aggregate size and volume on the fracture behavior and brittleness of self-compacting concrete

    SciTech Connect

    Beygi, Morteza H.A.; Kazemi, Mohammad Taghi; Nikbin, Iman M.; Vaseghi Amiri, Javad; Rabbanifar, Saeed; Rahmani, Ebrahim

    2014-12-15

    This paper presents the results of an experimental investigation on fracture characteristics and brittleness of self-compacting concrete (SCC), involving the tests of 185 three point bending beams with different coarse aggregate size and content. Generally, the parameters were analyzed by the work of fracture method (WFM) and the size effect method (SEM). The results showed that with increase of size and content of coarse aggregate, (a) the fracture energy increases which is due to the change in fractal dimensions, (b) behavior of SCC beams approaches strength criterion, (c) characteristic length, which is deemed as an index of brittleness, increases linearly. It was found with decrease of w/c ratio that fracture energy increases which may be explained by the improvement in structure of aggregate-paste transition zone. Also, the results showed that there is a correlation between the fracture energy measured by WFM (G{sub F}) and the value measured through SEM (G{sub f}) (G{sub F} = 3.11G{sub f})

  6. Mechanisms and Kinetics of Amyloid Aggregation Investigated by a Phenomenological Coarse-Grained Model

    NASA Astrophysics Data System (ADS)

    Magno, Andrea; Pellarin, Riccardo; Caflisch, Amedeo

    Amyloid fibrils are ordered polypeptide aggregates that have been implicated in several neurodegenerative pathologies, such as Alzheimer's, Parkinson's, Huntington's, and prion diseases, [1, 2] and, more recently, also in biological functionalities. [3, 4, 5] These findings have paved the way for a wide range of experimental and computational studies aimed at understanding the details of the fibril-formation mechanism. Computer simulations using low-resolution models, which employ a simplified representation of protein geometry and energetics, have provided insights into the basic physical principles underlying protein aggregation in general [6, 7, 8] and ordered amyloid aggregation. [9, 10, 11, 12, 13, 14, 15] For example, Dokholyan and coworkers have used the Discrete Molecular Dynamics method [16, 17] to shed light on the mechanisms of protein oligomerization [18] and the conformational changes that take place in proteins before the aggregation onset. [19, 20] One challenging observation, which is difficult to observe by computer simulations, is the wide range of aggregation scenarios emerging from a variety of biophysical measurements. [21, 22] Atomistic models have been employed to study the conformational space of amyloidogenic polypeptides in the monomeric state, [23, 24, 25] the very initial steps of amyloid formation, [26, 27, 28, 29, 30, 31, 32] and the structural stability of fibril models. [33, 34, 35) However, all-atom simulations of the kinetics of fibril formation are beyond what can be done with modern computers.

  7. The Feasibility of Palm Kernel Shell as a Replacement for Coarse Aggregate in Lightweight Concrete

    NASA Astrophysics Data System (ADS)

    Itam, Zarina; Beddu, Salmia; Liyana Mohd Kamal, Nur; Ashraful Alam, Md; Issa Ayash, Usama

    2016-03-01

    Implementing sustainable materials into the construction industry is fast becoming a trend nowadays. Palm Kernel Shell is a by-product of Malaysia’s palm oil industry, generating waste as much as 4 million tons per annum. As a means of producing a sustainable, environmental-friendly, and affordable alternative in the lightweight concrete industry, the exploration of the potential of Palm Kernel Shell to be used as an aggregate replacement was conducted which may give a positive impact to the Malaysian construction industry as well as worldwide concrete usage. This research investigates the feasibility of PKS as an aggregate replacement in lightweight concrete in terms of compressive strength, slump test, water absorption, and density. Results indicate that by using PKS for aggregate replacement, it increases the water absorption but decreases the concrete workability and strength. Results however, fall into the range acceptable for lightweight aggregates, hence it can be concluded that there is potential to use PKS as aggregate replacement for lightweight concrete.

  8. Effects of Macromolecular Crowding on Amyloid Beta (16–22) Aggregation Using Coarse-Grained Simulations

    PubMed Central

    2015-01-01

    To examine the effect of crowding on protein aggregation, discontinuous molecular dynamics (DMD) simulations combined with an intermediate resolution protein model, PRIME20, were applied to a peptide/crowder system. The systems contained 192 Aβ(16–22) peptides and crowders of diameters 5, 20, and 40 Å, represented here by simple hard spheres, at crowder volume fractions of 0.00, 0.10, and 0.20. Results show that both crowder volume fraction and crowder diameter have a large impact on fibril and oligomer formation. The addition of crowders to a system of peptides increases the rate of oligomer formation, shifting from a slow ordered formation of oligomers in the absence of crowders, similar to nucleated polymerization, to a fast collapse of peptides and subsequent rearrangement characteristic of nucleated conformational conversion with a high maximum in the number of peptides in oligomers as the total crowder surface area increases. The rate of conversion from oligomers to fibrils also increases with increasing total crowder surface area, giving rise to an increased rate of fibril growth. In all cases, larger volume fractions and smaller crowders provide the greatest aggregation enhancement effects. We also show that the size of the crowders influences the formation of specific oligomer sizes. In our simulations, the 40 Å crowders enhance the number of dimers relative to the numbers of trimers, hexamers, pentamers, and hexamers, while the 5 Å crowders enhance the number of hexamers relative to the numbers of dimers, trimers, tetramers, and pentamers. These results are in qualitative agreement with previous experimental and theoretical work. PMID:25347801

  9. A Study on Suitability of EAF Oxidizing Slag in Concrete: An Eco-Friendly and Sustainable Replacement for Natural Coarse Aggregate.

    PubMed

    Sekaran, Alan; Palaniswamy, Murthi; Balaraju, Sivagnanaprakash

    2015-01-01

    Environmental and economic factors increasingly encourage higher utility of industrial by-products. The basic objective of this study was to identify alternative source for good quality aggregates which is depleting very fast due to fast pace of construction activities in India. EAF oxidizing slag as a by-product obtained during the process in steel making industry provides great opportunity to utilize it as an alternative to normally available coarse aggregates. The primary aim of this research was to evaluate the physical, mechanical, and durability properties of concrete made with EAF oxidizing slag in addition to supplementary cementing material fly ash. This study presents the experimental investigations carried out on concrete grades of M20 and M30 with three mixes: (i) Mix A, conventional concrete mix with no material substitution, (ii) Mix B, 30% replacement of cement with fly ash, and (iii) Mix C, 30% replacement of cement with fly ash and 50% replacement of coarse aggregate with EAF oxidizing slag. Tests were conducted to determine mechanical and durability properties up to the age of 90 days. The test results concluded that concrete made with EAF oxidizing slag and fly ash (Mix C) had greater strength and durability characteristics when compared to Mix A and Mix B. Based on the overall observations, it could be recommended that EAF oxidizing slag and fly ash could be effectively utilized as coarse aggregate replacement and cement replacement in all concrete applications. PMID:26421315

  10. A Study on Suitability of EAF Oxidizing Slag in Concrete: An Eco-Friendly and Sustainable Replacement for Natural Coarse Aggregate

    PubMed Central

    Sekaran, Alan; Palaniswamy, Murthi; Balaraju, Sivagnanaprakash

    2015-01-01

    Environmental and economic factors increasingly encourage higher utility of industrial by-products. The basic objective of this study was to identify alternative source for good quality aggregates which is depleting very fast due to fast pace of construction activities in India. EAF oxidizing slag as a by-product obtained during the process in steel making industry provides great opportunity to utilize it as an alternative to normally available coarse aggregates. The primary aim of this research was to evaluate the physical, mechanical, and durability properties of concrete made with EAF oxidizing slag in addition to supplementary cementing material fly ash. This study presents the experimental investigations carried out on concrete grades of M20 and M30 with three mixes: (i) Mix A, conventional concrete mix with no material substitution, (ii) Mix B, 30% replacement of cement with fly ash, and (iii) Mix C, 30% replacement of cement with fly ash and 50% replacement of coarse aggregate with EAF oxidizing slag. Tests were conducted to determine mechanical and durability properties up to the age of 90 days. The test results concluded that concrete made with EAF oxidizing slag and fly ash (Mix C) had greater strength and durability characteristics when compared to Mix A and Mix B. Based on the overall observations, it could be recommended that EAF oxidizing slag and fly ash could be effectively utilized as coarse aggregate replacement and cement replacement in all concrete applications. PMID:26421315

  11. Aggregation in complex triacylglycerol oils: coarse-grained models, nanophase separation, and predicted x-ray intensities

    NASA Astrophysics Data System (ADS)

    Quinn, Bonnie; Peyronel, Fernanda; Gordon, Tyler; Marangoni, Alejandro; Hanna, Charles B.; Pink, David A.

    2014-11-01

    Triacylglycerols (TAGs) are biologically important molecules which form crystalline nanoplatelets (CNPs) and, ultimately, fat crystal networks in edible oils. Characterizing the self-assembled hierarchies of these networks is important to understanding their functionality and oil binding capacity. We have modelled CNPs in multicomponent oils and studied their aggregation. The oil comprises (a) a liquid componentt, and (b) components which phase separately on a nano-scale (nano-phase separation) to coat the surfaces of the CNPs impenetrably, either isotropically or anisotropically, with either liquid-like coatings or crystallites, forming a coating of thickness Δ. We modelled three cases: (i) liquid-liquid nano-phase separation, (ii) solid-liquid nano-phase separation, with CNPs coated isotropically, and (iii) CNPs coated anisotropically. The models were applied to mixes of tristearin and triolein with fully hydrogenated canola oil, shea butter with high oleic sunflower oil, and cotton seed oil. We performed Monte Carlo simulations, computed structure functions and concluded: (1) three regimes arose: (a) thin coating regime, Δ \\lt 0.0701 u (b) transition regime, 0.0701 u≤slant Δ ≤slant 0.0916 u and (c) thick coating regime, Δ \\gt 0.0916 u . (arbitrary units, u) (2) The thin coating regime exhibits 1D TAGwoods, which aggregate, via DLCA/RLCA, into fractal structures which are uniformly distributed in space. (3) In the thick coating regime, for an isotropic coating, TAGwoods are not formed and coated CNPs will not aggregate but will be uniformly distributed in space. For anisotropic coating, TAGwoods can be formed and might form 1D strings but will not form DLCA/RLCA clusters. (4) The regimes are, approximately: thin coating, 0\\lt Δ \\lt 7.0 \\text{nm} transition regime, 7.0\\ltΔ \\lt 9.2 \\text{nm} and thick coating, Δ \\gt 9.2 \\text{nm} (5) The minimum minority TAG concentration required to undergo nano-phase separation is, approximately, 0.29% (thin

  12. Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field.

    PubMed

    Rojas, Ana; Liwo, Adam; Browne, Dana; Scheraga, Harold A

    2010-12-01

    The growth mechanism of β-amyloid (Aβ) peptide fibrils was studied by a physics-based coarse-grained united-residue model and molecular dynamics (MD) simulations. To identify the mechanism of monomer addition to an Aβ(1-40) fibril, we placed an unstructured monomer at a distance of 20 Å from a fibril template and allowed it to interact freely with the latter. The monomer was not biased towards fibril conformation by either the force field or the MD algorithm. With the use of a coarse-grained model with replica-exchange molecular dynamics, a longer timescale was accessible, making it possible to observe how the monomers probe different binding modes during their search for the fibril conformation. Although different assembly pathways were seen, they all follow a dock-lock mechanism with two distinct locking stages, consistent with experimental data on fibril elongation. Whereas these experiments have not been able to characterize the conformations populating the different stages, we have been able to describe these different stages explicitly by following free monomers as they dock onto a fibril template and to adopt the fibril conformation (i.e., we describe fibril elongation step by step at the molecular level). During the first stage of the assembly ("docking"), the monomer tries different conformations. After docking, the monomer is locked into the fibril through two different locking stages. In the first stage, the monomer forms hydrogen bonds with the fibril template along one of the strands in a two-stranded β-hairpin; in the second stage, hydrogen bonds are formed along the second strand, locking the monomer into the fibril structure. The data reveal a free-energy barrier separating the two locking stages. The importance of hydrophobic interactions and hydrogen bonds in the stability of the Aβ fibril structure was examined by carrying out additional canonical MD simulations of oligomers with different numbers of chains (4-16 chains), with the fibril

  13. Coarse grained study of pluronic F127: Comparison with shorter co-polymers in its interaction with lipid bilayers and self-aggregation in water

    NASA Astrophysics Data System (ADS)

    Wood, I.; Martini, M. F.; Albano, J. M. R.; Cuestas, M. L.; Mathet, V. L.; Pickholz, M.

    2016-04-01

    The aim of this work is to understand the interactions of the poloxamer Pluronic F127, with lipid bilayers and its ability to self-associate in an aqueous environment. Molecular dynamics simulations at the coarse-grain scale were performed to address the behavior of single Pluronic F127 and shorter poloxamers unimers in palmitoyl-oleoyl-phosphatidyl-choline model membranes. According to the initial conditions and the poly-ethylene oxide/poly-propylene oxide composition, in water phase the unimer chain collapses into a coil conformation or adopts an interphacial U-shaped - or membrane spanning - distribution. A combination of poly-propylene oxide length, and the poly-ethylene oxide ability to cover poly-propylene oxide, is determinant for the conformation adopted by the unimer in each phase. Results of the simulations showed molecular evidence of strong interaction between Pluronic F127 and model membranes both in stable U-shaped and span conformations. The knowledge of this interaction could contribute to improve drug permeation. Additionally, we investigated the aggregation of one hundred Pluronic F127 unimers in water forming a micelle-like structure, suitable to be used as drug delivery system models.

  14. Thermodynamics of Protein Aggregation

    NASA Astrophysics Data System (ADS)

    Osborne, Kenneth L.; Barz, Bogdan; Bachmann, Michael; Strodel, Birgit

    Amyloid protein aggregation characterizes many neurodegenerative disorders, including Alzheimer's, Parkinson's, and Creutz- feldt-Jakob disease. Evidence suggests that amyloid aggregates may share similar aggregation pathways, implying simulation of full-length amyloid proteins is not necessary for understanding amyloid formation. In this study we simulate GNNQQNY, the N-terminal prion-determining domain of the yeast protein Sup35 to investigate the thermodynamics of structural transitions during aggregation. We use a coarse-grained model with replica-exchange molecular dynamics to investigate the association of 3-, 6-, and 12-chain GNNQQNY systems and we determine the aggregation pathway by studying aggregation states of GN- NQQNY. We find that the aggregation of the hydrophilic GNNQQNY sequence is mainly driven by H-bond formation, leading to the formation of /3-sheets from the very beginning of the assembly process. Condensation (aggregation) and ordering take place simultaneously, which is underpinned by the occurrence of a single heat capacity peak only.

  15. Coarse graining in micromagnetics.

    PubMed

    Grinstein, G; Koch, R H

    2003-05-23

    Numerical solutions of the micromagnetic Landau-Lifshitz-Gilbert equations provide valuable information at low temperatures (T), but produce egregious errors at higher T. For example, Curie temperatures are often overestimated by an order of magnitude. We show that these errors result from the use of block or coarse-grained variables, without a concomitant renormalization of the system parameters to account for the block size. Renormalization solves the problem of the Curie-point anomaly and improves the accuracy of more complicated micromagnetic simulations, even at low T. PMID:12785922

  16. The Aerosol Coarse Mode Initiative

    NASA Astrophysics Data System (ADS)

    Arnott, W. P.; Adhikari, N.; Air, D.; Kassianov, E.; Barnard, J.

    2014-12-01

    Many areas of the world show an aerosol volume distribution with a significant coarse mode and sometimes a dominant coarse mode. The large coarse mode is usually due to dust, but sea salt aerosol can also play an important role. However, in many field campaigns, the coarse mode tends to be ignored, because it is difficult to measure. This lack of measurements leads directly to a concomitant "lack of analysis" of this mode. Because, coarse mode aerosols can have significant effects on radiative forcing, both in the shortwave and longwave spectrum, the coarse mode -- and these forcings -- should be accounted for in atmospheric models. Forcings based only on fine mode aerosols have the potential to be misleading. In this paper we describe examples of large coarse modes that occur in areas of large aerosol loading (Mexico City, Barnard et al., 2010) as well as small loadings (Sacramento, CA; Kassianov et al., 2012; and Reno, NV). We then demonstrate that: (1) the coarse mode can contribute significantly to radiative forcing, relative to the fine mode, and (2) neglecting the coarse mode may result in poor comparisons between measurements and models. Next we describe -- in general terms -- the limitations of instrumentation to measure the coarse mode. Finally, we suggest a new initiative aimed at examining coarse mode aerosol generation mechanisms; transport and deposition; chemical composition; visible and thermal IR refractive indices; morphology; microphysical behavior when deposited on snow and ice; and specific instrumentation needs. Barnard, J. C., J. D. Fast, G. Paredes-Miranda, W. P. Arnott, and A. Laskin, 2010: Technical Note: Evaluation of the WRF-Chem "Aerosol Chemical to Aerosol Optical Properties" Module using data from the MILAGRO campaign, Atmospheric Chemistry and Physics, 10, 7325-7340. Kassianov, E. I., M. S. Pekour, and J. C. Barnard, 2012: Aerosols in Central California: Unexpectedly large contribution of coarse mode to aerosol radiative forcing

  17. Coarse frequency comb interferometry

    NASA Astrophysics Data System (ADS)

    Schwider, J.

    2008-08-01

    Real wedge interferometers of the Fizeau-type do not allow for fringes in case of a spectral broad band source - or in short: for white light fringes. Here, the use of a suitable frequency comb source will help to overcome this limitation on the one hand and on the other will offer the capability for enhanced phase sensitivity in high precision measurements of surface deviations. Frequency combs can be produced either by using a pulse train from a fs-laser or by passive filtering of the light emitted by a broad band source as a superlum-diode or a fs-laser. The frequency comb produced by a common fs-laser is extremely fine, i.e., the frequency difference of consecutive peaks is very small or the distance of consecutive pulses of the pulse train might be of the order of 1m. Therefore, the coarse pulse train produced by passive filtering of a broad band source is better adapted to the needs of surface testing interferometers. White light fringes are either applied for the profiling of discontinuous surfaces and/or can serve as an indication for the correct choice of multiplication factors in superposition interferometry. During the last decennium it became more and more clear that spatially incoherent sources provide better measuring accuracy in surface measurements due to the reduced influence of dust diffraction patterns. The advantage of laser illumination can nevertheless be maintained if the laser light is made spatially incoherent through moving scatterers in the light path. Here, we will discuss the application of spatially incoherent broad band light frequency filtered through a Fabry-Perot filter. The main applications are in the following fields: (1) surface profiling applications using two-beam Fizeau interferometers, (2) selection of single cavities out of a series of interlaced cavities, and (3) sensitivity enhancement for multi-beam interferometers for planeness or sphericity measurements. Some of the discussed possibilities will be experimentally

  18. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1995-01-01

    Part of the 1994 Industrial Minerals Review. The production, consumption, and applications of construction aggregates are reviewed. In 1994, the production of construction aggregates, which includes crushed stone and construction sand and gravel combined, increased 7.7 percent to 2.14 Gt compared with the previous year. These record production levels are mostly a result of funding for highway construction work provided by the Intermodal Surface Transportation Efficiency Act of 1991. Demand is expected to increase for construction aggregates in 1995.

  19. COMPARATIVE TOXICITY OF COARSE PARTICLES

    EPA Science Inventory

    As determined in preliminary studies, we expect that coarse particle toxicity will be influenced by a variety of factors including particle components (e.g., crustal material vs. metals vs. biologics), particle concentration, and the differing composition of urban and ru...

  20. Weighted aggregation

    NASA Technical Reports Server (NTRS)

    Feiveson, A. H. (Principal Investigator)

    1979-01-01

    The use of a weighted aggregation technique to improve the precision of the overall LACIE estimate is considered. The manner in which a weighted aggregation technique is implemented given a set of weights is described. The problem of variance estimation is discussed and the question of how to obtain the weights in an operational environment is addressed.

  1. Coarse-graining in peridynamics.

    SciTech Connect

    Silling, Stewart Andrew

    2010-11-01

    The peridynamic theory is an extension of traditional solid mechanics that treats discontinuous media, including the evolution of discontinuities due to fracture, on the same mathematical basis as classically smooth media. A recent advance in the linearized peridynamic theory permits the reduction of the number of degrees of freedom modeled within a body. Under equilibrium conditions, this coarse graining method exactly reproduces the internal forces on the coarsened degrees of freedom, including the effect of the omitted material that is no longer explicitly modeled. The method applies to heterogeneous as well as homogeneous media and accounts for defects in the material. The coarse graining procedure can be repeated over and over, resulting in a hierarchically coarsened description that, at each stage, continues to reproduce the exact internal forces present in the original, detailed model. Each coarsening step results in reduced computational cost. This talk will describe the new peridynamic coarsening method and show computational examples.

  2. Continuous coarse ash depressurization system

    DOEpatents

    Liu, Guohai; Peng, Wan Wang; Vimalchand, Pannalal

    2012-11-13

    A system for depressurizing and cooling a high pressure, high temperature dense phase solids stream having coarse solid particles with entrained gas therein. In one aspect, the system has an apparatus for at least partially depressurizing and cooling the high pressure, high temperature dense phase solids stream having gas entrained therein and a pressure letdown device for further depressurization and separating cooled coarse solid particles from a portion of the entrained gas, resulting in a lower temperature, lower pressure outlet of solid particles for downstream processing or discharge to a storage silo for future use and/or disposal. There are no moving parts in the flow path of the solids stream in the system.

  3. Impact into Coarse Grained Spheres

    NASA Technical Reports Server (NTRS)

    Barnouin-Jha, O. S.; Cintala, M.; Crawford, D. A.

    2005-01-01

    Several experimental studies [1,2,3] indicate that differences in the grain size of the target relative to the projectile could influence the cratering process. Impacts into coarse sand grains of size comparable to the projectile show some discrepancies with existing relationships for crater growth [e.g. 4]. Similarly, targets of ne grained, uniform in diameter glass spheres show differences in crater depth, transient crater diameter, and volume of ejecta excavated as a function of grain size [2,3]. The purpose of this work is to continue investigating how the relative grain size may influence early time coupling between a projectile and target, with implications for subsequent ejecta excavation and crater growth. In previous efforts we used numerical techniques to focus on the propagation of shock waves in coarse, granular media emphasizing the influence of relative grain size on crater growth, ejecta production, cratering efficiency, target strength, and crater shape [5,6,7]. In this study, we use experimental techniques - in part as a reality check for the numerical studies - to report on how coarse grained targets might influence ejecta excavation and crater shape. This body of work possesses important implications for ejecta excavation and cratering efficiency on asteroids that may possess rubble pile-like structures, and on planets that may possess either pre-fractured surfaces or large-scale heterogeneities in shock impedance.

  4. How coarse is too coarse for salmon spawning substrates?

    NASA Astrophysics Data System (ADS)

    Wooster, J. K.; Riebe, C. S.; Ligon, F. K.; Overstreet, B. T.

    2009-12-01

    Populations of Pacific salmon species have declined sharply in many rivers of the western US. Reversing these declines is a top priority and expense of many river restoration projects. To help restore salmon populations, managers often inject gravel into rivers, to supplement spawning habitat that has been depleted by gravel mining and the effects of dams—which block sediment and thus impair habitat downstream by coarsening the bed where salmon historically spawned. However, there is little quantitative understanding nor a methodology for determining when a river bed has become too coarse for salmon spawning. Hence there is little scientific basis for selecting sites that would optimize the restoration benefits of gravel injection (e.g., sites where flow velocities are suitable but bed materials are too coarse for spawning). To develop a quantitative understanding of what makes river beds too coarse for salmon spawning, we studied redds and spawning use in a series of California and Washington rivers where salmon spawning ability appears to be affected by coarse bed material. Our working hypothesis is that for a given flow condition, there is a maximum “threshold” particle size that a salmon of a given size is able to excavate and/or move as she builds her redd. A second, related hypothesis is that spawning use should decrease and eventually become impossible with increasing percent coverage by immovable particles. To test these hypotheses, we quantified the sizes and spatial distributions of immovably coarse particles in a series of salmon redds in each river during the peak of spawning. We also quantified spawning use and how it relates to percent coverage by immovable particles. Results from our studies of fall-run chinook salmon (Oncorhynchus tshawytsha) in the Feather River suggest that immovable particle size varies as a function of flow velocity over the redd, implying that faster water helps fish move bigger particles. Our Feather River study also

  5. Construction aggregates

    USGS Publications Warehouse

    Langer, W.H.; Tepordei, V.V.; Bolen, W.P.

    2000-01-01

    Construction aggregates consist primarily of crushed stone and construction sand and gravel. Total estimated production of construction aggregates increased in 1999 by about 2% to 2.39 Gt (2.64 billion st) compared with 1998. This record production level continued an expansion that began in 1992. By commodities, crushed stone production increased 3.3%, while sand and gravel production increased by about 0.5%.

  6. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1994-01-01

    Part of a special section on industrial minerals in 1993. The 1993 production of construction aggregates increased 6.3 percent over the 1992 figure, to reach 2.01 Gt. This represents the highest estimated annual production of combined crushed stone and construction sand and gravel ever recorded in the U.S. The outlook for construction aggregates and the issues facing the industry are discussed.

  7. Coarse Layering at 'Home Plate'

    NASA Technical Reports Server (NTRS)

    2006-01-01

    This image shows coarse-grained layers from around the edge of a low plateau called 'Home Plate' inside Mars' Gusev Crater. One possible origin is material falling to the ground after being thrown aloft by an explosion such as a volcanic eruption or meteorite impact.

    The panoramic camera (Pancam) on NASA's Mars Exploration Rover Spirit acquired the exposures for this image on Spirit's 749th Martian day (Feb. 10, 2006). This view is an approximately true-color rendering mathematically generated from separate images taken through all of the left Pancam's 432-nanometer to 753-nanometer filters.

  8. Coarse-graining the structure of polycyclic aromatic hydrocarbons clusters.

    PubMed

    Hernández-Rojas, J; Calvo, F; Wales, D J

    2016-05-18

    Clusters of polycyclic aromatic hydrocarbons (PAHs) are essential components of soot and may concentrate a significant fraction of carbon matter in the interstellar medium. In this contribution, coarse-grained potentials are parameterized using all-atom reference data to model PAH molecules, such as coronene (C24H12) or circumcoronene (C54H18), and their aggregates. Low-energy structures of pure coronene or circumcoronene clusters obtained using basin-hopping global optimization are found to agree with atomistic results, and consist of finite 1D columnar motifs, sometimes juxtaposed in larger clusters. The structures are only weakly perturbed when quadrupolar interactions are included. π-Stacking also dominates in binary coronene/circumcoronene aggregates, although intriguing motifs are predicted in which one or more molecules are sandwiched between the other PAH species. The coarse-grained model is also extended to account for interaction with a flat graphitic substrate. In this case, binding is stronger with the substrate than with other molecules, and the PAHs are predicted to arrange into a flat triangular monolayer. PMID:27055581

  9. Coarse-graining stiff bonds

    NASA Astrophysics Data System (ADS)

    Español, P.; de la Torre, J. A.; Ferrario, M.; Ciccotti, G.

    2011-11-01

    The method of constraints in molecular dynamics is useful because it avoids the resolution of high frequency motions with very small time steps. However, the price to pay is that both the dynamics and the statistics of a constrained system differ from those of the unconstrained one. Instead of using constraints, we propose to dispose of high frequency motions by a coarse-graining procedure in which fast variables are eliminated. These fast variables are thus modeled as friction and thermal fluctuations. We illustrate the methodology with a simple model case, a diatomic molecule in a monoatomic solvent, in which the bond between the atoms of a diatomic molecule is stiff. Although the example is very simple and does not display the interesting effects of "wrong" statistics of the constrained system (i.e. the well-known issue connected to the Fixman potential), it is well suited to give the proof of concept of the whole procedure.

  10. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1993-01-01

    Part of a special section on the market performance of industrial minerals in 1992. Production of construction aggregates increased by 4.6 percent in 1992. This increase was due, in part, to the increased funding for transportation and infrastructure projects. The U.S. produced about 1.05 Gt of crushed stone and an estimated 734 Mt of construction sand and gravel in 1992. Demand is expected to increase by about 5 percent in 1993.

  11. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1996-01-01

    Part of the Annual Commodities Review 1995. Production of construction aggregates such as crushed stone and construction sand and gravel showed a marginal increase in 1995. Most of the 1995 increases were due to funding for highway construction work. The major areas of concern to the industry included issues relating to wetlands classification and the classification of crystalline silica as a probable human carcinogen. Despite this, an increase in demand is anticipated for 1996.

  12. Construction aggregates

    USGS Publications Warehouse

    Nelson, T.I.; Bolen, W.P.

    2007-01-01

    Construction aggregates, primarily stone, sand and gravel, are recovered from widespread naturally occurring mineral deposits and processed for use primarily in the construction industry. They are mined, crushed, sorted by size and sold loose or combined with portland cement or asphaltic cement to make concrete products to build roads, houses, buildings, and other structures. Much smaller quantities are used in agriculture, cement manufacture, chemical and metallurgical processes, glass production and many other products.

  13. FAST FLOW IN UNSATURATED COARSE SEDIMENTS

    EPA Science Inventory

    This research proposal was developed to improve our understanding of the physics of unsaturated flow in coarse- to very coarse-textured sediments, and through this meet practical needs related to contaminant transport in such vadose environments. This is a critical area for impr...

  14. Mesoscale Simulation of Asphaltene Aggregation.

    PubMed

    Wang, Jiang; Ferguson, Andrew L

    2016-08-18

    Asphaltenes constitute a heavy aromatic crude oil fraction with a propensity to aggregate and precipitate out of solution during petroleum processing. Aggregation is thought to proceed according to the Yen-Mullins hierarchy, but the molecular mechanisms underlying mesoscopic assembly remain poorly understood. By combining coarse-grained molecular models parametrized using all-atom data with high-performance GPU hardware, we have performed molecular dynamics simulations of the aggregation of hundreds of asphaltenes over microsecond time scales. Our simulations reveal a hierarchical self-assembly mechanism consistent with the Yen-Mullins model, but the details are sensitive and depend on asphaltene chemistry and environment. At low concentrations asphaltenes exist predominantly as dispersed monomers. Upon increasing concentration, we first observe parallel stacking into 1D rod-like nanoaggregates, followed by the formation of clusters of nanoaggregates associated by offset, T-shaped, and edge-edge stacking. Asphaltenes possessing long aliphatic side chains cannot form nanoaggregate clusters due to steric repulsions between their aliphatic coronae. At very high concentrations, we observe a porous percolating network of rod-like nanoaggregates suspended in a sea of interpenetrating aliphatic side chains with a fractal dimension of ∼2. The lifetime of the rod-like aggregates is described by an exponential distribution reflecting a dynamic equilibrium between coagulation and fragmentation. PMID:27455391

  15. Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity

    NASA Astrophysics Data System (ADS)

    Frigori, Rafael B.; Rizzi, Leandro G.; Alves, Nelson A.

    2013-01-01

    The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid β-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid β isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process.

  16. Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity.

    PubMed

    Frigori, Rafael B; Rizzi, Leandro G; Alves, Nelson A

    2013-01-01

    The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid β-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid β isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process. PMID:23298062

  17. Construction aggregates

    USGS Publications Warehouse

    Bolen, W.P.; Tepordei, V.V.

    2001-01-01

    The estimated production during 2000 of construction aggregates, crushed stone, and construction sand and gravel increased by about 2.6% to 2.7 Gt (3 billion st), compared with 1999. The expansion that started in 1992 continued with record production levels for the ninth consecutive year. By commodity, construction sand and gravel production increased by 4.5% to 1.16 Gt (1.28 billion st), while crushed stone production increased by 1.3% to 1.56 Gt (1.72 billion st).

  18. Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

    PubMed Central

    Spijker, Peter; van Hoof, Bram; Debertrand, Michel; Markvoort, Albert J.; Vaidehi, Nagarajan; Hilbers, Peter A.J.

    2010-01-01

    Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide. PMID:20640160

  19. Biomembranes in atomistic and coarse-grained simulations

    NASA Astrophysics Data System (ADS)

    Pluhackova, Kristyna; Böckmann, Rainer A.

    2015-08-01

    The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.

  20. Thermodynamically Consistent Coarse-Graining of Polymers

    NASA Astrophysics Data System (ADS)

    Guenza, Marina

    2015-03-01

    Structural and dynamical properties of macromolecular liquids, melts and mixtures, bridge an extensive range of length- and time-scales. For these systems, the computational limitations of the atomistic description prevent the study of the properties of interest and coarse-grained models remain the only viable approach. In coarse-grained models, structural and thermodynamic consistency across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. This talk presents a coarse-graining approach that conserves structural and thermodynamic quantities independent of the extent of coarse-graining, and describes a model for the reconstruction of the dynamics measured in mesoscale simulations of the coarse-grained system. Some of the general challenges of preserving structural and thermodynamic consistency in coarse-grained models are discussed together with the conditions by which the problem is lessened. This material is based upon work partially supported by the National Science Foundation under Grant No. CHE-1362500.

  1. Coarse-graining methods for computational biology.

    PubMed

    Saunders, Marissa G; Voth, Gregory A

    2013-01-01

    Connecting the molecular world to biology requires understanding how molecular-scale dynamics propagate upward in scale to define the function of biological structures. To address this challenge, multiscale approaches, including coarse-graining methods, become necessary. We discuss here the theoretical underpinnings and history of coarse-graining and summarize the state of the field, organizing key methodologies based on an emerging paradigm for multiscale theory and modeling of biomolecular systems. This framework involves an integrated, iterative approach to couple information from different scales. The primary steps, which coincide with key areas of method development, include developing first-pass coarse-grained models guided by experimental results, performing numerous large-scale coarse-grained simulations, identifying important interactions that drive emergent behaviors, and finally reconnecting to the molecular scale by performing all-atom molecular dynamics simulations guided by the coarse-grained results. The coarse-grained modeling can then be extended and refined, with the entire loop repeated iteratively if necessary. PMID:23451897

  2. A technique for estimating spatial sampling errors in coarse-scale soil moisture estimates derived from point-scale observations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The validation of satellite surface soil moisture retrievals requires the spatial aggregation of point-scale ground soil moisture measurements up to coarse resolution satellite footprint scales (>10 km). In regions containing a limited number of ground measurements per satellite footprint, a large c...

  3. Contrasting effects of nanoparticle-protein attraction on amyloid aggregation

    PubMed Central

    Radic, Slaven; Davis, Thomas P; Ke, Pu Chun; Ding, Feng

    2015-01-01

    Nanoparticles (NPs) have been experimentally found to either promote or inhibit amyloid aggregation of proteins, but the molecular mechanisms for such complex behaviors remain unknown. Using coarse-grained molecular dynamics simulations, we investigated the effects of varying the strength of nonspecific NP-protein attraction on amyloid aggregation of a model protein, the amyloid-beta peptide implicated in Alzheimer's disease. Specifically, with increasing NP-peptide attraction, amyloid aggregation on the NP surface was initially promoted due to increased local protein concentration on the surface and destabilization of the folded state. However, further increase of NP-peptide attraction decreased the stability of amyloid fibrils and reduced their lateral diffusion on the NP surface necessary for peptide conformational changes and self-association, thus prohibiting amyloid aggregation. Moreover, we found that the relative concentration between protein and NPs also played an important role in amyloid aggregation. With a high NP/protein ratio, NPs that intrinsically promote protein aggregation may display an inhibitive effect by depleting the proteins in solution while having a low concentration of the proteins on each NP's surface. Our coarse-grained molecular dynamics simulation study offers a molecular mechanism for delineating the contrasting and seemingly conflicting effects of NP-protein attraction on amyloid aggregation and highlights the potential of tailoring anti-aggregation nanomedicine against amyloid diseases. PMID:26989481

  4. Quasiclassical coarse graining and thermodynamic entropy

    SciTech Connect

    Gell-Mann, Murray; Hartle, James B.

    2007-08-15

    Our everyday descriptions of the universe are highly coarse grained, following only a tiny fraction of the variables necessary for a perfectly fine-grained description. Coarse graining in classical physics is made natural by our limited powers of observation and computation. But in the modern quantum mechanics of closed systems, some measure of coarse graining is inescapable because there are no nontrivial, probabilistic, fine-grained descriptions. This essay explores the consequences of that fact. Quantum theory allows for various coarse-grained descriptions, some of which are mutually incompatible. For most purposes, however, we are interested in the small subset of 'quasiclassical descriptions' defined by ranges of values of averages over small volumes of densities of conserved quantities such as energy and momentum and approximately conserved quantities such as baryon number. The near-conservation of these quasiclassical quantities results in approximate decoherence, predictability, and local equilibrium, leading to closed sets of equations of motion. In any description, information is sacrificed through the coarse graining that yields decoherence and gives rise to probabilities for histories. In quasiclassical descriptions, further information is sacrificed in exhibiting the emergent regularities summarized by classical equations of motion. An appropriate entropy measures the loss of information. For a 'quasiclassical realm' this is connected with the usual thermodynamic entropy as obtained from statistical mechanics. It was low for the initial state of our universe and has been increasing since.

  5. Convergent Coarseness Regulation for Segmented Images

    SciTech Connect

    Paglieroni, D W

    2004-05-27

    In segmentation of remotely sensed images, the number of pixel classes and their spectral representations are often unknown a priori. Even with prior knowledge, pixels with spectral components from multiple classes lead to classification errors and undesired small region artifacts. Coarseness regulation for segmented images is proposed as an efficient novel technique for handling these problems. Beginning with an over-segmented image, perceptually similar connected regions are iteratively merged using a method reminiscent of region growing, except the primitives are regions, not pixels. Interactive coarseness regulation is achieved by specifying the area {alpha} of the largest region eligible for merging. A region with area less than {alpha} is merged with the most spectrally similar connected region, unless the regions are perceived as spectrally dissimilar. In convergent coarseness regulation, which requires no user interaction, {alpha} is specified as the total number of pixels in the image, and the coarseness regulation output converges to a steady-state segmentation that remains unchanged as {alpha} is further increased. By applying convergent coarseness regulation to AVIRIS, IKONOS and DigitalGlobe images, and quantitatively comparing computer-generated segmentations to segmentations generated manually by a human analyst, it was found that the quality of the input segmentations was consistently and dramatically improved.

  6. Calibration and validation of coarse-grained models of atomic systems: application to semiconductor manufacturing

    NASA Astrophysics Data System (ADS)

    Farrell, Kathryn; Oden, J. Tinsley

    2014-07-01

    Coarse-grained models of atomic systems, created by aggregating groups of atoms into molecules to reduce the number of degrees of freedom, have been used for decades in important scientific and technological applications. In recent years, interest in developing a more rigorous theory for coarse graining and in assessing the predictivity of coarse-grained models has arisen. In this work, Bayesian methods for the calibration and validation of coarse-grained models of atomistic systems in thermodynamic equilibrium are developed. For specificity, only configurational models of systems in canonical ensembles are considered. Among major challenges in validating coarse-grained models are (1) the development of validation processes that lead to information essential in establishing confidence in the model's ability predict key quantities of interest and (2), above all, the determination of the coarse-grained model itself; that is, the characterization of the molecular architecture, the choice of interaction potentials and thus parameters, which best fit available data. The all-atom model is treated as the "ground truth," and it provides the basis with respect to which properties of the coarse-grained model are compared. This base all-atom model is characterized by an appropriate statistical mechanics framework in this work by canonical ensembles involving only configurational energies. The all-atom model thus supplies data for Bayesian calibration and validation methods for the molecular model. To address the first challenge, we develop priors based on the maximum entropy principle and likelihood functions based on Gaussian approximations of the uncertainties in the parameter-to-observation error. To address challenge (2), we introduce the notion of model plausibilities as a means for model selection. This methodology provides a powerful approach toward constructing coarse-grained models which are most plausible for given all-atom data. We demonstrate the theory and

  7. Fractal dimension and mechanism of aggregation of apple juice particles.

    PubMed

    Benítez, E I; Lozano, J E; Genovese, D B

    2010-04-01

    Turbidity of freshly squeezed apple juice is produced by a polydisperse suspension of particles coming from the cellular tissue. After precipitation of coarse particles by gravity, only fine-colloidal particles remain in suspension. Aggregation of colloidal particles leads to the formation of fractal structures. The fractal dimension is a measure of the internal density of these aggregates and depends on their mechanism of aggregation. Digitized images of primary particles and aggregates of depectinized, diafiltered cloudy apple juice were obtained by scanning electron microscopy (SEM). Average radius of the primary particles was found to be a = 40 ± 11 nm. Maximum radius of the aggregates, R(L), ranged between 250 and 7750 nm. Fractal dimension of the aggregates was determined by analyzing SEM images with the variogram method, obtaining an average value of D(f) = 2.3 ± 0.1. This value is typical of aggregates formed by rapid flocculation or diffusion limited aggregation. Diafiltration process was found to reduce the average size and polydispersity of the aggregates, determined by photon correlation spectroscopy. Average gyration radius of the aggregates before juice diafiltration was found to be R(g) = 629 ± 87 nm. Average number of primary particles per aggregate was calculated to be N = 1174. PMID:21339133

  8. Influence of pH and sequence in peptide aggregation via molecular simulation

    SciTech Connect

    Enciso, Marta; Schütte, Christof; Delle Site, Luigi

    2015-12-28

    We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to describe the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse-grained model can account for these details.

  9. VERIFICATION OF 3-PHASES COMPOSITE MODEL FOR DRYING SHRINKAGE OF CONCRETE WITH DEFFERENT AGGREGATE PROPERTIES

    NASA Astrophysics Data System (ADS)

    Tanaka, Kie; Shima, Hiroshi

    Properties of aggregate are not taken into account in current codes for drying shrinkage of concrete although the drying shrinkage is affected by the properties of aggregate. Aggregate restrains cement paste from shrinkage so that the drying shrinkage of concrete is controlled by drying shrinkage and Young's modulus of aggregate itself. The effect of the aggregate properties on drying shrinkage of concrete can be calculated by composite model in which concrete consists of cement paste and aggregate. Several different kind of coarse aggregate were used in order to verify a 3-phases composite model for drying shrinkage. Drying shrinkage and Young's modulus of cement paste, aggregate and concrete were measured. It was verified that drying shrinkage of concrete can be estimated accurately by the composite model associating with both drying shrinkage and Young's modulus of aggregate.

  10. Interplay between the hydrophobic effect and dipole interactions in peptide aggregation at interfaces.

    PubMed

    Ganesan, Sai J; Matysiak, Silvina

    2016-01-28

    Protein misfolding is an intrinsic property of polypeptides, and misfolded conformations have a propensity to aggregate. In the past decade, the development of various coarse-grained models for proteins has provided key insights into the driving forces in folding and aggregation. We recently developed a low resolution Water Explicit Polarizable PROtein coarse-grained Model (WEPPROM) by adding oppositely charged dummy particles inside protein backbone beads. With this model, we were able to achieve significant α/β secondary structure content, without any added bias. We now extend the model to study peptide aggregation at hydrophobic-hydrophilic interfaces and draw comparisons to aggregation in explicit water solvent. Elastin-like octapeptides (GV)4 are used as a model system for this study. A condensation-ordering mechanism of aggregation is observed in water. Our results suggest that backbone interpeptide dipolar interactions, not hydrophobicity, plays a more significant role in fibril-like peptide aggregation. We observe a cooperative effect in hydrogen bonding or dipolar interactions, with an increase in aggregate size in water and at interfaces. Based on this cooperative effect, we provide a potential explanation for the observed nucleus size in peptide aggregation pathways. The presence of a hydrophobic-hydrophilic interface increases both (a) order of aggregates formed, and (b) rate of the aggregation process. Without dipolar particles, peptide aggregation is not observed at the hydrophilic-hydrophobic interface. Thus, the presence of dipoles, not hydrophobicity, plays a key role in aggregation observed at hydrophobic interfaces. PMID:26698374

  11. Acoustic emission monitoring of recycled aggregate concrete under bending

    NASA Astrophysics Data System (ADS)

    Tsoumani, A. A.; Barkoula, N.-M.; Matikas, T. E.

    2015-03-01

    The amount of construction and demolition waste has increased considerably over the last few years, making desirable the reuse of this waste in the concrete industry. In the present study concrete specimens are subjected at the age of 28 days to four-point bending with concurrent monitoring of their acoustic emission (AE) activity. Several concrete mixtures prepared using recycled aggregates at various percentages of the total coarse aggregate and also a reference mix using natural aggregates, were included to investigate their influence of the recycled aggregates on the load bearing capacity, as well as on the fracture mechanisms. The results reveal that for low levels of substitution the influence of using recycled aggregates on the flexural strength is negligible while higher levels of substitution lead into its deterioration. The total AE activity, as well as the AE signals emitted during failure, was related to flexural strength. The results obtained during test processing were found to be in agreement with visual observation.

  12. Mesoscale simulation of asphaltene aggregation

    NASA Astrophysics Data System (ADS)

    Wang, Jiang; Ferguson, Andrew

    Asphaltenes constitute a heavy aromatic crude oil fraction that can aggregate and precipitate out of solution. Association is thought to proceed hierarchically according to the Yen-Mullins model, but the molecular mechanisms and pathways remain poorly understood. In this study, we perform molecular dynamics simulations of the aggregation of hundreds of asphaltenes over microseconds using the coarse-grained Martini force field. We identified a hierarchical self-assembly mechanism consistent with Yen-Mullins model, but the details of which are strongly dependent on asphaltene molecular structure. Monomeric asphaltenes first self-assemble into 1-D rod-like nanoaggregates, followed by the formation of clusters of nanoaggregates. At high concentrations, asphaltenes with short aliphatic side chains assemble into a percolating network with the binding of 1-D rods. Conversely, molecules with more and longer side chains cannot efficiently stack, producing a fractal network of 1-D rods suspended in a sea of interpenetrating aliphatic side chains. Our results provide the first molecularly-detailed validation of the full Yen-Mullins hierarchy, and are in good agreement with recent computational and experimental studies. ACS Petroleum Research Fund.

  13. Unconstrained Structure Formation in Coarse-Grained Protein Simulations

    NASA Astrophysics Data System (ADS)

    Bereau, Tristan

    The ability of proteins to fold into well-defined structures forms the basis of a wide variety of biochemical functions in and out of the cell membrane. Many of these processes, however, operate at time- and length-scales that are currently unattainable by all-atom computer simulations. To cope with this difficulty, increasingly more accurate and sophisticated coarse-grained models are currently being developed. In the present thesis, we introduce a solvent-free coarse-grained model for proteins. Proteins are modeled by four beads per amino acid, providing enough backbone resolution to allow for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. By studying both helical and extended conformations we make sure the force field is not biased towards any particular secondary structure. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed. The model is subsequently applied to various biophysical problems: (i) kinetics of folding of two model peptides, (ii) large-scale amyloid-beta oligomerization, and (iii) protein folding cooperativity. The last topic---defined by the nature of the finite-size thermodynamic transition exhibited upon folding---was investigated from a microcanonical perspective: the accurate evaluation of the density of states can unambiguously characterize the nature of the transition, unlike its corresponding canonical analysis. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition. Finally, we combine the peptide model with a high-resolution, solvent-free, lipid

  14. Insights into DNA-mediated interparticle interactions from a coarse-grained model.

    PubMed

    Ding, Yajun; Mittal, Jeetain

    2014-11-14

    DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA-functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions. PMID:25399156

  15. Determination of the dynamic elastic constants of recycled aggregate concrete

    NASA Astrophysics Data System (ADS)

    Tsoumani, A. A.; Barkoula, N.-M.; Matikas, T. E.

    2015-03-01

    Nowadays, construction and demolition waste constitutes a major portion of the total solid waste production in the world. Due to both environmental and economical reasons, an increasing interest concerning the use of recycled aggregate to replace aggregate from natural sources is generated. This paper presents an investigation on the properties of recycled aggregate concrete. Concrete mixes are prepared using recycled aggregates at a substitution level between 0 and 100% of the total coarse aggregate. The influence of this replacement on strengthened concrete's properties is being investigated. The properties estimated are: density and dynamic modulus of elasticity at the age of both 7 and 28 days. Also, flexural strength of 28 days specimens is estimated. The determination of the dynamic elastic modulus was made using the ultrasonic pulse velocity method. The results reveal that the existence of recycled aggregates affects the properties of concrete negatively; however, in low levels of substitution the influence of using recycled aggregates is almost negligible. Concluding, the controlled use of recycled aggregates in concrete production may help solve a vital environmental issue apart from being a solution to the problem of inadequate concrete aggregates.

  16. Investigations on Fresh and Hardened Properties of Recycled Aggregate Self Compacting Concrete

    NASA Astrophysics Data System (ADS)

    Revathi, P.; Selvi, R. S.; Velin, S. S.

    2013-09-01

    In the recent years, construction and demolition waste management issues have attracted the attention from researchers around the world. In the present study, the potential usage of recycled aggregate obtained from crushed demolition waste for making self compacting concrete (SCC) was researched. The barriers in promoting the use of recycled material in new construction are also discussed. In addition, the results of an experimental study involving the use of recycled concrete aggregate as coarse aggregates for producing self-compacting concrete to study their flow and strength characteristics are also presented. Five series of mixture were prepared with 0, 25, 50, 75, and 100 % coarse recycled aggregate adopting Nan Su's mix proportioning method. The fresh concrete properties were evaluated through the slump flow, J-ring and V-funnel tests. Compressive and tensile strengths were also determined. The results obtained showed that SCC could be successfully developed by incorporating recycled aggregates.

  17. A closed-loop life cycle assessment of recycled aggregate concrete utilization in China.

    PubMed

    Ding, Tao; Xiao, Jianzhuang; Tam, Vivian W Y

    2016-10-01

    This paper studies the potential environmental impact of recycled coarse aggregate (RCA) for concrete production in China. According to the cradle-to-cradle theory, a closed-loop life cycle assessment (LCA) on recycled aggregate concrete (RAC) utilization in China with entire local life cycle inventory (LCI) is performed, regarding the environmental influence of cement content, aggregate production, transportation and waste landfilling. Special attention is paid on the primary resource and energy conservation, as well as climate protection induced by RAC applications. Environmental impact between natural aggregate concrete (NAC) and RAC are also compared. It is shown that cement proportion and transportation are the top two contributors for carbon dioxide (CO2) emissions and energy consumption for both NAC and RAC. Sensitivity analysis also proves that long delivery distances for natural coarse aggregate (NCA) leave a possible opportunity for lowering environmental impact of RAC in China. PMID:27297045

  18. Coarse-graining Landau-Lifshitz damping

    NASA Astrophysics Data System (ADS)

    Feng, Xuebing; Visscher, P. B.

    2001-06-01

    High speed switching in magnetic materials is usually studied with the Landau-Lifshitz (LL) equation, which describes damping through a phenomenological coefficient. The results of micromagnetic calculations based on the LL equation have been observed to depend strongly on the cell size. We take a coarse-graining or renormalization-group approach to this cell size dependence: from a simulation using cell size L, we look at the dynamics of a cell of size 2L and determine an effective damping coefficient that describes the larger-scale dynamics. This can be thought of as a Green-Kubo calculation of the effective damping coefficient. In principle, this makes it possible to coarse grain from the atomic scale to determine the micromagnetic damping coefficient.

  19. On the evolution of coarse categories.

    PubMed

    Mengel, Friederike

    2012-08-21

    We compare the evolutionary fitness of different cultures (or populations), where we think of culture as partitioning a set of decision situations into categories of situations treated the same. Information about optimal behavior in each category is passed on via a process of noisy cultural transmission. We show that coarse partitions (distinguishing less situations) can provide higher evolutionary fitness even if there are no explicit costs to holding finer partitions. PMID:22659044

  20. Measuring Crack Length in Coarse Grain Ceramics

    NASA Technical Reports Server (NTRS)

    Salem, Jonathan A.; Ghosn, Louis J.

    2010-01-01

    Due to a coarse grain structure, crack lengths in precracked spinel specimens could not be measured optically, so the crack lengths and fracture toughness were estimated by strain gage measurements. An expression was developed via finite element analysis to correlate the measured strain with crack length in four-point flexure. The fracture toughness estimated by the strain gaged samples and another standardized method were in agreement.

  1. Platelet aggregation test

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/003669.htm Platelet aggregation test To use the sharing features on this page, please enable JavaScript. The platelet aggregation blood test checks how well platelets , a ...

  2. Platelet aggregation test

    MedlinePlus

    The platelet aggregation blood test checks how well platelets , a part of blood, clump together and cause blood to clot. ... Decreased platelet aggregation may be due to: Autoimmune ... Fibrin degradation products Inherited platelet function defects ...

  3. Critical time scale of coarse-graining entropy production

    NASA Astrophysics Data System (ADS)

    Sohn, Jang-il

    2016-04-01

    We study coarse-grained entropy production in an asymmetric random walk system on a periodic one-dimensional lattice. In coarse-grained systems, the original dynamics are unavoidably destroyed, but the coarse-grained entropy production is not hidden below the critical time-scale separation. The hidden entropy production is rapidly increasing near the critical time-scale separation.

  4. Coarse mode aerosols in the High Arctic

    NASA Astrophysics Data System (ADS)

    Baibakov, K.; O'Neill, N. T.; Chaubey, J. P.; Saha, A.; Duck, T. J.; Eloranta, E. W.

    2014-12-01

    Fine mode (submicron) aerosols in the Arctic have received a fair amount of scientific attention in terms of smoke intrusions during the polar summer and Arctic haze pollution during the polar winter. Relatively little is known about coarse mode (supermicron) aerosols, notably dust, volcanic ash and sea salt. Asian dust is a regular springtime event whose optical and radiative forcing effects have been fairly well documented at the lower latitudes over North America but rarely reported for the Arctic. Volcanic ash, whose socio-economic importance has grown dramatically since the fear of its effects on aircraft engines resulted in the virtual shutdown of European civil aviation in the spring of 2010 has rarely been reported in the Arctic in spite of the likely probability that ash from Iceland and the Aleutian Islands makes its way into the Arctic and possibly the high Arctic. Little is known about Arctic sea salt aerosols and we are not aware of any literature on the optical measurement of these aerosols. In this work we present preliminary results of the combined sunphotometry-lidar analysis at two High Arctic stations in North America: PEARL (80°N, 86°W) for 2007-2011 and Barrow (71°N,156°W) for 2011-2014. The multi-years datasets were analyzed to single out potential coarse mode incursions and study their optical characteristics. In particular, CIMEL sunphotometers provided coarse mode optical depths as well as information on particle size and refractive index. Lidar measurements from High Spectral Resolution lidars (AHSRL at PEARL and NSHSRL at Barrow) yielded vertically resolved aerosol profiles and gave an indication of particle shape and size from the depolarization ratio and color ratio profiles. Additionally, we employed supplementary analyses of HYSPLIT backtrajectories, OMI aerosol index, and NAAPS (Navy Aerosol Analysis and Prediction System) outputs to study the spatial context of given events.

  5. A Coarse Pointing Assembly for Optical Communication

    NASA Technical Reports Server (NTRS)

    Szekely, G.; Blum, D.; Humphries, M.; Koller, A.; Mussett, D.; Schuler, S.; Vogt, P.

    2010-01-01

    In the framework of a contract with the European Space Agency, RUAG Space are developing a Coarse Pointing Assembly for an Optical Communication Terminal with the goal to enable high-bandwidth data exchange between GEO and/or LEO satellites as well as to earth-bound ground stations. This paper describes some development and testing aspects of such a high precision opto-mechanical device, with emphasis on the influence of requirements on the final design, the usage of a Bearing Active Preload System, some of the lessons learned on the BAPS implementation, the selection of a flex print design as rotary harness and some aspects of functional and environmental testing.

  6. Coarse-grained modelling of supercoiled RNA

    NASA Astrophysics Data System (ADS)

    Matek, Christian; Šulc, Petr; Randisi, Ferdinando; Doye, Jonathan P. K.; Louis, Ard A.

    2015-12-01

    We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.

  7. Coarse grained open system quantum dynamics

    SciTech Connect

    Thanopulos, Ioannis; Brumer, Paul; Shapiro, Moshe

    2008-11-21

    We show that the quantum dynamics of a system comprised of a subspace Q coupled to a larger subspace P can be recast as a reduced set of 'coarse grained' ordinary differential equations with constant coefficients. These equations can be solved by a single diagonalization of a general complex matrix. The method makes no assumptions about the strength of the couplings between the Q and the P subspaces, nor is there any limitation on the initial population in P. The utility of the method is demonstrated via computations in three following areas: molecular compounds, photonic materials, and condensed phases.

  8. Coarse-grained modelling of surface nanobubbles

    NASA Astrophysics Data System (ADS)

    Grosfils, Patrick

    2013-05-01

    Surface nanobubbles are nanoscale gaseous objects that form on hydrophobic surfaces in contact with water. Understanding nanobubble formation and stability remains challenging due to the lack of appropriate theoretical framework and adequate modelling. Here we present a non-equilibrium coarse-grained model for nanobubbles at hydrophobic surfaces. The model is based on a lattice-gas model that has been proposed to understand the hydrophobic effect to which dynamical properties are added. The results presented demonstrate the ability of the model to reproduce the basic features of stable surface nanobubbles, which, thereby, supports the dynamical origin of these objects.

  9. The effect of recycled concrete aggregate properties on the bond strength between RCA concrete and steel reinforcement

    SciTech Connect

    Butler, L. West, J.S.; Tighe, S.L.

    2011-10-15

    The purpose of this study was to investigate the influence that replacing natural coarse aggregate with recycled concrete aggregate (RCA) has on concrete bond strength with reinforcing steel. Two sources of RCA were used along with one natural aggregate source. Numerous aggregate properties were measured for all aggregate sources. Two types of concrete mixture proportions were developed replacing 100% of the natural aggregate with RCA. The first type maintained the same water-cement ratios while the second type was designed to achieve the same compressive strengths. Beam-end specimens were tested to determine the relative bond strength of RCA and natural aggregate concrete. On average, natural aggregate concrete specimens had bond strengths that were 9 to 19% higher than the equivalent RCA specimens. Bond strength and the aggregate crushing value seemed to correlate well for all concrete types.

  10. Effects of maximum aggregate size on UPV of brick aggregate concrete.

    PubMed

    Mohammed, Tarek Uddin; Mahmood, Aziz Hasan

    2016-07-01

    Investigation was carried out to study the effects of maximum aggregate size (MAS) (12.5mm, 19.0mm, 25.0mm, 37.5mm, and 50.0mm) on ultrasonic pulse velocity (UPV) of concrete. For investigation, first class bricks were collected and broken to make coarse aggregate. The aggregates were tested for specific gravity, absorption capacity, unit weight, and abrasion resistance. Cylindrical concrete specimens were made with different sand to aggregate volume ratio (s/a) (0.40 and 0.45), W/C ratio (0.45, 0.50, and 0.55), and cement content (375kg/m(3) and 400kg/m(3)). The specimens were tested for compressive strength and Young's modulus. UPV through wet specimen was measured using Portable Ultrasonic Non-destructive Digital Indicating Tester (PUNDIT). Results indicate that the pulse velocity through concrete increases with an increase in MAS. Relationships between UPV and compressive strength; and UPV and Young's modulus of concrete are proposed for different maximum sizes of brick aggregate. PMID:27085110

  11. Temporal stability of a coarse sediment community in the Central Eastern English Channel Paleovalleys

    NASA Astrophysics Data System (ADS)

    Lozach, Sophie; Dauvin, Jean-Claude

    2012-07-01

    The natural variation of the benthic community of eastern Channel paleovalleys was investigated over a four-year period in the context of an aggregate extraction licence for the French side of the English Channel. Six surveys were conducted: twice a year (mid-April: pre-recruitment and the end of August: post-recruitment) in 2007, 2009 and 2010. The area showed similar features of community structural parameters, to other coarse sediment areas in the eastern English Channel. This area also presented an outstanding constancy over time. The baseline obtained allows the identification of cause-effect relationships between the impact of aggregate dredging and environmental changes and also highlights the consequences of dredging on key ecological attributes. The long-term biological recovery rate will thereby be easier to assess. The use of this baseline is discussed in terms of implications for future management of the study area.

  12. Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.

    PubMed

    Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone

    2015-04-14

    A novel simulation framework that integrates the OPEP coarse-grained (CG) model for proteins with the Lattice Boltzmann (LB) methodology to account for the fluid solvent at mesoscale level is presented. OPEP is a very efficient, water-free and electrostatic-free force field that reproduces at quasi-atomistic detail processes like peptide folding, structural rearrangements, and aggregation dynamics. The LB method is based on the kinetic description of the solvent in order to solve the fluid mechanics under a wide range of conditions, with the further advantage of being highly scalable on parallel architectures. The capabilities of the approach are presented, and it is shown that the strategy is effective in exploring the role of hydrodynamics on protein relaxation and peptide aggregation. The end result is a strategy for modeling systems of thousands of proteins, such as in the case of dense protein suspensions. The future perspectives of the multiscale approach are also discussed. PMID:26574390

  13. Coarse-grained distributions and superstatistics

    NASA Astrophysics Data System (ADS)

    Chavanis, Pierre-Henri

    2006-01-01

    We show an interesting connection between non-standard (non-Boltzmannian) distribution functions arising in the theory of violent relaxation for collisionless stellar systems [D. Lynden-Bell, Mon. Not. R. Astron. Soc. 136 (1967) 101.] and the notion of superstatistics recently introduced by [Beck and Cohen Physica A 322 (2003) 267]. The common link between these two theories is the emergence of coarse-grained distributions arising out of fine-grained distributions. The coarse-grained distribution functions are written as a superposition of Boltzmann factors weighted by a non-universal function. Even more general distributions can arise in case of incomplete violent relaxation (non-ergodicity). They are stable stationary solutions of the Vlasov equation. We also discuss analogies and differences between the statistical equilibrium state of a multi-components self-gravitating system and the metaequilibrium (or quasi-equilibrium) states of a collisionless stellar system. Finally, we stress the important distinction between entropies, generalized entropies, relative entropies and H-functions. We discuss applications of these ideas in two-dimensional turbulence and for other systems with long-range interactions.

  14. Coarse-Grain Modeling of Energetic Materials

    NASA Astrophysics Data System (ADS)

    Brennan, John

    2015-06-01

    Mechanical and thermal loading of energetic materials can incite responses over a wide range of spatial and temporal scales due to inherent nano- and microscale features. Many energy transfer processes within these materials are atomistically governed, yet the material response is manifested at the micro- and mesoscale. The existing state-of-the-art computational methods include continuum level approaches that rely on idealized field-based formulations that are empirically based. Our goal is to bridge the spatial and temporal modeling regimes while ensuring multiscale consistency. However, significant technical challenges exist, including that the multiscale methods linking the atomistic and microscales for molecular crystals are immature or nonexistent. To begin addressing these challenges, we have implemented a bottom-up approach for deriving microscale coarse-grain models directly from quantum mechanics-derived atomistic models. In this talk, a suite of computational tools is described for particle-based microscale simulations of the nonequilibrium response of energetic solids. Our approach builds upon recent advances both in generating coarse-grain models under high strains and in developing a variant of dissipative particle dynamics that includes chemical reactions.

  15. Compressive strength and resistance to chloride ion penetration and carbonation of recycled aggregate concrete with varying amount of fly ash and fine recycled aggregate.

    PubMed

    Sim, Jongsung; Park, Cheolwoo

    2011-11-01

    Construction and demolition waste has been dramatically increased in the last decade, and social and environmental concerns on the recycling have consequently been increased. Recent technology has greatly improved the recycling process for waste concrete. This study investigates the fundamental characteristics of concrete using recycled concrete aggregate (RCA) for its application to structural concrete members. The specimens used 100% coarse RCA, various replacement levels of natural aggregate with fine RCA, and several levels of fly ash addition. Compressive strength of mortar and concrete which used RCA gradually decreased as the amount of the recycled materials increased. Regardless of curing conditions and fly ash addition, the 28 days strength of the recycled aggregate concrete was greater than the design strength, 40 MPa, with a complete replacement of coarse aggregate and a replacement level of natural fine aggregate by fine RCA up to 60%. The recycled aggregate concrete achieved sufficient resistance to the chloride ion penetration. The measured carbonation depth did not indicate a clear relationship to the fine RCA replacement ratio but the recycled aggregate concrete could also attain adequate carbonation resistance. Based on the results from the experimental investigations, it is believed that the recycled aggregate concrete can be successfully applied to structural concrete members. PMID:21784626

  16. Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly.

    PubMed

    Frederix, Pim W J M; Ulijn, Rein V; Hunt, Neil T; Tuttle, Tell

    2011-10-01

    Several short peptide sequences are known to self-assemble into supramolecular nanostructures with interesting properties. In this study, coarse-grained molecular dynamics is employed to rapidly screen all 400 dipeptide combinations and predict their ability to aggregate as a potential precursor to their self-assembly. The simulation protocol and scoring method proposed allows a rapid determination of whether a given peptide sequence is likely to aggregate (an indicator for the ability to self-assemble) under aqueous conditions. Systems that show strong aggregation tendencies in the initial screening are selected for longer simulations, which result in good agreement with the known self-assembly or aggregation of dipeptides reported in the literature. Our extended simulations of the diphenylalanine system show that the coarse-grain model is able to reproduce salient features of nanoscale systems and provide insight into the self-assembly process for this system. PMID:23795243

  17. Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly

    PubMed Central

    2011-01-01

    Several short peptide sequences are known to self-assemble into supramolecular nanostructures with interesting properties. In this study, coarse-grained molecular dynamics is employed to rapidly screen all 400 dipeptide combinations and predict their ability to aggregate as a potential precursor to their self-assembly. The simulation protocol and scoring method proposed allows a rapid determination of whether a given peptide sequence is likely to aggregate (an indicator for the ability to self-assemble) under aqueous conditions. Systems that show strong aggregation tendencies in the initial screening are selected for longer simulations, which result in good agreement with the known self-assembly or aggregation of dipeptides reported in the literature. Our extended simulations of the diphenylalanine system show that the coarse-grain model is able to reproduce salient features of nanoscale systems and provide insight into the self-assembly process for this system. PMID:23795243

  18. Organic carbon, water repellency and soil stability to slaking at aggregate and intra-aggregate scales

    NASA Astrophysics Data System (ADS)

    Jordán López, Antonio; García-Moreno, Jorge; Gordillo-Rivero, Ángel J.; Zavala, Lorena M.; Cerdà, Artemi; Alanís, Nancy; Jiménez-Compán, Elizabeth

    2015-04-01

    intensity of WR in aggregates of different sizes. [ii] the intra-aggregate distribution of OC and the intensity of WR and [iii] the structural stability of soil aggregates relative to the OC content and the intensity of WR in soils under different crops (apricot, citrus and wheat) and different treatments (conventional tilling and mulching). Soil samples were collected from an experimental area (Luvic Calcisols and Calcic Luvisols) in the province of Sevilla (Southern Spain) under different crops (apricot, citrus and wheat) and different management types (conventional tillage with moldboard plow) and mulching (no-tilling and addition of wheat residues at rates varying between 5 and 8 Mg/ha/year). At each sampling site, soil blocks (50 cm long × 50 cm wide × 10 cm deep) were carefully collected to avoid disturbance of aggregates as much as possible and transported to the laboratory. At field moist condition, undisturbed soil aggregates were separated by hand. In order to avoid possible interferences due to disturbance by handling, aggregates broken during this process were discarded. Individual aggregates were arranged in paper trays and air-dried during 7 days under laboratory standard conditions. After air-drying, part of each sample was carefully divided for different analyses: [i] part of the original samples was sieved (2 mm) to eliminate coarse soil particles and homogenized for characterization of OC and N contents, C/N ratio and texture; [ii] part of the aggregates were dry-sieved (0.25-0.5, 0.5-1 and 1-2 mm) or measured with a caliper (2-5, 5-10 and 10-15 mm) and separated in different sieve-size classes for determination of WR and OC content; [iii] aggregates 10-15 mm in size were selected for obtaining aggregate layers using a soil aggregate erosion (SAE) apparatus and WR and OC content were determined at each layer; finally, [iv] in order to study the relation between stability to slaking, WR and OC, these properties were determined in 90 air-dried aggregates

  19. Effect of Coarse Materials Percentage in the Shear Strength

    NASA Astrophysics Data System (ADS)

    Alshameri, B.; Bakar, I.; Madun, A.; Abdeldjouad, L.; Haimi Dahlan, S.

    2016-07-01

    There are several factors that affecting the shear strength and shear strength parameters (i.e. cohesion and friction angle). In this study, the effect of coarse material percentage was tested. Six different mixtures of soils (clay and sand) with different coarse material percentages (i.e. from 80% to 30% of coarse material percentage) were tested via using direct shear test under different moisture content percentage. The results indicated that the shear strength and friction angle were decreased by the increment of the percentage of coarse materials (sand). However, the cohesion results showed unique behavior. The cohesion (at every moisture content values) increased with the increment of the percentage of coarse materials until specific point then it started to decrease with the increment of the percentage of coarse materials.

  20. Aggregate-mediated charge transport in ionomeric electrolytes

    NASA Astrophysics Data System (ADS)

    Lu, Keran; Maranas, Janna; Milner, Scott

    Polymers such PEO can conduct ions, and have been studied as possible replacements for organic liquid electrolytes in rechargeable metal-ion batteries. More generally, fast room-temperature ionic conduction has been reported for a variety of materials, from liquids to crystalline solids. Unfortunately, polymer electrolytes generally have limited conductivity; these polymers are too viscous to have fast ion diffusion like liquids, and too unstructured to promote cooperative transport like crystalline solids. Ionomers are polymer electrolytes in which ionic groups are covalently bound to the polymer backbone, neutralized by free counterions. These materials also conduct ions, and can exhibit strong ionic aggregation. Using coarse-grained molecular dynamics, we explore the forces driving ionic aggregation, and describe the role ion aggregates have in mediating charge transport. The aggregates are string-like such that ions typically have two neighbors. We find ion aggregates self-assemble like worm-like micelles. Excess charge, or free ions, occasionally coordinate with aggregates and are transported along the chain in a Grotthuss-like mechanism. We propose that controlling ionomer aggregate structure through materials design can enhance cooperative ion transport.

  1. Coarse-grained modeling of DNA curvature

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    The interaction of DNA with proteins occurs over a wide range of length scales, and depends critically on its local structure. In particular, recent experimental work suggests that the intrinsic curvature of DNA plays a significant role on its protein-binding properties. In this work, we present a coarse grained model of DNA that is capable of describing base-pairing, hybridization, major and minor groove widths, and local curvature. The model represents an extension of the recently proposed 3SPN.2 description of DNA [D. M. Hinckley, G. S. Freeman, J. K. Whitmer, and J. J. de Pablo, J. Chem. Phys. 139, 144903 (2013)], into which sequence-dependent shape and mechanical properties are incorporated. The proposed model is validated against experimental data including melting temperatures, local flexibilities, dsDNA persistence lengths, and minor groove width profiles.

  2. Aggregations in Flatworms.

    ERIC Educational Resources Information Center

    Liffen, C. L.; Hunter, M.

    1980-01-01

    Described is a school project to investigate aggregations in flatworms which may be influenced by light intensity, temperature, and some form of chemical stimulus released by already aggregating flatworms. Such investigations could be adopted to suit many educational levels of science laboratory activities. (DS)

  3. Comparative environmental assessment of natural and recycled aggregate concrete.

    PubMed

    Marinković, S; Radonjanin, V; Malešev, M; Ignjatović, I

    2010-11-01

    Constant and rapid increase in construction and demolition (C&D) waste generation and consumption of natural aggregate for concrete production became one of the biggest environmental problems in the construction industry. Recycling of C&D waste represents one way to convert a waste product into a resource but the environment benefits through energy consumption, emissions and fallouts reductions are not certain. The main purpose of this study is to determine the potentials of recycled aggregate concrete (concrete made with recycled concrete aggregate) for structural applications and to compare the environmental impact of the production of two types of ready-mixed concrete: natural aggregate concrete (NAC) made entirely with river aggregate and recycled aggregate concrete (RAC) made with natural fine and recycled coarse aggregate. Based on the analysis of up-to-date experimental evidence, including own tests results, it is concluded that utilization of RAC for low-to-middle strength structural concrete and non-aggressive exposure conditions is technically feasible. The Life Cycle Assessment (LCA) is performed for raw material extraction and material production part of the concrete life cycle including transport. Assessment is based on local LCI data and on typical conditions in Serbia. Results of this specific case study show that impacts of aggregate and cement production phases are slightly larger for RAC than for NAC but the total environmental impacts depend on the natural and recycled aggregates transport distances and on transport types. Limit natural aggregate transport distances above which the environmental impacts of RAC can be equal or even lower than the impacts of NAC are calculated for the specific case study. PMID:20434898

  4. Interfacial adsorption and aggregation of amphiphilic proteins

    NASA Astrophysics Data System (ADS)

    Cheung, David

    2012-02-01

    The adsorption and aggregation on liquid interfaces of proteins is important in many biological contexts, such as the formation of aerial structures, immune response, and catalysis. Likewise the adsorption of proteins onto interfaces has applications in food technology, drug delivery, and in personal care products. As such there has been much interest in the study of a wide range of biomolecules at liquid interfaces. One class of proteins that has attracted particular attention are hydrophobins, small, fungal proteins with a distinct, amphiphilic surface structure. This makes these proteins highly surface active and they recently attracted much interest. In order to understand their potential applications a microscopic description of their interfacial and self-assembly is necessary and molecular simulation provides a powerful tool for providing this. In this presentation I will describe some recent work using coarse-grained molecular dynamics simulations to study the interfacial and aggregation behaviour of hydrophobins. Specifically this will present the calculation of their adsorption strength at oil-water and air-water interfaces, investigate the stability of hydrophobin aggregates in solution and their interaction with surfactants.

  5. Charged Dust Aggregate Interactions

    NASA Astrophysics Data System (ADS)

    Matthews, Lorin; Hyde, Truell

    2015-11-01

    A proper understanding of the behavior of dust particle aggregates immersed in a complex plasma first requires a knowledge of the basic properties of the system. Among the most important of these are the net electrostatic charge and higher multipole moments on the dust aggregate as well as the manner in which the aggregate interacts with the local electrostatic fields. The formation of elongated, fractal-like aggregates levitating in the sheath electric field of a weakly ionized RF generated plasma discharge has recently been observed experimentally. The resulting data has shown that as aggregates approach one another, they can both accelerate and rotate. At equilibrium, aggregates are observed to levitate with regular spacing, rotating about their long axis aligned parallel to the sheath electric field. Since gas drag tends to slow any such rotation, energy must be constantly fed into the system in order to sustain it. A numerical model designed to analyze this motion provides both the electrostatic charge and higher multipole moments of the aggregate while including the forces due to thermophoresis, neutral gas drag, and the ion wakefield. This model will be used to investigate the ambient conditions leading to the observed interactions. This research is funded by NSF Grant 1414523.

  6. Effect of β-sheet propensity on peptide aggregation

    NASA Astrophysics Data System (ADS)

    Bellesia, Giovanni; Shea, Joan-Emma

    2009-04-01

    The effect of β-sheet propensity on the structural features of peptide aggregates was investigated using an off-lattice coarse-grained peptide model. A phase diagram as a function of temperature and β-sheet propensity reveals a diverse family of supramolecular assemblies. Highly rigid peptides (peptides with high β-sheet propensity) are seen to assemble predominantly into fibrillar structures. Increasing the flexibility of the peptide (reducing β-sheet propensity) leads to a variety of structures, including fibrils, β-barrel structures, and amorphous aggregates. Nonfibrillar entities have been suggested as primary causative agents in amyloid diseases and our simulations indicate that mutations that decrease β-sheet propensity will decrease fibril formation and favor the formation of such toxic oligomers. Parallels between β-sheet aggregates and nematic liquid crystals are discussed.

  7. Aggregate and the environment

    USGS Publications Warehouse

    Langer, William H.; Drew, Lawrence J.; Sachs, J.S.

    2004-01-01

    This book is designed to help you understand our aggregate resources-their importance, where they come from, how they are processed for our use, the environmental concerns related to their mining and processing, how those concerns are addressed, and the policies and regulations designed to safeguard workers, neighbors, and the environment from the negative impacts of aggregate mining. We hope this understanding will help prepare you to be involved in decisions that need to be made-individually and as a society-to be good stewards of our aggregate resources and our living planet.

  8. Airborne Measurements of Coarse Mode Aerosol Composition and Abundance

    NASA Astrophysics Data System (ADS)

    Froyd, K. D.; Murphy, D. M.; Brock, C. A.; Ziemba, L. D.; Anderson, B. E.; Wilson, J. C.

    2015-12-01

    Coarse aerosol particles impact the earth's radiative balance by direct scattering and absorption of light and by promoting cloud formation. Modeling studies suggest that coarse mode mineral dust and sea salt aerosol are the dominant contributors to aerosol optical depth throughout much of the globe. Lab and field studies indicate that larger aerosol particles tend to be more efficient ice nuclei, and recent airborne measurements confirm the dominant role of mineral dust on cirrus cloud formation. However, our ability to simulate coarse mode particle abundance in large scale models is limited by a lack of validating measurements above the earth's surface. We present airborne measurements of coarse mode aerosol abundance and composition over several mid-latitude, sub-tropical, and tropical regions from the boundary layer to the stratosphere. In the free troposphere the coarse mode constitutes 10-50% of the total particulate mass over a wide range of environments. Above North America mineral dust typically dominates the coarse mode, but biomass burning particles and sea salt also contribute. In remote environments coarse mode aerosol mainly consists of internally mixed sulfate-organic particles. Both continental and marine convection can enhance coarse aerosol mass through direct lofting of primary particles and by secondary accumulation of aerosol material through cloud processing.

  9. Coarse grained dynamics in the glass phase

    NASA Astrophysics Data System (ADS)

    Smessaert, Anton; Rottler, Jörg

    2013-03-01

    Atomic scale dynamics in glasses is dominated by extended periods of localized vibration, where the crowded surroundings of a particle act as a cage. Collective motion is necessary to escape the cage, and the succession of particle jumps or hops leads to diffusion. Each jump is an elementary relaxation event since the local structure is stable until a jump occurs. The link between local dynamics and structural properties has become of increasing interest in recent years. Aging of the mechanical response has been tied to a power-law distribution of persistence times in the cages, and concentration of hops into dynamical heterogeneities (DH) was observed in granular media and simulations of supercooled liquids in 2D. These studies were limited to small systems or hop detection in subsets, because of the post processing requirements. We present results based on a new algorithm that allows us to detect the hops of all particles during a molecular dynamics simulation. This complete coarse-grained ``map'' of the dynamics allows us to directly investigate temporal and spatial correlations between relaxation events. Furthermore, we can readily identify DH using a cluster algorithm and we explore the impact of aging and deformation on the size and shape of DH.

  10. Coarse-grained models for biological simulations

    NASA Astrophysics Data System (ADS)

    Wu, Zhe; Cui, Qiang; Yethiraj, Arun

    2011-03-01

    The large timescales and length-scales of interest in biophysics preclude atomistic study of many systems and processes. One appealing approach is to use coarse-grained (CG) models where several atoms are grouped into a single CG site. In this work we describe a new CG force field for lipids, surfactants, and amino acids. The topology of CG sites is the same as in the MARTINI force field, but the new model is compatible with a recently developed CG electrostatic water (Big Multiple Water, BMW) model. The model not only gives correct structural, elastic properties and phase behavior for lipid and surfactants, but also reproduces electrostatic properties at water-membrane interface that agree with experiment and atomistic simulations, including the potential of mean force for charged amino acid residuals at membrane. Consequently, the model predicts stable attachment of cationic peptides (i.e., poly-Arg) on lipid bilayer surface, which is not shown in previous models with non-electrostatic water.

  11. Protein Colloidal Aggregation Project

    NASA Technical Reports Server (NTRS)

    Oliva-Buisson, Yvette J. (Compiler)

    2014-01-01

    To investigate the pathways and kinetics of protein aggregation to allow accurate predictive modeling of the process and evaluation of potential inhibitors to prevalent diseases including cataract formation, chronic traumatic encephalopathy, Alzheimer's Disease, Parkinson's Disease and others.

  12. Creep of dry clinopyroxene aggregates

    NASA Astrophysics Data System (ADS)

    Bystricky, Misha; Mackwell, Stephen

    2001-01-01

    We have determined diffusional and dislocation creep rheologies for clinopyroxenite Ca1.0Mg0.8Fe0.2Si2O6 under dry conditions by deforming natural and hot-pressed samples at confining pressures of 300-430 MPa and temperatures of 1100°-1250°C with the oxygen fugacity buffered by either nickel-nickel oxide or iron-wüstite powders. The coarse-grained natural Sleaford Bay clinopyroxenite yielded a stress exponent of n = 4.7 ± 0.2 and an activation energy for creep of Q = 760 ± 40 kJ mol-1, consistent with deformation in the dislocation creep regime. The strength of the natural clinopyroxenite is consistent with previous high-temperature measurements of dislocation creep behavior of Sleaford Bay clinopyroxenite by Kirby and Kronenberg [1984] and Boland and Tullis [1986]. Fine-grained clinopyroxenite was prepared from ground powders of the natural clinopyroxenite. Hot-pressed samples were deformed under similar conditions to the natural samples. Mixed-mode deformation behavior was observed, with diffusional creep (n = 1) at lower differential stresses and dislocation creep (with n and Q similar to those of the natural samples) at higher differential stresses. Within the dislocation creep field the predried hot-pressed samples generally yielded creep rates that were about an order of magnitude faster than the natural samples. Thus, even at the highest differential stresses, a component of strain accommodation by grain boundary diffusion was present in the hot-pressed samples. Optical and electron microscope investigations of the deformation microstructures of the natural and hot-pressed samples show evidence for mechanical twinning and activation of dislocation slip systems. When extrapolated to geological conditions expected in the deep crust and upper mantle on Earth and other terrestrial planets, the strength of dry single-phase clinopyroxene aggregates is very high, exceeding that of dry olivine-rich rocks.

  13. PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.

    PubMed

    Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto

    2015-12-01

    Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins. PMID:26597989

  14. Multi-scale morphology in self-assembly of peptides to proteins via a coarse-grain model

    NASA Astrophysics Data System (ADS)

    Pandey, Ras; Farmer, Barry

    2015-03-01

    Self-organizing structures of short peptides (6-7 residues) and proteins (136 residues) are studied by a coarse-grained Monte Carlo simulation. Peptides and proteins are described by coarse-grained chains of residues whose interactions are described by a knowledge-based residue-residue interaction potential that captures the compositional specificity. Large-scale computer simulations are performed to study the structural evolution e.g. aggregation, network, etc. at a range of temperatures and concentrations. A number of local and global physical quantities including structure factor are examined. We find that the residue interactions, concentration, and size of chains are very important in modulating the structure of emerging morphologies in the specified temperature range. Estimates are provided for the effective (fractal) dimension of the assembly over various length scales as a function of temperature. This work is supported by the Air Force Research Laboratory.

  15. Interlaced coarse-graining for the dynamic cluster approximation

    NASA Astrophysics Data System (ADS)

    Staar, P.; Jiang, M.; Hähner, U. R.; Schulthess, T. C.; Maier, T. A.

    2016-04-01

    The dynamical cluster approximation (DCA) and its DCA+ extension use coarse-graining of the momentum space to reduce the complexity of quantum many-body problems, thereby mapping the bulk lattice to a cluster embedded in a dynamical mean-field host. Here, we introduce a new form of an interlaced coarse-graining and compare it with the traditional coarse-graining. While it gives a more localized self-energy for a given cluster size, we show that it leads to more controlled results with weaker cluster shape and smoother cluster size dependence, which converge to the results obtained from the standard coarse-graining with increasing cluster size. Most importantly, the new coarse-graining reduces the severity of the fermionic sign problem of the underlying quantum Monte Carlo cluster solver and thus allows for calculations on larger clusters. This enables the treatment of correlations longer ranged than those accessible with the standard coarse-graining and thus can allow for the evaluation of the exact infinite cluster size result via finite size scaling. As a demonstration, we study the hole-doped two-dimensional Hubbard model and show that the interlaced coarse-graining in combination with the extended DCA+ algorithm permits the determination of the superconducting Tc on cluster sizes for which the results can be fit with a Kosterlitz-Thouless scaling law.

  16. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals.

    PubMed

    Singh, Amit Kumar; Singh, Rakesh; Subramani, Rajkumar; Kumar, Rajesh; Wankhede, Dhammaprakash P

    2016-06-01

    Coarse grains are important group of crops that constitutes staple food for large population residing primarily in the arid and semi-arid regions of the world. Coarse grains are designated as nutri-cereals as they are rich in essential amino acids, minerals and vitamins. In spite of having several nutritional virtues in coarse grain as mentioned above, there is still scope for improvement in quality parameters such as cooking qualities, modulation of nutritional constituents and reduction or elimination of anti-nutritional factors. Besides its use in traditional cooking, coarse grains have been used mainly in the weaning food preparation and other malted food production. Improvement in quality parameters will certainly increase consumer's preference for coarse grains and increase their demand. The overall genetic gain in quality traits of economic importance in the cultivated varieties will enhance their industrial value and simultaneously increase income of farmers growing these varieties. The urgent step for improvement of quality traits in coarse grains requires a detailed understanding of molecular mechanisms responsible for varied level of different nutritional contents in different genotypes of these crops. In this review we have discussed the progresses made in understanding of coarse grain biology with various omics tool coupled with modern breeding approaches and the current status with regard to our effort towards dissecting traits related to improvement of quality and nutritional constituents of grains. PMID:27252585

  17. Non-Galerkin Coarse Grids for Algebraic Multigrid

    SciTech Connect

    Falgout, Robert D.; Schroder, Jacob B.

    2014-06-26

    Algebraic multigrid (AMG) is a popular and effective solver for systems of linear equations that arise from discretized partial differential equations. And while AMG has been effectively implemented on large scale parallel machines, challenges remain, especially when moving to exascale. Particularly, stencil sizes (the number of nonzeros in a row) tend to increase further down in the coarse grid hierarchy, and this growth leads to more communication. Therefore, as problem size increases and the number of levels in the hierarchy grows, the overall efficiency of the parallel AMG method decreases, sometimes dramatically. This growth in stencil size is due to the standard Galerkin coarse grid operator, $P^T A P$, where $P$ is the prolongation (i.e., interpolation) operator. For example, the coarse grid stencil size for a simple three-dimensional (3D) seven-point finite differencing approximation to diffusion can increase into the thousands on present day machines, causing an associated increase in communication costs. We therefore consider algebraically truncating coarse grid stencils to obtain a non-Galerkin coarse grid. First, the sparsity pattern of the non-Galerkin coarse grid is determined by employing a heuristic minimal “safe” pattern together with strength-of-connection ideas. Second, the nonzero entries are determined by collapsing the stencils in the Galerkin operator using traditional AMG techniques. The result is a reduction in coarse grid stencil size, overall operator complexity, and parallel AMG solve phase times.

  18. Coarse-grained Simulations of Viral Assembly

    NASA Astrophysics Data System (ADS)

    Elrad, Oren M.

    2011-12-01

    The formation of viral capsids is a marvel of natural engineering and design. A large number (from 60 to thousands) of protein subunits assemble into complete, reproducible structures under a variety of conditions while avoiding kinetic and thermodynamic traps. Small single-stranded RNA viruses not only assemble their coat proteins in this fashion but also package their genome during the self-assembly process. Recent experiments have shown that the coat proteins are competent to assemble not merely around their own genomes but heterologous RNA, synthetic polyanions and even functionalized gold nanoparticles. Remarkably these viruses can even assemble around cargo not commensurate with their native state by adopting different morphologies. Understanding the properties that confer such exquisite precision and flexibility to the assembly process could aid biomedical research in the search for novel antiviral remedies, drug-delivery vehicles and contrast agents used in bioimaging. At the same time, viral assembly provides an excellent model system for the development of a statistical mechanical understanding of biological self-assembly, in the hopes of that we will identify some universal principles that underly such processes. This work consists of computational studies using coarse-grained representations of viral coat proteins and their cargoes. We find the relative strength of protein-cargo and protein-protein interactions has a profound effect on the assembly pathway, in some cases leading to assembly mechanisms that are markedly different from those found in previous work on the assembly of empty capsids. In the case of polymeric cargo, we find the first evidence for a previously theorized mechanism in which the polymer actively participates in recruiting free subunits to the assembly process through cooperative polymer-protein motions. We find that successful assembly is non-monotonic in protein-cargo affinity, such affinity can be detrimental to assembly if it

  19. Arbuscular mycorrhizal fungi make a complex contribution to soil aggregation

    NASA Astrophysics Data System (ADS)

    McGee, Peter; Daynes, Cathal; Damien, Field

    2013-04-01

    Soil aggregates contain solid and fluid components. Aggregates develop as a consequence of the organic materials, plants and hyphae of arbuscular mycorrhizal (AM) fungi acting on the solid phase. Various correlative studies indicate hyphae of AM fungi enmesh soil particles, but their impact on the pore space is poorly understood. Hyphae may penetrate between particles, remove water from interstitial spaces, and otherwise re-arrange the solid phase. Thus we might predict that AM fungi also change the pore architecture of aggregates. Direct observations of pore architecture of soil, such as by computer-aided tomography (CT), is difficult. The refractive natures of solid and biological material are similar. The plant-available water in various treatments allows us to infer changes in pore architecture. Our experimental studies indicate AM fungi have a complex role in the formation and development of aggregates. Soils formed from compost and coarse subsoil materials were planted with mycorrhizal or non-mycorrhizal seedlings and the resultant soils compared after 6 or 14 months in separate experiments. As well as enmeshing particles, AM fungi were associated with the development of a complex pore space and greater pore volume. Even though AM fungi add organic matter to soil, the modification of pore space is not correlated with organic carbon. In a separate study, we visualised hyphae of AM fungi in a coarse material using CT. In this study, hyphae appeared to grow close to the surfaces of particles with limited ramification across the pore spaces. Hyphae of AM fungi appear to utilise soil moisture for their growth and development of mycelium. The strong correlation between moisture and hyphae has profound implications for soil aggregation, plant utilisation of soil water, and the distribution of water as water availability declines.

  20. Generalization of the DLA process with different immiscible components by time-scale coarse graining

    NASA Astrophysics Data System (ADS)

    Postnikov, E. B.; Ryabov, A. B.; Loskutov, A.

    2007-10-01

    In the framework of the mean-field approximation we propose a new approach to the description of the growth of fractal structures which are formed as a result of the process of diffusion limited aggregation. Our approach is based on the coarse graining of the time scale which takes into account the property of discreteness of such structures. The obtained system of partial differential equations allows us to evaluate numerically the fractal dimension and the cluster density depending on the distance from the cluster center. The results are in a quite good agreement with values found by the direct numerical simulations. The proposed approach is generalized for the case of the cluster description with different immiscible particles.

  1. Kinetics of formation of bile salt micelles from coarse-grained Langevin dynamics simulations.

    PubMed

    Vila Verde, Ana; Frenkel, Daan

    2016-06-21

    We examine the mechanism of formation of micelles of dihydroxy bile salts using a coarse-grained, implicit solvent model and Langevin dynamics simulations. We find that bile salt micelles primarily form via addition and removal of monomers, similarly to surfactants with typical head-tail molecular structures, and not via a two-stage mechanism - involving formation of oligomers and their subsequent aggregation to form larger micelles - originally proposed for bile salts. The free energy barrier to removal of single bile monomers from micelles is ≈2kBT, much less than what has been observed for head-tail surfactants. Such a low barrier may be biologically relevant: it allows for rapid release of bile monomers into the intestine, possibly enabling the coverage of fat droplets by bile salt monomers and subsequent release of micelles containing fats and bile salts - a mechanism that is not possible for ionic head-tail surfactants of similar critical micellar concentrations. PMID:27199094

  2. Coarse-grained dynamics of alignment in animal group models

    NASA Astrophysics Data System (ADS)

    Moon, Sung Joon; Levin, Simon; Kevrekidis, Yannis

    2006-03-01

    Coordinated motion in animal groups, such as bird flocks and fish schools, and their models gives rise to remarkable coherent structures. Using equation-free computational tools we explore the coarse-grained dynamics of a model for the orientational movement decision in animal groups, consisting of a small number of informed "leaders" and a large number of uninformed, nonidentical ``followers.'' The direction in which each group member is headed is characterized by a phase angle of a limit-cycle oscillator, whose dynamics are nonlinearly coupled with those of all the other group members. We identify a small number of proper coarse-grained variables (using uncertainty quantification methods) that describe the collective dynamics, and perform coarse projective integration and equation-free bifurcation analysis of the coarse-grained model behavior in these variables.

  3. Two-level method with coarse space size independent convergence

    SciTech Connect

    Vanek, P.; Brezina, M.; Tezaur, R.; Krizkova, J.

    1996-12-31

    The basic disadvantage of the standard two-level method is the strong dependence of its convergence rate on the size of the coarse-level problem. In order to obtain the optimal convergence result, one is limited to using a coarse space which is only a few times smaller than the size of the fine-level one. Consequently, the asymptotic cost of the resulting method is the same as in the case of using a coarse-level solver for the original problem. Today`s two-level domain decomposition methods typically offer an improvement by yielding a rate of convergence which depends on the ratio of fine and coarse level only polylogarithmically. However, these methods require the use of local subdomain solvers for which straightforward application of iterative methods is problematic, while the usual application of direct solvers is expensive. We suggest a method diminishing significantly these difficulties.

  4. Technology meets aggregate

    SciTech Connect

    Wilson, C.; Swan, C.

    2007-07-01

    New technology carried out at Tufts University and the University of Massachusetts on synthetic lightweight aggregate has created material from various qualities of fly ash from coal-fired power plants for use in different engineered applications. In pilot scale manufacturing tests an 'SLA' containing 80% fly ash and 20% mixed plastic waste from packaging was produced by 'dry blending' mixed plastic with high carbon fly ash. A trial run was completed to produce concrete masonry unit (CMU) blocks at a full-scale facility. It has been shown that SLA can be used as a partial substitution of a traditional stone aggregate in hot asphalt mix. 1 fig., 2 photos.

  5. Polarisation mode dispersion correlations with the coarse-step method

    NASA Astrophysics Data System (ADS)

    Braimiotis, Christos; Eberhard, Marc; Blow, Keith

    2006-06-01

    Having a fixed differential-group delay (DGD) term b‧ in the coarse-step method results in a repetitive pattern in the autocorrelation function (ACF). We solve this problem by inserting a varying DGD term at each integration step. Furthermore we compute the range of values needed for b‧ and simulate the phenomenon of polarisation mode dispersion for different statistical distributions of b‧. We examine systematically the modified coarse-step method compared to the analytical model, through our simulation results.

  6. Hot Mix Asphalt Using Light Weight Aggregate Concrete

    NASA Astrophysics Data System (ADS)

    Awwad, Mohammad T.

    Hot mix asphalt concrete is produced by properly blending asphalt, coarse and fine aggregates in addition to filler at temperatures ranging from 80 to 165°C. This research is directed to study the effect of replacing the conventional aggregates by the recycled Light Weight Aggregate Concrete (LWAC) on the properties of the produced asphalt mix. The research studied the optimum asphalt content and the effect of some parameters on the properties of the recycled LWAC. The research included studying thirty-six Marshal Specimens lie in four main groups. Each group was made from crushed LWAC in addition to a comparison group used the pumice instead of the crushed LWAC. The LWAC mixes contained (0, 10, 15 and 20%) of silica powder content. The density, stability, flow, percentages of the air Voids in the Compacted Mixture (VTM), compacted mineral aggregate (VMA) and the Voids Filled by Asphalt (VFA) were investigated for all the studied specimens. The main conclusions drawn from the current research implies that the optimum percent of asphalt was 7.5% for the different percentages of silica powder ratios. The presence of voids in the light weight aggregates and the porosity of the obtained concrete affected largely the behavior of the obtained mix.

  7. Interlaced coarse-graining for the dynamical cluster approximation

    NASA Astrophysics Data System (ADS)

    Haehner, Urs; Staar, Peter; Jiang, Mi; Maier, Thomas; Schulthess, Thomas

    The negative sign problem remains a challenging limiting factor in quantum Monte Carlo simulations of strongly correlated fermionic many-body systems. The dynamical cluster approximation (DCA) makes this problem less severe by coarse-graining the momentum space to map the bulk lattice to a cluster embedded in a dynamical mean-field host. Here, we introduce a new form of an interlaced coarse-graining and compare it with the traditional coarse-graining. We show that it leads to more controlled results with weaker cluster shape and smoother cluster size dependence, which with increasing cluster size converge to the results obtained using the standard coarse-graining. In addition, the new coarse-graining reduces the severity of the fermionic sign problem. Therefore, it enables calculations on much larger clusters and can allow the evaluation of the exact infinite cluster size result via finite size scaling. To demonstrate this, we study the hole-doped two-dimensional Hubbard model and show that the interlaced coarse-graining in combination with the DCA+ algorithm permits the determination of the superconducting Tc on cluster sizes, for which the results can be fitted with the Kosterlitz-Thouless scaling law. This research used resources of the Oak Ridge Leadership Computing Facility (OLCF) awarded by the INCITE program, and of the Swiss National Supercomputing Center. OLCF is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725.

  8. Energy-conserving coarse-graining of complex molecules.

    PubMed

    Español, Pep; Serrano, Mar; Pagonabarraga, Ignacio; Zúñiga, Ignacio

    2016-05-25

    Coarse-graining (CG) of complex molecules is a method to reach time scales that would be impossible to access through brute force molecular simulations. In this paper, we formulate a coarse-grained model for complex molecules using first principles caculations that ensures energy conservation. Each molecule is described in a coarse way by a thermal blob characterized by the position and momentum of the center of mass of the molecule, together with its internal energy as an additional degree of freedom. This level of description gives rise to an entropy-based framework instead of the usual one based on the configurational free energy (i.e. potential of mean force). The resulting dynamic equations, which account for an appropriate description of heat transfer at the coarse-grained level, have the structure of the dissipative particle dynamics with energy conservation (DPDE) model but with a clear microscopic underpinning. Under suitable approximations, we provide explicit microscopic expressions for each component (entropy, mean force, friction and conductivity coefficients) appearing in the coarse-grained model. These quantities can be computed directly using MD simulations. The proposed non-isothermal coarse-grained model is thermodynamically consistent and opens up a first principles CG strategy for the study of energy transport issues that are not accessible using current isothermal models. PMID:27127809

  9. Bayesian parametrization of coarse-grain dissipative dynamics models

    NASA Astrophysics Data System (ADS)

    Dequidt, Alain; Solano Canchaya, Jose G.

    2015-08-01

    We introduce a new bottom-up method for the optimization of dissipative coarse-grain models. The method is based on Bayesian optimization of the likelihood to reproduce a coarse-grained reference trajectory obtained from analysis of a higher resolution molecular dynamics trajectory. This new method is related to force matching techniques, but using the total force on each grain averaged on a coarse time step instead of instantaneous forces. It has the advantage of not being limited to pairwise short-range interactions in the coarse-grain model and also yields an estimation of the friction parameter controlling the dynamics. The theory supporting the method is exposed in a practical perspective, with an analytical solution for the optimal set of parameters. The method was first validated by using it on a system with a known optimum. The new method was then tested on a simple system: n-pentane. The local molecular structure of the optimized model is in excellent agreement with the reference system. An extension of the method allows to get also an excellent agreement for the equilibrium density. As for the dynamic properties, they are also very satisfactory, but more sensitive to the choice of the coarse-grain representation. The quality of the final force field depends on the definition of the coarse grain degrees of freedom and interactions. We consider this method as a serious alternative to other methods like iterative Boltzmann inversion, force matching, and Green-Kubo formulae.

  10. Wavelets as basis functions to represent the coarse-graining potential in multiscale coarse graining approach

    NASA Astrophysics Data System (ADS)

    Maiolo, M.; Vancheri, A.; Krause, R.; Danani, A.

    2015-11-01

    In this paper, we apply Multiresolution Analysis (MRA) to develop sparse but accurate representations for the Multiscale Coarse-Graining (MSCG) approximation to the many-body potential of mean force. We rigorously framed the MSCG method into MRA so that all the instruments of this theory become available together with a multitude of new basis functions, namely the wavelets. The coarse-grained (CG) force field is hierarchically decomposed at different resolution levels enabling to choose the most appropriate wavelet family for each physical interaction without requiring an a priori knowledge of the details localization. The representation of the CG potential in this new efficient orthonormal basis leads to a compression of the signal information in few large expansion coefficients. The multiresolution property of the wavelet transform allows to isolate and remove the noise from the CG force-field reconstruction by thresholding the basis function coefficients from each frequency band independently. We discuss the implementation of our wavelet-based MSCG approach and demonstrate its accuracy using two different condensed-phase systems, i.e. liquid water and methanol. Simulations of liquid argon have also been performed using a one-to-one mapping between atomistic and CG sites. The latter model allows to verify the accuracy of the method and to test different choices of wavelet families. Furthermore, the results of the computer simulations show that the efficiency and sparsity of the representation of the CG force field can be traced back to the mathematical properties of the chosen family of wavelets. This result is in agreement with what is known from the theory of multiresolution analysis of signals.

  11. Aggregates, broccoli and cauliflower

    NASA Astrophysics Data System (ADS)

    Grey, Francois; Kjems, Jørgen K.

    1989-09-01

    Naturally grown structures with fractal characters like broccoli and cauliflower are discussed and compared with DLA-type aggregates. It is suggested that the branching density can be used to characterize the growth process and an experimental method to determine this parameter is proposed.

  12. Concrete using waste oil palm shells as aggregate

    SciTech Connect

    Basri, H.B.; Mannan, M.A.; Zain, M.F.M.

    1999-04-01

    Concrete with oil palm shells (OPS) as coarse aggregate was investigated for its workability, density, and compressive strength development over 56 days under three curing conditions. The effect of fly ash as partial cement replacement was also studied. Fresh OPS concrete was found to have better workability while its 28-day air-dry density was 19--20% lower than ordinary concrete. Compressive strength after 56 days was found to be 41--50% lower than ordinary concrete. These results were still within the normal range for structural lightweight concrete. Fly ash was found to lower the compressive strength of OPS concrete, which was the opposite of its effect on normal concrete.

  13. Coarse-grained simulations of the solution-phase self-assembly of poly(3-hexylthiophene) nanostructures

    NASA Astrophysics Data System (ADS)

    Schwarz, Kyra N.; Kee, Tak W.; Huang, David M.

    2013-02-01

    Under certain conditions the conjugated polymer poly(3-hexylthiophene) (P3HT) self-assembles into high-aspect-ratio nanostructures (known as nanofibres, nanowires, or nanoribbons) when cooled below its solubility limit in a marginal solvent such as anisole. Such nanostructures are potentially beneficial for organic photovoltaic device performance. In this work, Langevin dynamics simulations of a coarse-grained model of P3HT in implicit anisole solvent are used to study the self-assembly of P3HT nanostructures for polymer chain lengths and concentrations used experimentally to prepare P3HT nanofibres. The coarse-grained model is parametrised to match the local structure and dynamics of an atomistic model with explicit solvent. Nanofibres are also prepared experimentally and characterised by atomic force microscopy and UV-vis spectroscopy. The simulations match the experimental phase behaviour of P3HT in anisole, showing aggregation of P3HT at 293 and 308 K but not at 323 or 353 K. Single-chain simulations at 293 K reveal two distinct nano-scale aggregate morphologies: hairpins and helices. Hairpin aggregates, which are the precursors of nanofibres, are slightly favoured energetically at 293 K for nuclei of the critical size of ~80 monomers for aggregation. Consequently, chains in multi-chain aggregates adopt the hairpin morphology exclusively in simulations at experimental concentrations at 293 K. The simulated aggregate sizes match experimentally measured nanofibre widths. An estimate of the shift in UV-vis absorption of P3HT due to the change in conjugation length with aggregation in the simulations agrees reasonably well with experiment and shows that most of the spectral red shift that occurs with nanofibre formation is due to increased planarisation of the P3HT chains. In addition to providing insight into the mechanisms of nanofibre formation, the simulations resolve details of the molecular-level organisation of chains in P3HT nanofibres hitherto inaccessible

  14. Properties of concrete blocks prepared with low grade recycled aggregates.

    PubMed

    Poon, Chi-Sun; Kou, Shi-cong; Wan, Hui-wen; Etxeberria, Miren

    2009-08-01

    Low grade recycled aggregates obtained from a construction waste sorting facility were tested to assess the feasibility of using these in the production of concrete blocks. The characteristics of the sorted construction waste are significantly different from that of crushed concrete rubbles that are mostly derived from demolition waste streams. This is due to the presence of higher percentages of non-concrete components (e.g. >10% soil, brick, tiles etc.) in the sorted construction waste. In the study reported in this paper, three series of concrete block mixtures were prepared by using the low grade recycled aggregates to replace (i) natural coarse granite (10mm), and (ii) 0, 25, 50, 75 and 100% replacement levels of crushed stone fine (crushed natural granite <5mm) in the concrete blocks. Test results on properties such as density, compressive strength, transverse strength and drying shrinkage as well as strength reduction after exposure to 800 degrees C are presented below. The results show that the soil content in the recycled fine aggregate was an important factor in affecting the properties of the blocks produced and the mechanical strength deceased with increasing low grade recycled fine aggregate content. But the higher soil content in the recycled aggregates reduced the reduction of compressive strength of the blocks after exposure to high temperature due probably to the formation of a new crystalline phase. The results show that the low grade recycled aggregates obtained from the construction waste sorting facility has potential to be used as aggregates for making non-structural pre-cast concrete blocks. PMID:19398196

  15. Exploring energy landscapes of protein folding and aggregation.

    PubMed

    Mousseau, Normand; Derreumaux, Philippe

    2008-01-01

    Human diseases, such as Alzheimer's and Creutzfeldt-Jakob's are associated with misfolding and aggregation of specific proteins into amyloid fibrils sharing a generic cross-beta structure. The self-assembly process is complex, but once a nucleus is formed, rapid fibril formation occurs. Insight into the structures of the oligomers during the lag phase, varying between hours and days, is very difficult experimentally because these species are transient, and numerically using all-atom molecular dynamics because the time scale explored is on the order of 10-100 ns. It is therefore important to develop simplified protein models and alternative methods to sample more efficiently the conformational space. In the past few years, we have developed the activation-relaxation technique (ART nouveau) coupled to the OPEP coarse-grained force field. This review reports the application of ART-OPEP on protein folding and aggregation. PMID:18508525

  16. Photophoretic force on aggregate grains

    NASA Astrophysics Data System (ADS)

    Matthews, Lorin S.; Kimery, Jesse B.; Wurm, Gerhard; de Beule, Caroline; Kuepper, Markus; Hyde, Truell W.

    2016-01-01

    The photophoretic force may impact planetary formation by selectively moving solid particles based on their composition and structure. This generates collision velocities between grains of different sizes and sorts the dust in protoplanetary discs by composition. This numerical simulation studied the photophoretic force acting on fractal dust aggregates of μm-scale radii. Results show that aggregates tend to have greater photophoretic drift velocities than spheres of similar mass or radii, though with a greater spread in the velocity. While the drift velocities of compact aggregates continue to increase as the aggregates grow larger in size, fluffy aggregates have drift velocities which are relatively constant with size. Aggregates formed from an initially polydisperse size distribution of dust grains behave differently from aggregates formed from a monodisperse population, having smaller drift velocities with directions which deviate substantially from the direction of illumination. Results agree with microgravity experiments which show the difference of photophoretic forces with aggregation state.

  17. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    SciTech Connect

    Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet; Peter, Christine

    2013-12-21

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

  18. A transferable coarse-grained model for diphenylalanine: how to represent an environment driven conformational transition.

    PubMed

    Dalgicdir, Cahit; Sensoy, Ozge; Peter, Christine; Sayar, Mehmet

    2013-12-21

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties. PMID:24359360

  19. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    NASA Astrophysics Data System (ADS)

    Dalgicdir, Cahit; Sensoy, Ozge; Peter, Christine; Sayar, Mehmet

    2013-12-01

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

  20. Proteins aggregation and human diseases

    NASA Astrophysics Data System (ADS)

    Hu, Chin-Kun

    2015-04-01

    Many human diseases and the death of most supercentenarians are related to protein aggregation. Neurodegenerative diseases include Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), frontotemporallobar degeneration, etc. Such diseases are due to progressive loss of structure or function of neurons caused by protein aggregation. For example, AD is considered to be related to aggregation of Aβ40 (peptide with 40 amino acids) and Aβ42 (peptide with 42 amino acids) and HD is considered to be related to aggregation of polyQ (polyglutamine) peptides. In this paper, we briefly review our recent discovery of key factors for protein aggregation. We used a lattice model to study the aggregation rates of proteins and found that the probability for a protein sequence to appear in the conformation of the aggregated state can be used to determine the temperature at which proteins can aggregate most quickly. We used molecular dynamics and simple models of polymer chains to study relaxation and aggregation of proteins under various conditions and found that when the bending-angle dependent and torsion-angle dependent interactions are zero or very small, then protein chains tend to aggregate at lower temperatures. All atom models were used to identify a key peptide chain for the aggregation of insulin chains and to find that two polyQ chains prefer anti-parallel conformation. It is pointed out that in many cases, protein aggregation does not result from protein mis-folding. A potential drug from Chinese medicine was found for Alzheimer's disease.

  1. Organic carbon, water repellency and soil stability to slaking at aggregate and intra-aggregate scales

    NASA Astrophysics Data System (ADS)

    Jordán López, Antonio; García-Moreno, Jorge; Gordillo-Rivero, Ángel J.; Zavala, Lorena M.; Cerdà, Artemi; Alanís, Nancy; Jiménez-Compán, Elizabeth

    2015-04-01

    intensity of WR in aggregates of different sizes. [ii] the intra-aggregate distribution of OC and the intensity of WR and [iii] the structural stability of soil aggregates relative to the OC content and the intensity of WR in soils under different crops (apricot, citrus and wheat) and different treatments (conventional tilling and mulching). Soil samples were collected from an experimental area (Luvic Calcisols and Calcic Luvisols) in the province of Sevilla (Southern Spain) under different crops (apricot, citrus and wheat) and different management types (conventional tillage with moldboard plow) and mulching (no-tilling and addition of wheat residues at rates varying between 5 and 8 Mg/ha/year). At each sampling site, soil blocks (50 cm long × 50 cm wide × 10 cm deep) were carefully collected to avoid disturbance of aggregates as much as possible and transported to the laboratory. At field moist condition, undisturbed soil aggregates were separated by hand. In order to avoid possible interferences due to disturbance by handling, aggregates broken during this process were discarded. Individual aggregates were arranged in paper trays and air-dried during 7 days under laboratory standard conditions. After air-drying, part of each sample was carefully divided for different analyses: [i] part of the original samples was sieved (2 mm) to eliminate coarse soil particles and homogenized for characterization of OC and N contents, C/N ratio and texture; [ii] part of the aggregates were dry-sieved (0.25-0.5, 0.5-1 and 1-2 mm) or measured with a caliper (2-5, 5-10 and 10-15 mm) and separated in different sieve-size classes for determination of WR and OC content; [iii] aggregates 10-15 mm in size were selected for obtaining aggregate layers using a soil aggregate erosion (SAE) apparatus and WR and OC content were determined at each layer; finally, [iv] in order to study the relation between stability to slaking, WR and OC, these properties were determined in 90 air-dried aggregates

  2. Coarse-grained interaction potentials for anisotropic molecules.

    PubMed

    Babadi, M; Everaers, R; Ejtehadi, M R

    2006-05-01

    We have proposed an efficient parametrization method for a recent variant of the Gay Berne potential for dissimilar and biaxial particles [Phys. Rev. E 67, 041710 (2003)] and demonstrated it for a set of small organic molecules. Compared with the previously proposed coarse-grained models, the new potential exhibits a superior performance in close contact and large distant interactions. The repercussions of thermal vibrations and elasticity have been studied through a statistical method. The study justifies that the potential of mean force is representable with the same functional form, extending the application of this coarse-grained description to a broader range of molecules. Moreover, the advantage of employing coarse-grained models over truncated atomistic summations with large distance cutoffs has been briefly studied. PMID:16689591

  3. Molecular dynamics studies of protein folding and aggregation

    NASA Astrophysics Data System (ADS)

    Ding, Feng

    This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism

  4. Dynamics of fire ant aggregations

    NASA Astrophysics Data System (ADS)

    Tennenbaum, Michael; Hu, David; Fernandez-Nieves, Alberto

    Fire ant aggregations are an inherently active system. Each ant harvests its own energy and can convert it into motion. The motion of individual ants contributes non-trivially to the bulk material properties of the aggregation. We have measured some of these properties using plate-plate rheology, where the response to an applied external force or deformation is measured. In this talk, we will present data pertaining to the aggregation behavior in the absence of any external force. We quantify the aggregation dynamics by monitoring the rotation of the top plate and by measuring the normal force. We then compare the results with visualizations of 2D aggregations.

  5. A Transferable Coarse-Grained Model for Hydrogen Bonding Liquids

    PubMed Central

    Golubkov, Pavel A.; Wu, Johnny C.; Ren, Pengyu

    2008-01-01

    We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effectivepotential based approaches. The previous center-of-mass framework1 is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic .level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations. PMID:18688358

  6. Role of Ionic Clusters in Dynamics of Ionomer Melts: From Atomistic to Coarse Grained Simulations

    NASA Astrophysics Data System (ADS)

    Agrawal, Anupriya

    Ionomers, polymers decorated with ionizable groups, have found application in numerous technologies where ionic transport is required. The ionic groups associate into random clusters resulting in substantial effect on structure, dynamics and transport of these materials. The effects of topology, size and dynamics of these aggregates however remain an open question. Here we probe cluster formation correlated with polymer dynamics through a model system of randomly sulfonated polystyrene (SPS) melts with molecular dynamics (MD) simulations over a broad time and length scales ranging from that within the ionic clusters through polymer segmental dynamics to the motion of the entire molecules. The cluster evolution was probed by fully atomistic studies. We find ladder-like aggregates that transform to globule-like with increasing the dielectric constant of media for sodium neutralized SPS. With increasing dielectric constant, the size of the aggregates decrease and their number increases. Concurrently, the mobility of the polymer increases. The counterion radius and valency affect both morphology and dynamics as is evident in the calculated static and dynamic structure factors. It is further manifested in the results of viscosity obtained through non-equilibrium molecular dynamics technique. Finally, to access larger length scales a three bead coarse-grained model to describe sulfonated styrene that we have developed will be discussed in view of the outstanding challenges in ionic polymers. Supported in part by DOE Grant No. DE-SC007908. This work was carried out in collaboration with Dvora Perahia and Gary Grest while I was a postdoc at Clemson University. I gratefully acknowledge both of them for their support and encouragement.

  7. Applied Electric Fields and the Aggregation of Highly Charged Proteins

    NASA Astrophysics Data System (ADS)

    Nemzer, Louis; Flanders, Bret; Sorensen, Christopher

    2011-03-01

    The abnormal aggregation of misfolded proteins is associated with the onset of Alzheimer's disease, along with other neurodegenerative disorders, and there is increasing evidence that prefibrillar clusters, rather than fully-formed amyloid plaques, are primarily responsible. Therefore, weakly invasive methods, such as dynamic light scattering, which can probe the size distribution and structure factor of early nuclei and proto-aggregate clusters, can serve an important role in understanding this process, and may lead to insights regarding future therapeutic interventions. Here we study a highly charged model protein, lysozyme, under the influence of applied AC and DC fields in an effort to evaluate general models of protein aggregation, including the coarse-grained ``patchy protein'' method of visualizing charge heterogeneity. This anisotropy in the interprotein interaction can lead to frustrated crystalline order, resulting in low density phases. Dynamic measurements of the size distribution and structure factor can reveal local ordering, hierarchical clustering, and fractal properties of the aggregates. Early results show that applied fields affect early cluster growth by modulating local protein and counterion concentrations, in addition to their influence on protein alignment.

  8. Coarse-grid selection for parallel algebraic multigrid

    SciTech Connect

    Cleary, A. J., LLNL

    1998-06-01

    The need to solve linear systems arising from problems posed on extremely large, unstructured grids has sparked great interest in parallelizing algebraic multigrid (AMG) To date, however, no parallel AMG algorithms exist We introduce a parallel algorithm for the selection of coarse-grid points, a crucial component of AMG, based on modifications of certain paallel independent set algorithms and the application of heuristics designed to insure the quality of the coarse grids A prototype serial version of the algorithm is implemented, and tests are conducted to determine its effect on multigrid convergence, and AMG complexity

  9. Relation between Molecular Shape and the Morphology of Self-Assembling Aggregates: A Simulation Study

    PubMed Central

    Vácha, Robert; Frenkel, Daan

    2011-01-01

    Proteins can aggregate in a wide variety of structures, both compact and extended. We present simulations of a coarse-grained anisotropic model that reproduce many of the experimentally observed aggregate structures. Conversely, all structures predicted by our model have experimental counterparts (ribbons, multistranded fibrils, and vesicles). The model we use is that of a rodlike particle with an attractive (hydrophobic) stripe on its side. Our Monte Carlo simulations show that aggregate morphologies crucially depend on two parameters. The first one is the width of the attractive stripe and the second one is a presence or absence of attractive interactions at the particle ends. These results provide us with a generic insight into the relation between the shape of protein-protein interaction potential and the morphology of protein aggregates. PMID:21943424

  10. Characterization of coarse particulate matter in school gyms

    SciTech Connect

    Branis, Martin; Safranek, Jiri

    2011-05-15

    We investigated the mass concentration, mineral composition and morphology of particles resuspended by children during scheduled physical education in urban, suburban and rural elementary school gyms in Prague (Czech Republic). Cascade impactors were deployed to sample the particulate matter. Two fractions of coarse particulate matter (PM{sub 10-2.5} and PM{sub 2.5-1.0}) were characterized by gravimetry, energy dispersive X-ray spectrometry and scanning electron microscopy. Two indicators of human activity, the number of exercising children and the number of physical education hours, were also recorded. Lower mass concentrations of coarse particulate matter were recorded outdoors (average PM{sub 10-2.5} 4.1-7.4 {mu}g m{sup -3} and PM{sub 2.5-1.0} 2.0-3.3 {mu}g m{sup -3}) than indoors (average PM{sub 10-2.5} 13.6-26.7 {mu}g m{sup -3} and PM{sub 2.5-1.0} 3.7-7.4 {mu}g m{sup -3}). The indoor concentrations of coarse aerosol were elevated during days with scheduled physical education with an average indoor-outdoor (I/O) ratio of 2.5-16.3 for the PM{sub 10-2.5} and 1.4-4.8 for the PM{sub 2.5-1.0} values. Under extreme conditions, the I/O ratios reached 180 (PM{sub 10-2.5}) and 19.1 (PM{sub 2.5-1.0}). The multiple regression analysis based on the number of students and outdoor coarse PM as independent variables showed that the main predictor of the indoor coarse PM concentrations is the number of students in the gym. The effect of outdoor coarse PM was weak and inconsistent. The regression models for the three schools explained 60-70% of the particular dataset variability. X-ray spectrometry revealed 6 main groups of minerals contributing to resuspended indoor dust. The most abundant particles were those of crustal origin composed of Si, Al, O and Ca. Scanning electron microscopy showed that, in addition to numerous inorganic particles, various types of fibers and particularly skin scales make up the main part of the resuspended dust in the gyms. In conclusion, school

  11. The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

    PubMed Central

    Noid, W. G.; Liu, Pu; Wang, Yanting; Chu, Jhih-Wei; Ayton, Gary S.; Izvekov, Sergei; Andersen, Hans C.; Voth, Gregory A.

    2008-01-01

    The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+∕NO3− ionic liquid are provided to illustrate the method. PMID:18601325

  12. Making Graphene Resist Aggregation

    NASA Astrophysics Data System (ADS)

    Luo, Jiayan

    Graphene-based sheets have stimulated great interest in many scientific disciplines and shown promise for wide potential applications. Among various ways of creating single atomic layer carbon sheets, a promising route for bulk production is to first chemically exfoliate graphite powders to graphene oxide (GO) sheets, followed by reduction to form chemically modified graphene (CMG). Due to the strong van der Waals attraction between graphene sheets, CMG tends to aggregate. The restacking of sheets is largely uncontrollable and irreversible, thus it reduces their processability and compromises properties such as accessible surface area. Strategies based on colloidal chemistry have been applied to keep CMG dispersed in solvents by introducing electrostatic repulsion to overcome the van der Waals attraction or adding spacers to increase the inter-sheet spacing. In this dissertation, two very different ideas that can prevent CMG aggregation without extensively modifying the material or introducing foreign spacer materials are introduced. The van der Waals potential decreases with reduced overlapping area between sheets. For CMG, reducing the lateral dimension from micrometer to nanometer scale should greatly enhance their colloidal stability with additional advantages of increased charge density and decreased probability to interact. The enhanced colloidal stability of GO and CMG nanocolloids makes them especially promising for spectroscopy based bio-sensing applications. For potential applications in a compact bulk solid form, the sheets were converted into paper-ball like structure using capillary compression in evaporating aerosol droplets. The crumpled graphene balls are stabilized by locally folded pi-pi stacked ridges, and do not unfold or collapse during common processing steps. They can tightly pack without greatly reducing the surface area. This form of graphene leads to scalable performance in energy storage. For example, planer sheets tend to aggregate and

  13. Structure of Viral Aggregates

    NASA Astrophysics Data System (ADS)

    Barr, Stephen; Luijten, Erik

    2010-03-01

    The aggregation of virus particles is a particular form of colloidal self-assembly, since viruses of a give type are monodisperse and have identical, anisotropic surface charge distributions. In small-angle X-ray scattering experiments, the Qbeta virus was found to organize in different crystal structures in the presence of divalent salt and non-adsorbing polymer. Since a simple isotropic potential cannot explain the occurrence of all observed phases, we employ computer simulations to investigate how the surface charge distribution affects the virus interactions. Using a detailed model of the virus particle, we find an asymmetric ion distribution around the virus which gives rise to the different phases observed.

  14. The Optimum Production Method for Quality Improvement of Recycled Aggregates Using Sulfuric Acid and the Abrasion Method.

    PubMed

    Kim, Haseog; Park, Sangki; Kim, Hayong

    2016-01-01

    There has been increased deconstruction and demolition of reinforced concrete structures due to the aging of the structures and redevelopment of urban areas resulting in the generation of massive amounts of construction. The production volume of waste concrete is projected to increase rapidly over 100 million tons by 2020. However, due to the high cement paste content, recycled aggregates have low density and high absorption ratio. They are mostly used for land reclamation purposes with low added value instead of multiple approaches. This study was performed to determine an effective method to remove cement paste from recycled aggregates by using the abrasion and substituting the process water with acidic water. The aim of this study is to analyze the quality of the recycled fine aggregates produced by a complex method and investigate the optimum manufacturing conditions for recycled fine aggregates based on the design of experiment. The experimental parameters considered were water ratio, coarse aggregate ratio, and abrasion time and, as a result of the experiment, data concerning the properties of recycled sand were obtained. It was found that high-quality recycled fine aggregates can be obtained with 8.57 min of abrasion-crusher time and a recycled coarse aggregate ratio of over 1.5. PMID:27483298

  15. The Optimum Production Method for Quality Improvement of Recycled Aggregates Using Sulfuric Acid and the Abrasion Method

    PubMed Central

    Kim, Haseog; Park, Sangki; Kim, Hayong

    2016-01-01

    There has been increased deconstruction and demolition of reinforced concrete structures due to the aging of the structures and redevelopment of urban areas resulting in the generation of massive amounts of construction. The production volume of waste concrete is projected to increase rapidly over 100 million tons by 2020. However, due to the high cement paste content, recycled aggregates have low density and high absorption ratio. They are mostly used for land reclamation purposes with low added value instead of multiple approaches. This study was performed to determine an effective method to remove cement paste from recycled aggregates by using the abrasion and substituting the process water with acidic water. The aim of this study is to analyze the quality of the recycled fine aggregates produced by a complex method and investigate the optimum manufacturing conditions for recycled fine aggregates based on the design of experiment. The experimental parameters considered were water ratio, coarse aggregate ratio, and abrasion time and, as a result of the experiment, data concerning the properties of recycled sand were obtained. It was found that high-quality recycled fine aggregates can be obtained with 8.57 min of abrasion-crusher time and a recycled coarse aggregate ratio of over 1.5. PMID:27483298

  16. Quantum particles from coarse grained classical probabilities in phase space

    SciTech Connect

    Wetterich, C.

    2010-07-15

    Quantum particles can be obtained from a classical probability distribution in phase space by a suitable coarse graining, whereby simultaneous classical information about position and momentum can be lost. For a suitable time evolution of the classical probabilities and choice of observables all features of a quantum particle in a potential follow from classical statistics. This includes interference, tunneling and the uncertainty relation.

  17. Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations

    SciTech Connect

    Nemenman, Ilya; Sinitsyn, Nikolai; Hengartner, Nick

    2008-01-01

    We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscoplc, non-Poissonian fluctuations of the slow ones. Our approach, which is similar to the Born-Oppenhelmer approximation in quantum mechanics, follows from the stochastic path Integral representation of the cumulant generating function of reaction events. In applications with a small number of chemIcal reactions, It produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, Interpretable representation and can be used for coarse-grained numerical simulation schemes with a small computational complexity and yet high accuracy. As an example, we derive the coarse-grained description for a chain of biochemical reactions, and show that the coarse-grained and the microscopic simulations are in an agreement, but the coarse-gralned simulations are three orders of magnitude faster.

  18. Terrain aided navigation for autonomous underwater vehicles with coarse maps

    NASA Astrophysics Data System (ADS)

    Zhou, Ling; Cheng, Xianghong; Zhu, Yixian

    2016-09-01

    Terrain aided navigation (TAN) is a form of geophysical localization technique for autonomous underwater vehicles (AUVs) operating in GPS-denied environments. TAN performance on sensor-rich AUVs has been evaluated in sea trials. However, many challenges remain before TAN can be successfully implemented on sensor-limited AUVs, especially with coarse maps. To improve TAN performance over coarse maps, a Gaussian process (GP) is proposed for the modeling of bathymetric terrain and integrated into the particle filter (GP-PF). GP is applied to provide not only the bathymetric value prediction through learning a set of bathymetric data from coarse maps but also the variance of the prediction. As a measurement update, calculated on bathymetric deviation is performed through the PF to obtain absolute and bounded positioning accuracy. Through the analysis of TAN performance on experimental data for two different terrains with map resolutions of 10–50 m, both the ability of the proposed model to represent the actual bathymetric terrain with accuracy and the effect of the GP-PF for TAN on sensor-limited systems in suited terrain are demonstrated. The experiment results further verify that there is an inverse relationship between the coarseness of the map and the overall TAN accuracy in rough terrains, but there is hardly any relationship between them in relatively flat terrains.

  19. On coarse projective integration for atomic deposition in amorphous systems

    NASA Astrophysics Data System (ADS)

    Chuang, Claire Y.; Han, Sang M.; Zepeda-Ruiz, Luis A.; Sinno, Talid

    2015-10-01

    Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of time scales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity, and computational efficiency. Coarse projective integration, an example application of the "equation-free" framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute time derivatives of slowly evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to the application of this technique in realistic settings is the "lifting" operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO2 substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO2 using only a few measures of the island size distribution. The approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.

  20. On coarse projective integration for atomic deposition in amorphous systems.

    PubMed

    Chuang, Claire Y; Han, Sang M; Zepeda-Ruiz, Luis A; Sinno, Talid

    2015-10-01

    Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of time scales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity, and computational efficiency. Coarse projective integration, an example application of the "equation-free" framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute time derivatives of slowly evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to the application of this technique in realistic settings is the "lifting" operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO2 substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO2 using only a few measures of the island size distribution. The approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system. PMID:26450324

  1. Multiscale coarse graining of liquid-state systems

    NASA Astrophysics Data System (ADS)

    Izvekov, Sergei; Voth, Gregory A.

    2005-10-01

    A methodology is described to systematically derive coarse-grained (CG) force fields for molecular liquids from the underlying atomistic-scale forces. The coarse graining of an interparticle force field is accomplished by the application of a force-matching method to the trajectories and forces obtained from the atomistic trajectory and force data for the CG sites of the targeted system. The CG sites can be associated with the centers of mass of atomic groups because of the simplicity in the evaluation of forces acting on these sites from the atomistic data. The resulting system is called a multiscale coarse-grained (MS-CG) representation. The MS-CG method for liquids is applied here to water and methanol. For both liquids one-site and two-site CG representations without an explicit treatment of the long-ranged electrostatics have been derived. In addition, for water a two-site model having the explicit long-ranged electrostatics has been developed. To improve the thermodynamic properties (e.g., pressure and density) for the MS-CG models, the constraint for the instantaneous virial was included into the force-match procedure. The performance of the resulting models was evaluated against the underlying atomistic simulations and experiment. In contrast with existing approaches for coarse graining of liquid systems, the MS-CG approach is general, relies only on the interatomic interactions in the reference atomistic system.

  2. Personal Coarse Particulate Matter Exposures in an Adult Cohort

    EPA Science Inventory

    Volunteers associated with the North Carolina Adult Asthma and Environment Study (NCAAES) participated in an investigation of personal daily exposures to coarse and fine particulate matter size fractions (PM10-2.5, PM2.5). Data from these personal measuremen...

  3. 7 CFR 457.113 - Coarse grains crop insurance provisions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Grains Crop Provisions 1. Definitions Coarse grains. Corn, grain sorghum, and soybeans. Grain sorghum... cash grain price per bushel for the U.S. No. 2 yellow corn, U.S. No. 2 grain sorghum, or U.S. No. 1... yellow corn and grain sorghum, or U.S. No. 1 grade for soybeans. Factors not associated with...

  4. 7 CFR 457.113 - Coarse grains crop insurance provisions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Grains Crop Provisions 1. Definitions Coarse grains. Corn, grain sorghum, and soybeans. Grain sorghum... cash grain price per bushel for the U.S. No. 2 yellow corn, U.S. No. 2 grain sorghum, or U.S. No. 1... yellow corn and grain sorghum, or U.S. No. 1 grade for soybeans. Factors not associated with...

  5. 7 CFR 457.113 - Coarse grains crop insurance provisions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Grains Crop Provisions 1. Definitions Coarse grains— Corn, grain sorghum, and soybeans. Grain sorghum... cash grain price per bushel for the U.S. No. 2 yellow corn, U.S. No. 2 grain sorghum, or U.S. No. 1... yellow corn and grain sorghum, or U.S. No. 1 grade for soybeans. Factors not associated with...

  6. 7 CFR 457.113 - Coarse grains crop insurance provisions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... Grains Crop Provisions 1. Definitions Coarse grains. Corn, grain sorghum, and soybeans. Grain sorghum... cash grain price per bushel for the U.S. No. 2 yellow corn, U.S. No. 2 grain sorghum, or U.S. No. 1... yellow corn and grain sorghum, or U.S. No. 1 grade for soybeans. Factors not associated with...

  7. Evaluation of a Direct Personal Coarse Particulate Matter Monitor

    EPA Science Inventory

    One aspect of the North Carolina Adult Asthma and Environment study (NCAAES) was to evaluate personal exposures to coarse particulate matter (PM 10-2.5) and their associated variability. As part of this, we examined the ability of a community-based monitor to act as...

  8. On coarse projective integration for atomic deposition in amorphous systems

    SciTech Connect

    Chuang, Claire Y. E-mail: meister@unm.edu Sinno, Talid; Han, Sang M. E-mail: meister@unm.edu; Zepeda-Ruiz, Luis A. E-mail: meister@unm.edu

    2015-10-07

    Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of time scales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity, and computational efficiency. Coarse projective integration, an example application of the “equation-free” framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute time derivatives of slowly evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to the application of this technique in realistic settings is the “lifting” operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO{sub 2} substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO{sub 2} using only a few measures of the island size distribution. The approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.

  9. 7. DETAIL OF ROOM BELOW GRIZZLY SHOWING BOTTOM OF COARSE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. DETAIL OF ROOM BELOW GRIZZLY SHOWING BOTTOM OF COARSE ORE BIN AND CHUTE TO BEGINNING OF CONVEYOR BELT, SOUTH VIEW. - Vanadium Corporation of America (VCA) Naturita Mill, Sampling Building & Ore Receiving Platform, 3 miles Northwest of Naturita, between Highway 141 & San Miguel River, Naturita, Montrose County, CO

  10. COARSE PM EMISSIONS MODEL DEVELOPMENT AND INVENTORY VALIDATION

    EPA Science Inventory

    The proposed research will contribute to our understanding of the sources and controlling variables of coarse PM. This greater understanding, along with an increase in our ability to predict these emissions, will enable more efficient pollution control strategy development. Ad...

  11. Coarse-Grained and Atomistic Modeling of Polyimides

    NASA Technical Reports Server (NTRS)

    Clancy, Thomas C.; Hinkley, Jeffrey A.

    2004-01-01

    A coarse-grained model for a set of three polyimide isomers is developed. Each polyimide is comprised of BPDA (3,3,4,4' - biphenyltetracarboxylic dianhydride) and one of three APB isomers: 1,3-bis(4-aminophenoxy)benzene, 1,4-bis(4-aminophenoxy)benzene or 1,3-bis(3-aminophenoxy)benzene. The coarse-grained model is constructed as a series of linked vectors following the contour of the polymer backbone. Beads located at the midpoint of each vector define centers for long range interaction energy between monomer subunits. A bulk simulation of each coarse-grained polyimide model is performed with a dynamic Monte Carlo procedure. These coarsegrained models are then reverse-mapped to fully atomistic models. The coarse-grained models show the expected trends in decreasing chain dimensions with increasing meta linkage in the APB section of the repeat unit, although these differences were minor due to the relatively short chains simulated here. Considerable differences are seen among the dynamic Monte Carlo properties of the three polyimide isomers. Decreasing relaxation times are seen with increasing meta linkage in the APB section of the repeat unit.

  12. Taurine and platelet aggregation

    SciTech Connect

    Nauss-Karol, C.; VanderWende, C.; Gaut, Z.N.

    1986-03-01

    Taurine is a putative neurotransmitter or neuromodulator. The endogenous taurine concentration in human platelets, determined by amino acid analysis, is 15 ..mu..M/g. In spite of this high level, taurine is actively accumulated. Uptake is saturable, Na/sup +/ and temperature dependent, and suppressed by metabolic inhibitors, structural analogues, and several classes of centrally active substances. High, medium and low affinity transport processes have been characterized, and the platelet may represent a model system for taurine transport in the CNS. When platelets were incubated with /sup 14/C-taurine for 30 minutes, then resuspended in fresh medium and reincubated for one hour, essentially all of the taurine was retained within the cells. Taurine, at concentrations ranging from 10-1000 ..mu..M, had no effect on platelet aggregation induced by ADP or epinephrine. However, taurine may have a role in platelet aggregation since 35-39% of the taurine taken up by human platelets appears to be secreted during the release reaction induced by low concentrations of either epinephrine or ADP, respectively. This release phenomenon would imply that part of the taurine taken up is stored directly in the dense bodies of the platelet.

  13. Coarse-Grained Clustering Dynamics of Heterogeneously Coupled Neurons.

    PubMed

    Moon, Sung Joon; Cook, Katherine A; Rajendran, Karthikeyan; Kevrekidis, Ioannis G; Cisternas, Jaime; Laing, Carlo R

    2015-12-01

    The formation of oscillating phase clusters in a network of identical Hodgkin-Huxley neurons is studied, along with their dynamic behavior. The neurons are synaptically coupled in an all-to-all manner, yet the synaptic coupling characteristic time is heterogeneous across the connections. In a network of N neurons where this heterogeneity is characterized by a prescribed random variable, the oscillatory single-cluster state can transition-through [Formula: see text] (possibly perturbed) period-doubling and subsequent bifurcations-to a variety of multiple-cluster states. The clustering dynamic behavior is computationally studied both at the detailed and the coarse-grained levels, and a numerical approach that can enable studying the coarse-grained dynamics in a network of arbitrarily large size is suggested. Among a number of cluster states formed, double clusters, composed of nearly equal sub-network sizes are seen to be stable; interestingly, the heterogeneity parameter in each of the double-cluster components tends to be consistent with the random variable over the entire network: Given a double-cluster state, permuting the dynamical variables of the neurons can lead to a combinatorially large number of different, yet similar "fine" states that appear practically identical at the coarse-grained level. For weak heterogeneity we find that correlations rapidly develop, within each cluster, between the neuron's "identity" (its own value of the heterogeneity parameter) and its dynamical state. For single- and double-cluster states we demonstrate an effective coarse-graining approach that uses the Polynomial Chaos expansion to succinctly describe the dynamics by these quickly established "identity-state" correlations. This coarse-graining approach is utilized, within the equation-free framework, to perform efficient computations of the neuron ensemble dynamics. PMID:26458901

  14. Bridging scales: from atoms to coarse-grained models for soft matter systems

    NASA Astrophysics Data System (ADS)

    Peter, Christine

    2015-03-01

    Molecular simulation has extended to increasingly complex soft matter systems, and time-scale and system-size requirements have instigated the use of simulation models on multiple levels of resolution. On the classical particle-based level, a large variety of methods to develop coarse grained (CG) simulation models has emerged, an important subgroup being those scale-bridging methods where the CG model is derived from and systematically linked to an underlying atomistic description. In my talk, I will introduce a few of these methods, address the underlying concepts as well as some of the ongoing challenges that are inherent to coarse graining. A natural consequence of reducing the level of resolution in a simulation model is a loss of transferability, i.e. a decreasing ability to correctly describe a system at several thermodynamic state points. Intimately linked to this is a loss of the ability to correctly represent all structural, thermodynamic and dynamic properties of the system. Examples for these limitations are easily found in all CG simulations of multicomponent or multiphase soft matter systems - ranging from liquid crystals, biomolecular aggregates, biomaterials to hard/soft nanocomposites. A correct representation of phase transitions, phase coexistence, environment-induced conformational transitions, or effects due to surfaces and interfaces is a severe challenge for bottom-up CG models. Addressing this challenge requires both a method of generating CG potentials as well as finding and rationalizing an appropriate reference state point to start out from. I will illustrate several of these aspects using examples from the biomolecular and (biomimetic-) materials world.

  15. Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding.

    PubMed

    Pickard, Frank C; Miller, Benjamin T; Schalk, Vinushka; Lerner, Michael G; Woodcock, H Lee; Brooks, Bernard R

    2014-07-01

    A lesson utilizing a coarse-grained (CG) Gō-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org) to the Chemistry at HARvard Macromolecular Mechanics (CHARMM) molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool because they can provide qualitative descriptions of complex biophysical phenomena for a relatively cheap computational cost. As a proof of concept, this lesson demonstrates the construction of a CG model of a small globular protein, its simulation via Langevin dynamics, and the analysis of the resulting data. This lesson makes connections between modern molecular simulation techniques and topics commonly presented in an advanced undergraduate lecture on physical chemistry. It culminates in a straightforward analysis of a short dynamics trajectory of a small fast folding globular protein; we briefly describe the thermodynamic properties that can be calculated from this analysis. The assumptions inherent in the model and the data analysis are laid out in a clear, concise manner, and the techniques used are consistent with those employed by specialists in the field of CG modeling. One of the major tasks in building the Gō-like model is determining the relative strength of the nonbonded interactions between coarse-grained sites. New functionality has been added to CHARMMing to facilitate this process. The implementation of these features into CHARMMing helps automate many of the tedious aspects of constructing a CG Gō model. The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field. PMID:25058338

  16. Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding

    PubMed Central

    Schalk, Vinushka; Lerner, Michael G.; Woodcock, H. Lee; Brooks, Bernard R.

    2014-01-01

    A lesson utilizing a coarse-grained (CG) G-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org) to the Chemistry at HARvard Macromolecular Mechanics (CHARMM) molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool because they can provide qualitative descriptions of complex biophysical phenomena for a relatively cheap computational cost. As a proof of concept, this lesson demonstrates the construction of a CG model of a small globular protein, its simulation via Langevin dynamics, and the analysis of the resulting data. This lesson makes connections between modern molecular simulation techniques and topics commonly presented in an advanced undergraduate lecture on physical chemistry. It culminates in a straightforward analysis of a short dynamics trajectory of a small fast folding globular protein; we briefly describe the thermodynamic properties that can be calculated from this analysis. The assumptions inherent in the model and the data analysis are laid out in a clear, concise manner, and the techniques used are consistent with those employed by specialists in the field of CG modeling. One of the major tasks in building the G-like model is determining the relative strength of the nonbonded interactions between coarse-grained sites. New functionality has been added to CHARMMing to facilitate this process. The implementation of these features into CHARMMing helps automate many of the tedious aspects of constructing a CG G model. The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field. PMID:25058338

  17. Holographic characterization of protein aggregates

    NASA Astrophysics Data System (ADS)

    Wang, Chen; Zhong, Xiao; Ruffner, David; Stutt, Alexandra; Philips, Laura; Ward, Michael; Grier, David

    Holographic characterization directly measures the size distribution of subvisible protein aggregates in suspension and offers insights into their morphology. Based on holographic video microscopy, this analytical technique records and interprets holograms of individual aggregates in protein solutions as they flow down a microfluidic channel, without requiring labeling or other exceptional sample preparation. The hologram of an individual protein aggregate is analyzed in real time with the Lorenz-Mie theory of light scattering to measure that aggregate's size and optical properties. Detecting, counting and characterizing subvisible aggregates proceeds fast enough for time-resolved studies, and lends itself to tracking trends in protein aggregation arising from changing environmental factors. No other analytical technique provides such a wealth of particle-resolved characterization data in situ. Holographic characterization promises accelerated development of therapeutic protein formulations, improved process control during manufacturing, and streamlined quality assurance during storage and at the point of use. Mrsec and MRI program of the NSF, Spheryx Inc.

  18. Aggregation dynamics of rigid polyelectrolytes

    NASA Astrophysics Data System (ADS)

    Tom, Anvy Moly; Rajesh, R.; Vemparala, Satyavani

    2016-01-01

    Similarly charged polyelectrolytes are known to attract each other and aggregate into bundles when the charge density of the polymers exceeds a critical value that depends on the valency of the counterions. The dynamics of aggregation of such rigid polyelectrolytes are studied using large scale molecular dynamics simulations. We find that the morphology of the aggregates depends on the value of the charge density of the polymers. For values close to the critical value, the shape of the aggregates is cylindrical with height equal to the length of a single polyelectrolyte chain. However, for larger values of charge, the linear extent of the aggregates increases as more and more polymers aggregate. In both the cases, we show that the number of aggregates decrease with time as power laws with exponents that are not numerically distinguishable from each other and are independent of charge density of the polymers, valency of the counterions, density, and length of the polyelectrolyte chain. We model the aggregation dynamics using the Smoluchowski coagulation equation with kernels determined from the molecular dynamics simulations and justify the numerically obtained value of the exponent. Our results suggest that once counterions condense, effective interactions between polyelectrolyte chains short-ranged and the aggregation of polyelectrolytes are diffusion-limited.

  19. Simulation of Ionic Aggregation and Ion Dynamics in Model Ionomers

    NASA Astrophysics Data System (ADS)

    Frischknecht, Amalie L.

    2012-02-01

    Ionomers, polymers containing a small fraction of covalently bound ionic groups, are of interest as possible electrolytes in batteries. A single-ion conducting polymer electrolyte would be safer and have higher efficiency than the currently-used liquid electrolytes. However, to date ionomeric materials do not have sufficiently high conductivities for practical application. This is most likely because the ions tend to form aggregates, leading to slow ion transport. A key question is therefore how molecular structure affects the ionic aggregation and ion dynamics. To probe these structure-property relationships, we have performed molecular simulations of a set of recently synthesized poly(ethylene-co-acrylic acid) copolymers and ionomers, with a focus on the morphology of the ionic aggregates. The ionomers have a precise, constant spacing of charged groups, making them ideal for direct comparisons with simulations. Ab initio calculations give insight into the expected coordination of cations with fragments of the ionomers. All-atom molecular dynamics (MD) simulations of the ionomer melt show aggregation of the ionic groups into extended string-like clusters. An extensive set of coarse-grained molecular dynamics simulations extend the results to longer times and larger length scales. The structure factors calculated from the MD simulations compare favorably with x-ray scattering data. Furthermore, the simulations give a detailed picture of the sizes, shapes, and composition of the ionic aggregates, and how they depend on polymer architecture. Implications for ion transport will be discussed. [Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  20. A nucleotide-level coarse-grained model of RNA

    SciTech Connect

    Šulc, Petr; Ouldridge, Thomas E.; Louis, Ard A.; Romano, Flavio; Doye, Jonathan P. K.

    2014-06-21

    We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.

  1. Coarse-graining of proteins based on elastic network models

    NASA Astrophysics Data System (ADS)

    Sinitskiy, Anton V.; Voth, Gregory A.

    2013-08-01

    To simulate molecular processes on biologically relevant length- and timescales, coarse-grained (CG) models of biomolecular systems with tens to even hundreds of residues per CG site are required. One possible way to build such models is explored in this article: an elastic network model (ENM) is employed to define the CG variables. Free energy surfaces are approximated by Taylor series, with the coefficients found by force-matching. CG potentials are shown to undergo renormalization due to roughness of the energy landscape and smoothing of it under coarse-graining. In the case study of hen egg-white lysozyme, the entropy factor is shown to be of critical importance for maintaining the native structure, and a relationship between the proposed ENM-mode-based CG models and traditional CG-bead-based models is discussed. The proposed approach uncovers the renormalizable character of CG models and offers new opportunities for automated and computationally efficient studies of complex free energy surfaces.

  2. A nucleotide-level coarse-grained model of RNA

    NASA Astrophysics Data System (ADS)

    Šulc, Petr; Romano, Flavio; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.

    2014-06-01

    We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.

  3. Linear mixing model applied to coarse resolution satellite data

    NASA Technical Reports Server (NTRS)

    Holben, Brent N.; Shimabukuro, Yosio E.

    1992-01-01

    A linear mixing model typically applied to high resolution data such as Airborne Visible/Infrared Imaging Spectrometer, Thematic Mapper, and Multispectral Scanner System is applied to the NOAA Advanced Very High Resolution Radiometer coarse resolution satellite data. The reflective portion extracted from the middle IR channel 3 (3.55 - 3.93 microns) is used with channels 1 (0.58 - 0.68 microns) and 2 (0.725 - 1.1 microns) to run the Constrained Least Squares model to generate fraction images for an area in the west central region of Brazil. The derived fraction images are compared with an unsupervised classification and the fraction images derived from Landsat TM data acquired in the same day. In addition, the relationship betweeen these fraction images and the well known NDVI images are presented. The results show the great potential of the unmixing techniques for applying to coarse resolution data for global studies.

  4. Peptide aggregation in neurodegenerative disease.

    PubMed

    Murphy, Regina M

    2002-01-01

    In the not-so-distant past, insoluble aggregated protein was considered as uninteresting and bothersome as yesterday's trash. More recently, protein aggregates have enjoyed considerable scientific interest, as it has become clear that these aggregates play key roles in many diseases. In this review, we focus attention on three polypeptides: beta-amyloid, prion, and huntingtin, which are linked to three feared neurodegenerative diseases: Alzheimer's, "mad cow," and Huntington's disease, respectively. These proteins lack any significant primary sequence homology, yet their aggregates possess very similar features, specifically, high beta-sheet content, fibrillar morphology, relative insolubility, and protease resistance. Because the aggregates are noncrystalline, secrets of their structure at nanometer resolution are only slowly yielding to X-ray diffraction, solid-state NMR, and other techniques. Besides structure, the aggregates may possess similar pathways of assembly. Two alternative assembly pathways have been proposed: the nucleation-elongation and the template-assisted mode. These two modes may be complementary, not mutually exclusive. Strategies for interfering with aggregation, which may provide novel therapeutic approaches, are under development. The structural similarities between protein aggregates of dissimilar origin suggest that therapeutic strategies successful against one disease may have broad utility in others. PMID:12117755

  5. Topics in Probabilistic Judgment Aggregation

    ERIC Educational Resources Information Center

    Wang, Guanchun

    2011-01-01

    This dissertation is a compilation of several studies that are united by their relevance to probabilistic judgment aggregation. In the face of complex and uncertain events, panels of judges are frequently consulted to provide probabilistic forecasts, and aggregation of such estimates in groups often yield better results than could have been made…

  6. Mineral of the month: aggregates

    USGS Publications Warehouse

    Tepordei, Valentin V.

    2005-01-01

    Natural aggregates, consisting of crushed stone, and sand and gravel, are a major contributor to economic health, and have an amazing variety of uses. Aggregates are among the most abundant mineral resources and are major basic raw materials used by construction, agriculture and other industries that employ complex chemical and metallurgical processes.

  7. Enhancing physiologic simulations using supervised learning on coarse mesh solutions.

    PubMed

    Kolandaivelu, Kumaran; O'Brien, Caroline C; Shazly, Tarek; Edelman, Elazer R; Kolachalama, Vijaya B

    2015-03-01

    Computational modelling of physical and biochemical processes has emerged as a means of evaluating medical devices, offering new insights that explain current performance, inform future designs and even enable personalized use. Yet resource limitations force one to compromise with reduced order computational models and idealized assumptions that yield either qualitative descriptions or approximate, quantitative solutions to problems of interest. Considering endovascular drug delivery as an exemplary scenario, we used a supervised machine learning framework to process data generated from low fidelity coarse meshes and predict high fidelity solutions on refined mesh configurations. We considered two models simulating drug delivery to the arterial wall: (i) two-dimensional drug-coated balloons and (ii) three-dimensional drug-eluting stents. Simulations were performed on computational mesh configurations of increasing density. Supervised learners based on Gaussian process modelling were constructed from combinations of coarse mesh setting solutions of drug concentrations and nearest neighbourhood distance information as inputs, and higher fidelity mesh solutions as outputs. These learners were then used as computationally inexpensive surrogates to extend predictions using low fidelity information to higher levels of mesh refinement. The cross-validated, supervised learner-based predictions improved fidelity as compared with computational simulations performed at coarse level meshes--a result consistent across all outputs and computational models considered. Supervised learning on coarse mesh solutions can augment traditional physics-based modelling of complex physiologic phenomena. By obtaining efficient solutions at a fraction of the computational cost, this framework has the potential to transform how modelling approaches can be applied in the evaluation of medical technologies and their real-time administration in an increasingly personalized fashion. PMID:25652458

  8. Coarse pointing mechanism assembly for satellite interlink experiment

    NASA Technical Reports Server (NTRS)

    Maeusli, P. A.; Ivorra, M. T.; Gass, V.; Berthoud, J. F.

    1996-01-01

    Since 1975, MECANEX S.A. has been manufacturing components for solar array drives and mechanisms used in space applications. In 1991, work was started in an early phase C (Engineering Model) on a Coarse Pointing Mechanism Assembly (CPMA) for the Semiconductor-laser Inter-satellite Link EXperiment (SILEX). This paper deals with the history, the evolution, and the lessons learned from taking over a pre-design in 1991 to the delivery of last flight models (FM 5 & 6) in 1995.

  9. Coarse-Grained Molecular Dynamics: Dissipation Due to Internal Modes

    SciTech Connect

    Rudd, R E

    2001-12-21

    We describe progress on the issue of pathological elastic wave reflection in atomistic and multiscale simulation. First we briefly review Coarse-Grained Molecular Dynamics (CGMD). Originally CGMD was formulated as a Hamiltonian system in which energy is conserved. This formulation is useful for many applications, but recently CGMD has been extended to include generalized Langevin forces. Here we describe how Langevin dynamics arise naturally in CGMD, and we examine the implication for elastic wave scattering.

  10. Enhancing physiologic simulations using supervised learning on coarse mesh solutions

    PubMed Central

    Kolandaivelu, Kumaran; O'Brien, Caroline C.; Shazly, Tarek; Edelman, Elazer R.; Kolachalama, Vijaya B.

    2015-01-01

    Computational modelling of physical and biochemical processes has emerged as a means of evaluating medical devices, offering new insights that explain current performance, inform future designs and even enable personalized use. Yet resource limitations force one to compromise with reduced order computational models and idealized assumptions that yield either qualitative descriptions or approximate, quantitative solutions to problems of interest. Considering endovascular drug delivery as an exemplary scenario, we used a supervised machine learning framework to process data generated from low fidelity coarse meshes and predict high fidelity solutions on refined mesh configurations. We considered two models simulating drug delivery to the arterial wall: (i) two-dimensional drug-coated balloons and (ii) three-dimensional drug-eluting stents. Simulations were performed on computational mesh configurations of increasing density. Supervised learners based on Gaussian process modelling were constructed from combinations of coarse mesh setting solutions of drug concentrations and nearest neighbourhood distance information as inputs, and higher fidelity mesh solutions as outputs. These learners were then used as computationally inexpensive surrogates to extend predictions using low fidelity information to higher levels of mesh refinement. The cross-validated, supervised learner-based predictions improved fidelity as compared with computational simulations performed at coarse level meshes—a result consistent across all outputs and computational models considered. Supervised learning on coarse mesh solutions can augment traditional physics-based modelling of complex physiologic phenomena. By obtaining efficient solutions at a fraction of the computational cost, this framework has the potential to transform how modelling approaches can be applied in the evaluation of medical technologies and their real-time administration in an increasingly personalized fashion. PMID:25652458

  11. Mechanics of fire ant aggregations

    NASA Astrophysics Data System (ADS)

    Tennenbaum, Michael; Liu, Zhongyang; Hu, David; Fernandez-Nieves, Alberto

    2016-01-01

    Fire ants link their bodies to form aggregations; these can adopt a variety of structures, they can drip and spread, or withstand applied loads. Here, by using oscillatory rheology, we show that fire ant aggregations are viscoelastic. We find that, at the lowest ant densities probed and in the linear regime, the elastic and viscous moduli are essentially identical over the spanned frequency range, which highlights the absence of a dominant mode of structural relaxation. As ant density increases, the elastic modulus rises, which we interpret by alluding to ant crowding and subsequent jamming. When deformed beyond the linear regime, the aggregation flows, exhibiting shear-thinning behaviour with a stress load that is comparable to the maximum load the aggregation can withstand before individual ants are torn apart. Our findings illustrate the rich, collective mechanical behaviour that can arise in aggregations of active, interacting building blocks.

  12. Mechanics of fire ant aggregations.

    PubMed

    Tennenbaum, Michael; Liu, Zhongyang; Hu, David; Fernandez-Nieves, Alberto

    2016-01-01

    Fire ants link their bodies to form aggregations; these can adopt a variety of structures, they can drip and spread, or withstand applied loads. Here, by using oscillatory rheology, we show that fire ant aggregations are viscoelastic. We find that, at the lowest ant densities probed and in the linear regime, the elastic and viscous moduli are essentially identical over the spanned frequency range, which highlights the absence of a dominant mode of structural relaxation. As ant density increases, the elastic modulus rises, which we interpret by alluding to ant crowding and subsequent jamming. When deformed beyond the linear regime, the aggregation flows, exhibiting shear-thinning behaviour with a stress load that is comparable to the maximum load the aggregation can withstand before individual ants are torn apart. Our findings illustrate the rich, collective mechanical behaviour that can arise in aggregations of active, interacting building blocks. PMID:26501413

  13. Molecular aggregation of humic substances

    USGS Publications Warehouse

    Wershaw, R. L.

    1999-01-01

    Humic substances (HS) form molecular aggregates in solution and on mineral surfaces. Elucidation of the mechanism of formation of these aggregates is important for an understanding of the interactions of HS in soils arid natural waters. The HS are formed mainly by enzymatic depolymerization and oxidation of plant biopolymers. These reactions transform the aromatic and lipid plant components into amphiphilic molecules, that is, molecules that consist of separate hydrophobic (nonpolar) and hydrophilic (polar) parts. The nonpolar parts of the molecules are composed of relatively unaltered segments of plant polymers and the polar parts of carboxylic acid groups. These amphiphiles form membrane-like aggregates on mineral surfaces and micelle-like aggregates in solution. The exterior surfaces of these aggregates are hydrophilic, and the interiors constitute separate hydrophobic liquid-like phases.

  14. Imbibition kinetics of spherical aggregates

    NASA Astrophysics Data System (ADS)

    Hébraud, Pascal; Lootens, Didier; Debacker, Alban

    The imbibition kinetics of a millimeter-sized aggregate of 300 nm diameter colloidal particles by a wetting pure solvent is studied. Three successive regimes are observed : in the first one, the imbibition proceeds by compressing the air inside the aggregate. Then, the solvent stops when the pressure of the compressed air is equal to the Laplace pressure at the meniscus of the wetting solvent in the porous aggregate. The interface is pinned and the aggregate slowly degases, up to a point where the pressure of the entrapped air stops decreasing and is controlled by the Laplace pressure of small bubbles. Depending on the curvature of the bubble, the system may then be in an unstable state. The imbibition then starts again, but with an inner pressure in equilibrium with these bubbles. This last stage leads to the complete infiltration of the aggregate.

  15. Immunogenicity of Therapeutic Protein Aggregates.

    PubMed

    Moussa, Ehab M; Panchal, Jainik P; Moorthy, Balakrishnan S; Blum, Janice S; Joubert, Marisa K; Narhi, Linda O; Topp, Elizabeth M

    2016-02-01

    Therapeutic proteins have a propensity for aggregation during manufacturing, shipping, and storage. The presence of aggregates in protein drug products can induce adverse immune responses in patients that may affect safety and efficacy, and so it is of concern to both manufacturers and regulatory agencies. In this vein, there is a lack of understanding of the physicochemical determinants of immunological responses and a lack of standardized analytical methods to survey the molecular properties of aggregates associated with immune activation. In this review, we provide an overview of the basic immune mechanisms in the context of interactions with protein aggregates. We then critically examine the literature with emphasis on the underlying immune mechanisms as they relate to aggregate properties. Finally, we highlight the gaps in our current understanding of this issue and offer recommendations for future research. PMID:26869409

  16. Coarse-Grained Model for Colloidal Protein Interactions, B22, and Protein Cluster Formation

    PubMed Central

    Blanco, Marco A.; Sahin, Eric; Robinson, Anne S.; Roberts, Christopher J.

    2014-01-01

    Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semi-quantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as the osmotic second virial coefficient (B22). Based on earlier work, this CG model treats proteins as rigid bodies composed of one bead per amino acid, with each amino acid having specific parameters for its size, hydrophobicity, and charge. The net interactions are a combination of steric repulsions, short-range attractions, and screened long-range charge-charge interactions. Model parametrization was done by fitting simulation results against experimental values of the B22 as a function of solution ionic strength for α-chymotrypsinogen A and γD-crystallin (gD-Crys). The CG model is applied to characterize the pairwise interactions and dimerization of gD-Crys and the dependance on temperature, protein concentration, and ionic strength. The results illustrate that at experimentally relevant conditions where stable dimers do not form, the entropic contributions are predominant in the free-energy of protein cluster formation and colloidal protein interactions, arguing against interpretations that treat B22 primarily from energetic considerations alone. Additionally, the results suggest that electrostatic interactions help to modulate the population of the different stable configurations for protein nearest-neighbor pairs, while short-range attractions determine the relative orientations of proteins within these configurations. Finally, simulation results are combined with Principal Component Analysis to identify those amino-acids / surface patches that form inter-protein contacts

  17. Eco-friendly porous concrete using bottom ash aggregate for marine ranch application.

    PubMed

    Lee, Byung Jae; Prabhu, G Ganesh; Lee, Bong Chun; Kim, Yun Yong

    2016-03-01

    This article presents the test results of an investigation carried out on the reuse of coal bottom ash aggregate as a substitute material for coarse aggregate in porous concrete production for marine ranch applications. The experimental parameters were the rate of bottom ash aggregate substitution (30%, 50% and 100%) and the target void ratio (15%, 20% and 25%). The cement-coated granular fertiliser was substituted into a bottom ash aggregate concrete mixture to improve marine ranch applications. The results of leaching tests revealed that the bottom ash aggregate has only a negligible amount of the ten deleterious substances specified in the Ministry of Environment - Enforcement Regulation of the Waste Management Act of Republic Korea. The large amount of bubbles/air gaps in the bottom ash aggregate increased the voids of the concrete mixtures in all target void ratios, and decreased the compressive strength of the porous concrete mixture; however, the mixture substituted with 30% and 10% of bottom ash aggregate and granular fertiliser, respectively, showed an equal strength to the control mixture. The sea water resistibility of the bottom ash aggregate substituted mixture was relatively equal to that of the control mixture, and also showed a great deal of improvement in the degree of marine organism adhesion compared with the control mixture. No fatality of fish was observed in the fish toxicity test, which suggested that bottom ash aggregate was a harmless material and that the combination of bottom ash aggregate and granular fertiliser with substitution rates of 30% and 10%, respectively, can be effectively used in porous concrete production for marine ranch application. PMID:26687102

  18. Use of recycled fine aggregate in concretes with durable requirements.

    PubMed

    Zega, Claudio Javier; Di Maio, Angel Antonio

    2011-11-01

    The use of construction waste materials as aggregates for concrete production is highly attractive compared to the use of non-renewable natural resources, promoting environmental protection and allowing the development of a new raw material. Several countries have recommendations for the use of recycled coarse aggregate in structural concrete, whereas the use of the fine fraction is limited because it may produce significant changes in some properties of concrete. However, during the last decade the use of recycled fine aggregates (RFA) has achieved a great international interest, mainly because of economic implications related to the shortage of natural sands suitable for the production of concrete, besides to allow an integral use of this type of waste. In this study, the durable behaviour of structural concretes made with different percentage of RFA (0%, 20%, and 30%) is evaluated. Different properties related to the durability of concretes such as absorption, sorptivity, water penetration under pressure, and carbonation are determined. In addition, the results of compressive strength, static modulus of elasticity and drying shrinkage are presented. The obtained results indicate that the recycled concretes have a suitable resistant and durable behaviour, according to the limits indicated by different international codes for structural concrete. PMID:21775123

  19. Coarse graining of force fields for metal-organic frameworks.

    PubMed

    Dürholt, Johannes P; Galvelis, Raimondas; Schmid, Rochus

    2016-03-14

    We have adapted our genetic algorithm based optimization approach, originally developed to generate force field parameters from quantum mechanic reference data, to derive a first coarse grained force field for a MOF, taking the atomistic MOF-FF as a reference. On the example of the copper paddle-wheel based HKUST-1, a maximally coarse grained model, using a single bead for each three and four coordinated vertex, was developed as a proof of concept. By adding non-bonded interactions with a modified Buckingham potential, the resulting MOF-FF-CGNB is able to predict local deformation energies of the building blocks as well as bulk properties like the tbovs.pto energy difference or elastic constants in a semi-quantitative way. As expected, the negative thermal expansion of HKUST-1 is not reproduced by the maximally coarse grained model. At the expense of atomic resolution, substantially larger systems (up to tens of nanometers in size) can be simulated with respect to structural and mechanical properties, bridging the gap to the mesoscale. As an example the deformation of the [111] surface of HKUST-1 by a "tip" could be computed without artifacts from periodic images. PMID:26732756

  20. Coarse Point Cloud Registration by Egi Matching of Voxel Clusters

    NASA Astrophysics Data System (ADS)

    Wang, Jinhu; Lindenbergh, Roderik; Shen, Yueqian; Menenti, Massimo

    2016-06-01

    Laser scanning samples the surface geometry of objects efficiently and records versatile information as point clouds. However, often more scans are required to fully cover a scene. Therefore, a registration step is required that transforms the different scans into a common coordinate system. The registration of point clouds is usually conducted in two steps, i.e. coarse registration followed by fine registration. In this study an automatic marker-free coarse registration method for pair-wise scans is presented. First the two input point clouds are re-sampled as voxels and dimensionality features of the voxels are determined by principal component analysis (PCA). Then voxel cells with the same dimensionality are clustered. Next, the Extended Gaussian Image (EGI) descriptor of those voxel clusters are constructed using significant eigenvectors of each voxel in the cluster. Correspondences between clusters in source and target data are obtained according to the similarity between their EGI descriptors. The random sampling consensus (RANSAC) algorithm is employed to remove outlying correspondences until a coarse alignment is obtained. If necessary, a fine registration is performed in a final step. This new method is illustrated on scan data sampling two indoor scenarios. The results of the tests are evaluated by computing the point to point distance between the two input point clouds. The presented two tests resulted in mean distances of 7.6 mm and 9.5 mm respectively, which are adequate for fine registration.

  1. Moving Beyond Watson-Crick Models of Coarse Grained DNA

    NASA Astrophysics Data System (ADS)

    Dorfman, Kevin; Linak, Margaret; Tourdot, Richard

    2012-02-01

    DNA structure possesses several levels of complexity, ranging from the sequence of bases (primary structure) to base pairing (secondary structure) to its three-dimensional shape (tertiary structure) and can produce a wide variety of conformations in addition to canonical double stranded DNA. By including non-Watson-Crick interactions in a coarse-grained model, we developed a system that not only can capture the traditional B-form double helix, but also can adopt a wide variety of other DNA conformations. In our experimentally parameterized, coarse-grained DNA model we are able to reproduce the microscopic features of double-stranded DNA without the need for explicit constraints and capture experimental melting curves for a number of short DNA hairpins. We demonstrate the utility of the model by simulating more complex tertiary structures such as the folding of the thrombin aptamer, which includes G-quartets, and strand invasion during triplex formation. Our results highlight the importance of non-canonical interactions in DNA coarse- grained models.

  2. Bayesian calibration of coarse-grained forces: Efficiently addressing transferability

    NASA Astrophysics Data System (ADS)

    Patrone, Paul N.; Rosch, Thomas W.; Phelan, Frederick R.

    2016-04-01

    Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics. In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f0 of forces anchored by standard methods such as force-matching. Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our workflow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f0. In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.

  3. Components and activity of polysaccharides from coarse tea.

    PubMed

    Wang Dongfeng, W; Wang Chenghong, W; Li Jun, L; Zhao Guiwen, Z

    2001-01-01

    Coarse tea contained a high content of polysaccharide complex. Composed of polysaccharide and protein, the polysaccharide complex from tea (TPS) belonged to glycoprotein with the molecular weight () of (10.7-11.0) x 10(4). When mice (7 weeks old, C57BL/8) were injected with TPS, the levels of blood glucose (BG) in normal mice and model mice with high BG were decreased significantly by averages of 13.54 and 22.18%, respectively. The antibody concentration (OD(413 nm)) in the mice injected with 2.4 mg/mL TPS was increased evidently by 44.93% (p < 0.01). TPS treatment was beneficial not only for the subsequent production of interleukin (IL) 2 in spleen cells of adjuvant arthritis (AA) rats but also because it prohibited the body from producing too much IL-1 in AA rats. Treatment of diabetes with coarse tea in both China and Japan may be related to TPS and the content of TPS in coarse tea. PMID:11170619

  4. High capacitance of coarse-grained carbide derived carbon electrodes

    NASA Astrophysics Data System (ADS)

    Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; Zozulya, Yuliya; Simon, Patrice; Gogotsi, Yury

    2016-02-01

    We report exceptional electrochemical properties of supercapacitor electrodes composed of large, granular carbide-derived carbon (CDC) particles. Using a titanium carbide (TiC) precursor, we synthesized 70-250 μm sized particles with high surface area and a narrow pore size distribution. Electrochemical cycling of these coarse-grained powders defied conventional wisdom that a small particle size is strictly required for supercapacitor electrodes and allowed high charge storage densities, rapid transport, and good rate handling ability. The material showcased capacitance above 100 F g-1 at sweep rates as high as 250 mV s-1 in organic electrolyte. 250-1000 micron thick dense CDC films with up to 80 mg cm-2 loading showed superior areal capacitances. The material significantly outperformed its activated carbon counterpart in organic electrolytes and ionic liquids. Furthermore, large internal/external surface ratio of coarse-grained carbons allowed the resulting electrodes to maintain high electrochemical stability up to 3.1 V in ionic liquid electrolyte. In addition to presenting novel insights into the electrosorption process, these coarse-grained carbons offer a pathway to low-cost, high-performance implementation of supercapacitors in automotive and grid-storage applications.

  5. Coarse-Grained Model of SNARE-Mediated Docking

    PubMed Central

    Fortoul, Nicole; Singh, Pankaj; Hui, Chung-Yuen; Bykhovskaia, Maria; Jagota, Anand

    2015-01-01

    Synaptic transmission requires that vesicles filled with neurotransmitter molecules be docked to the plasma membrane by the SNARE protein complex. The SNARE complex applies attractive forces to overcome the long-range repulsion between the vesicle and membrane. To understand how the balance between the attractive and repulsive forces defines the equilibrium docked state we have developed a model that combines the mechanics of vesicle/membrane deformation with an apparently new coarse-grained model of the SNARE complex. The coarse-grained model of the SNARE complex is calibrated by comparison with all-atom molecular dynamics simulations as well as by force measurements in laser tweezer experiments. The model for vesicle/membrane interactions includes the forces produced by membrane deformation and hydration or electrostatic repulsion. Combining these two parts, the coarse-grained model of the SNARE complex with membrane mechanics, we study how the equilibrium docked state varies with the number of SNARE complexes. We find that a single SNARE complex is able to bring a typical synaptic vesicle to within a distance of ∼3 nm from the membrane. Further addition of SNARE complexes shortens this distance, but an overdocked state of >4–6 SNAREs actually increases the equilibrium distance. PMID:25954883

  6. Biomolecular pleiomorphism probed by spatial interpolation of coarse models.

    PubMed

    Rusu, Mirabela; Birmanns, Stefan; Wriggers, Willy

    2008-11-01

    In low resolution structures of biological assemblies one can often observe conformational deviations that require a flexible rearrangement of structural domains fitted at the atomic level. We are evaluating interpolation methods for the flexible alignment of atomic models based on coarse models. Spatial interpolation is well established in image-processing and visualization to describe the overall deformation or warping of an object or an image. Combined with a coarse representation of the biological system by feature vectors, such methods can provide a flexible approximation of the molecular structure. We have compared three well-known interpolation techniques and evaluated the results by comparing them with constrained molecular dynamics. One method, inverse distance weighting interpolation, consistently produced models that were nearly indistinguishable on the alpha carbon level from the molecular dynamics results. The method is simple to apply and enables flexing of structures by non-expert modelers. This is useful for the basic interpretation of volumetric data in biological applications such as electron microscopy. The method can be used as a general interpretation tool for sparsely sampled motions derived from coarse models. PMID:18757874

  7. The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation.

    PubMed

    Davtyan, Aram; Dama, James F; Sinitskiy, Anton V; Voth, Gregory A

    2014-12-01

    The increasing interest in the modeling of complex macromolecular systems in recent years has spurred the development of numerous coarse-graining (CG) techniques. However, many of the CG models are constructed assuming that all details beneath the resolution of CG degrees of freedom are fast and average out, which sets limits on the resolution of feasible coarse-grainings and on the range of applications of the CG models. Ultra-coarse-graining (UCG) makes it possible to construct models at any desired resolution while accounting for discrete conformational or chemical changes within the CG sites that can modulate the interactions between them. Here, we discuss the UCG methodology and its numerical implementation. We pay particular attention to the numerical mechanism for including state transitions between different conformations within CG sites because this has not been discussed previously. Using a simple example of 1,2-dichloroethane, we demonstrate the ability of the UCG model to reproduce the multiconfigurational behavior of this molecular liquid, even when each molecule is modeled with only one CG site. The methodology can also be applied to other molecular liquids and macromolecular systems with time scale separation between conformational transitions and other intramolecular motions and rotations. PMID:26583210

  8. Is Coarse-to-Fine Strategy Sensitive to Normal Aging?

    PubMed Central

    Musel, Benoit; Chauvin, Alan; Guyader, Nathalie; Chokron, Sylvie; Peyrin, Carole

    2012-01-01

    Theories on visual perception agree that visual recognition begins with global analysis and ends with detailed analysis. Different results from neurophysiological, computational, and behavioral studies all indicate that the totality of visual information is not immediately conveyed, but that information analysis follows a predominantly coarse-to-fine processing sequence (low spatial frequencies are extracted first, followed by high spatial frequencies). We tested whether such processing continues to occur in normally aging subjects. Young and aged participants performed a categorization task (indoor vs. outdoor scenes), using dynamic natural scene stimuli, in which they resorted to either a coarse-to-fine (CtF) sequence or a reverse fine-to-coarse sequence (FtC). The results show that young participants categorized CtF sequences more quickly than FtC sequences. However, sequence processing interacts with semantic category only for aged participants. The present data support the notion that CtF categorization is effective even in aged participants, but is constrained by the spatial features of the scenes, thus highlighting new perspectives in visual models. PMID:22675568

  9. Coarse bedload routing and dispersion through tributary confluences

    NASA Astrophysics Data System (ADS)

    Imhoff, Kurt S.; Wilcox, Andrew C.

    2016-07-01

    Sediment routing fundamentally influences channel morphology and the propagation of disturbances such as debris flows. The transport and storage of bedload particles across headwater channel confluences, which may be significant nodes of the channel network in terms of sediment routing, morphology, and habitat, are poorly understood, however. We investigated patterns and processes of sediment routing through headwater confluences by comparing them to published results from lower-gradient confluences and by comparing the dispersive behavior of coarse bedload particles between headwater confluence and non-confluence reaches. We addressed these questions with a field tracer experiment using passive-integrated transponder and radio-frequency identification technology in the East Fork Bitterroot River basin, Montana, USA. Within the confluence zone, tracers tended to be deposited towards scour-hole and channel margins, suggesting narrow, efficient transport corridors that mirror those observed in prior studies, many of which are from finer-grained systems. Coarse particles in some confluence reaches experienced reduced depositional probabilities within the confluence relative to upstream and downstream of the confluence. Analysis of particle transport data suggests that variation in the spatial distribution of coarse-sediment particles may be enhanced by passing through confluences, though further study is needed to evaluate confluence effects on dispersive regimes and sediment routing on broader spatial and temporal scales.

  10. Coarse-graining the electrostatic potential via distributed multipole expansions

    PubMed Central

    Gramada, Apostol; Bourne, Philip E.

    2011-01-01

    Multipole expansions offer a natural path to coarse-graining the electrostatic potential. However, the validity of the expansion is restricted to regions outside a spherical enclosure of the distribution of charge and, therefore, not suitable for most applications that demand accurate representation at arbitrary positions around the molecule. We propose and demonstrate a distributed multipole expansion approach that resolves this limitation. We also provide a practical algorithm for the computational implementation of this approach. The method allows the partitioning of the charge distribution into subsystems so that the multipole expansion of each component of the partition, and therefore of their superposition, is valid outside an enclosing surface of the molecule of arbitrary shape. The complexity of the resulting coarse-grained model of electrostatic potential is dictated by the area of the molecular surface and therefore, for a typical three-dimensional molecule, it scale as N2/3 with N, the number of charges in the system. This makes the method especially useful for coarse-grained studies of biological systems consisting of many large macromolecules provided that the configuration of the individual molecules can be approximated as fixed. PMID:21572587

  11. Insights on protein-DNA recognition by coarse grain modelling

    PubMed Central

    Poulain, Pierre; Saladin, Adrien; Hartmann, Brigitte; Prévost, Chantal

    2008-01-01

    Coarse grain modelling of macromolecules is a new approach potentially well adapted to answer numerous issues, ranging from physics to biology. We propose here an original DNA coarse grain model specifically dedicated to protein–DNA docking, a crucial, but still largely unresolved, question in molecular biology. Using a representative set of protein–DNA complexes, we first show that our model is able to predict the interaction surface between the macromolecular partners taken in their bound form. In a second part, the impact of the DNA sequence and electrostatics, together with the DNA and protein conformations on docking is investigated. Our results strongly suggest that the overall DNA structure mainly contributes in discriminating the interaction site on cognate proteins. Direct electrostatic interactions between phosphate groups and amino acids side chains strengthen the binding. Overall, this work demonstrates that coarse grain modelling can reveal itself a precious auxiliary for a general and complete description and understanding of protein–DNA association mechanisms. PMID:18478582

  12. High capacitance of coarse-grained carbide derived carbon electrodes

    DOE PAGESBeta

    Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; Zozulya, Yuliya; Simon, Patrice; Gogotsi, Yury

    2016-01-01

    Here, we report exceptional electrochemical properties of supercapacitor electrodes composed of large, granular carbide-derived carbon (CDC) particles. We synthesized 70–250 μm sized particles with high surface area and a narrow pore size distribution, using a titanium carbide (TiC) precursor. Electrochemical cycling of these coarse-grained powders defied conventional wisdom that a small particle size is strictly required for supercapacitor electrodes and allowed high charge storage densities, rapid transport, and good rate handling ability. Moreover, the material showcased capacitance above 100 F g-1 at sweep rates as high as 250 mV s-1 in organic electrolyte. 250–1000 micron thick dense CDC films withmore » up to 80 mg cm-2 loading showed superior areal capacitances. The material significantly outperformed its activated carbon counterpart in organic electrolytes and ionic liquids. Furthermore, large internal/external surface ratio of coarse-grained carbons allowed the resulting electrodes to maintain high electrochemical stability up to 3.1 V in ionic liquid electrolyte. In addition to presenting novel insights into the electrosorption process, these coarse-grained carbons offer a pathway to low-cost, high-performance implementation of supercapacitors in automotive and grid-storage applications.« less

  13. High capacitance of coarse-grained carbide derived carbon electrodes

    SciTech Connect

    Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; Zozulya, Yuliya; Simon, Patrice; Gogotsi, Yury

    2016-01-01

    Here, we report exceptional electrochemical properties of supercapacitor electrodes composed of large, granular carbide-derived carbon (CDC) particles. We synthesized 70–250 μm sized particles with high surface area and a narrow pore size distribution, using a titanium carbide (TiC) precursor. Electrochemical cycling of these coarse-grained powders defied conventional wisdom that a small particle size is strictly required for supercapacitor electrodes and allowed high charge storage densities, rapid transport, and good rate handling ability. Moreover, the material showcased capacitance above 100 F g-1 at sweep rates as high as 250 mV s-1 in organic electrolyte. 250–1000 micron thick dense CDC films with up to 80 mg cm-2 loading showed superior areal capacitances. The material significantly outperformed its activated carbon counterpart in organic electrolytes and ionic liquids. Furthermore, large internal/external surface ratio of coarse-grained carbons allowed the resulting electrodes to maintain high electrochemical stability up to 3.1 V in ionic liquid electrolyte. In addition to presenting novel insights into the electrosorption process, these coarse-grained carbons offer a pathway to low-cost, high-performance implementation of supercapacitors in automotive and grid-storage applications.

  14. Penetration Test Modelling in a Coarse Granular Medium

    NASA Astrophysics Data System (ADS)

    Breul, P.; Benz, M.; Gourvès, R.; Saussine, G.

    2009-06-01

    Penetration test is a simple and useful test to characterize soils and granular materials. Several studies have shown the link between cone penetration resistance and density for a given material if the relation connecting these two parameters has been established beforehand. A granular materials bank currently including more than 35 granular materials has been developed to this end. Unfortunately, to be able to generalize and cover the broadest possible material range, it would be necessary to multiply the tests and the number of materials. Moreover in coarse granular media, it is necessary to carry out a large number of tests in order to achieve a reliable relation between density and cone resistance.Consequently, being able to model this test in a realistic way will enable increasing the number of tests on a material and carry out more precise parametric studies to evaluate the influence of any parameter on the test response. This article presents the work carried out to model a penetration test within a coarse granular medium. The penetrometer used is a light penetrometer with a 2 cm2 cone. The first part will present the experimental protocol developed with the material bank in order to establish the relation between cone resistance and material density. The results obtained on a coarse material of a railway ballast type will be presented. The second part will present the test modelling using discrete elements and parameter identification to obtain the relation found in the experimental tests and connecting cone resistance to material density.

  15. Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models.

    PubMed

    Mereghetti, Paolo; Maccari, Giuseppe; Spampinato, Giulia Lia Beatrice; Tozzini, Valentina

    2016-08-25

    The increasing trend in the recent literature on coarse grained (CG) models testifies their impact in the study of complex systems. However, the CG model landscape is variegated: even considering a given resolution level, the force fields are very heterogeneous and optimized with very different parametrization procedures. Along the road for standardization of CG models for biopolymers, here we describe a strategy to aid building and optimization of statistics based analytical force fields and its implementation in the software package AsParaGS (Assisted Parameterization platform for coarse Grained modelS). Our method is based on the use and optimization of analytical potentials, optimized by targeting internal variables statistical distributions by means of the combination of different algorithms (i.e., relative entropy driven stochastic exploration of the parameter space and iterative Boltzmann inversion). This allows designing a custom model that endows the force field terms with a physically sound meaning. Furthermore, the level of transferability and accuracy can be tuned through the choice of statistical data set composition. The method-illustrated by means of applications to helical polypeptides-also involves the analysis of two and three variable distributions, and allows handling issues related to the FF term correlations. AsParaGS is interfaced with general-purpose molecular dynamics codes and currently implements the "minimalist" subclass of CG models (i.e., one bead per amino acid, Cα based). Extensions to nucleic acids and different levels of coarse graining are in the course. PMID:27150459

  16. Coarse-Grained Model of SNARE-Mediated Docking.

    PubMed

    Fortoul, Nicole; Singh, Pankaj; Hui, Chung-Yuen; Bykhovskaia, Maria; Jagota, Anand

    2015-05-01

    Synaptic transmission requires that vesicles filled with neurotransmitter molecules be docked to the plasma membrane by the SNARE protein complex. The SNARE complex applies attractive forces to overcome the long-range repulsion between the vesicle and membrane. To understand how the balance between the attractive and repulsive forces defines the equilibrium docked state we have developed a model that combines the mechanics of vesicle/membrane deformation with an apparently new coarse-grained model of the SNARE complex. The coarse-grained model of the SNARE complex is calibrated by comparison with all-atom molecular dynamics simulations as well as by force measurements in laser tweezer experiments. The model for vesicle/membrane interactions includes the forces produced by membrane deformation and hydration or electrostatic repulsion. Combining these two parts, the coarse-grained model of the SNARE complex with membrane mechanics, we study how the equilibrium docked state varies with the number of SNARE complexes. We find that a single SNARE complex is able to bring a typical synaptic vesicle to within a distance of ∼ 3 nm from the membrane. Further addition of SNARE complexes shortens this distance, but an overdocked state of >4-6 SNAREs actually increases the equilibrium distance. PMID:25954883

  17. Coarse-grained models for aqueous polyethylene glycol solutions.

    PubMed

    Choi, Eunsong; Mondal, Jagannath; Yethiraj, Arun

    2014-01-01

    A new coarse-grained force field is developed for polyethylene glycol (PEG) in water. The force field is based on the MARTINI model but with the big multipole water (BMW) model for the solvent. The polymer force field is reparameterized using the MARTINI protocol. The new force field removes the ring-like conformations seen in simulations of short chains with the MARTINI force field; these conformations are not observed in atomistic simulations. We also investigate the effect of using parameters for the end-group that are different from those for the repeat units, with the MARTINI and BMW/MARTINI models. We find that the new BMW/MARTINI force field removes the ring-like conformations seen in the MARTINI models and has more accurate predictions for the density of neat PEG. However, solvent-separated-pairs between chain ends and slow dynamics of the PEG reflect its own artifacts. We also carry out fine-grained simulations of PEG with bundled water clusters and show that the water bundling can lead to ring-like conformations of the polymer molecules. The simulations emphasize the pitfalls of coarse-graining several molecules into one site and suggest that polymer-solvent systems might be a stringent test for coarse-grained force fields. PMID:24350686

  18. Lung Response to Coarse PM: Bioassay in Mice

    PubMed Central

    Wegesser, Teresa C.; Last, Jerold A.

    2008-01-01

    Particulate matter (PM) elicits inflammatory and toxic responses in the lung specific to its constituents, which can vary by region, time, and particle size. To identify the mechanism of toxicity in PM collected in a rural area in the San Joaquin Valley of Central California, we studied coarse particles of 2.5 – 10 μm diameter (PM2.5-PM10). Potential pro-inflammatory and toxic effects of PM2.5-PM10 in the lung were investigated using intratracheally instilled mice. We determined total and differential cell profiles and inflammatory chemokines in lung lavage fluid, and biomarkers of toxicity resulting from coarse PM exposure. Responses of the mice were readily observed with total doses of 25–50 ug of PM per mouse. Changes in pro-inflammatory cellular profiles and chemokines showed both dose and time response; peak responses were observed 24 hours after PM instillation, with recovery as early as 48 hours. Furthermore, macrophage inflammatory protein (MIP-2) profiles following PM exposures were correlated to levels of measured macrophages and neutrophils recovered from lung lavage fluid of PM treated animals. Our data suggest that pro-inflammatory effects observed from coarse PM collected during the summer months from California’s hot and dry Central Valley are driven largely by the insoluble components of the PM mixture, and are not caused by endotoxin. PMID:18384828

  19. Experimental investigation of coarse particle conveying in pipes

    NASA Astrophysics Data System (ADS)

    Vlasak, Pavel; Chara, Zdenek; Konfrst, Jiri; Krupička, Jan

    2015-05-01

    The advanced knowledge of particle-water mixture flow behaviour is important for safe, reliable, and economical design and operation of the freight pipelines. The effect of the mixture velocity and concentration on the coarse particle - water mixtures flow behaviour was experimentally investigated on an experimental pipe loop of inner diameter D = 100 mm with horizontal, vertical, and inclined pipe sections. Narrow particle size distribution basalt pebbles were used as model of coarse-grained solid particles. The radiometric method was used to measure particle concentration distribution in pipe cross-section. Mixture flow behaviour and particles motion along the pipe invert were studied in a pipe viewing section. The study revealed that the coarse particlewater mixtures in the horizontal and inclined pipe sections were significantly stratified. The particles moved principally in a layer close to the pipe invert. However, for higher and moderate flow velocities the particles moved also in the central part of the pipe cross-section, and particle saltation was found to be dominant mode of particle conveying.

  20. Lung response to coarse PM: Bioassay in mice

    SciTech Connect

    Wegesser, Teresa C.; Last, Jerold A.

    2008-07-15

    Particulate matter (PM) elicits inflammatory and toxic responses in the lung specific to its constituents, which can vary by region, time, and particle size. To identify the mechanism of toxicity in PM collected in a rural area in the San Joaquin Valley of Central California, we studied coarse particles of 2.5-10 {mu}m diameter (PM{sub 2.5}-PM{sub 10}). Potential pro-inflammatory and toxic effects of PM{sub 2.5}-PM{sub 10} in the lung were investigated using intratracheally instilled mice. We determined total and differential cell profiles and inflammatory chemokines in lung lavage fluid, and biomarkers of toxicity resulting from coarse PM exposure. Responses of the mice were readily observed with total doses of 25-50 {mu}g of PM per mouse. Changes in pro-inflammatory cellular profiles and chemokines showed both dose and time responses; peak responses were observed 24 h after PM instillation, with recovery as early as 48 h. Furthermore, macrophage inflammatory protein (MIP-2) profiles following PM exposures were correlated to levels of measured macrophages and neutrophils recovered from lung lavage fluid of PM-treated animals. Our data suggest that pro-inflammatory effects observed from coarse PM collected during the summer months from California's hot and dry Central Valley are driven largely by the insoluble components of the PM mixture, and are not caused by endotoxin.

  1. Neutron attenuation characteristics of polyethylene, polyvinyl chloride, and heavy aggregate concrete and mortars

    SciTech Connect

    Abdul-Majid, S.; Othman, F.

    1994-03-01

    Polyethylene and polyvinyl chloride pellets were introduced into concrete to improve its neutron attenuation characteristics while several types of heavy coarse aggregates were used to improve its gamma ray attenuation properties. Neutron and gamma ray attenuation were studied in concrete samples containing coarse aggregates of barite, pyrite, basalt, hematite, and marble as well as polyethylene and polyvinyl chloride pellets in narrow-beam geometry. The highest neutron attenuation was shown by polyethylene mortar, followed by polyvinyl chloride mortar; barite and pyrite concrete showed higher gamma ray attenuation than ordinary concrete. Broad-beam and continuous (infinite) medium geometries were used to study the neutron attenuation of samples containing polymers at different concentrations with and without heavy aggregates, the fitting equations were established, and from these the neutron removal coefficients were deduced. In a radiation field of neutrons and gamma rays, the appropriate concentration of polymer and heavy aggregate can be selected to give the optimum total dose attenuation depending on the relative intensities of each type of radiation. This would give much better design flexibility over ordinary concrete. The compressive strength tests performed on mortar and concrete samples showed that their value, in general, decreases as polymer concentration increases and that the polyvinyl chloride mortar showed higher values than the polyethylene mortar. For general construction purposes, the compression strength was considered acceptable in these samples. 34 refs., 16 figs., 4 tabs.

  2. Perspectives on Preference Aggregation.

    PubMed

    Regenwetter, Michel

    2009-07-01

    For centuries, the mathematical aggregation of preferences by groups, organizations, or society itself has received keen interdisciplinary attention. Extensive theoretical work in economics and political science throughout the second half of the 20th century has highlighted the idea that competing notions of rational social choice intrinsically contradict each other. This has led some researchers to consider coherent democratic decision making to be a mathematical impossibility. Recent empirical work in psychology qualifies that view. This nontechnical review sketches a quantitative research paradigm for the behavioral investigation of mathematical social choice rules on real ballots, experimental choices, or attitudinal survey data. The article poses a series of open questions. Some classical work sometimes makes assumptions about voter preferences that are descriptively invalid. Do such technical assumptions lead the theory astray? How can empirical work inform the formulation of meaningful theoretical primitives? Classical "impossibility results" leverage the fact that certain desirable mathematical properties logically cannot hold in all conceivable electorates. Do these properties nonetheless hold true in empirical distributions of preferences? Will future behavioral analyses continue to contradict the expectations of established theory? Under what conditions do competing consensus methods yield identical outcomes and why do they do so? PMID:26158988

  3. The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites

    SciTech Connect

    Cao, Zhen; Voth, Gregory A.

    2015-12-28

    It is essential to be able to systematically construct coarse-grained (CG) models that can efficiently and accurately reproduce key properties of higher-resolution models such as all-atom. To fulfill this goal, a mapping operator is needed to transform the higher-resolution configuration to a CG configuration. Certain mapping operators, however, may lose information related to the underlying electrostatic properties. In this paper, a new mapping operator based on the centers of charge of CG sites is proposed to address this issue. Four example systems are chosen to demonstrate this concept. Within the multiscale coarse-graining framework, CG models that use this mapping operator are found to better reproduce the structural correlations of atomistic models. The present work also demonstrates the flexibility of the mapping operator and the robustness of the force matching method. For instance, important functional groups can be isolated and emphasized in the CG model.

  4. Efficient coarse simulation of a growing avascular tumor

    PubMed Central

    Kavousanakis, Michail E.; Liu, Ping; Boudouvis, Andreas G.; Lowengrub, John; Kevrekidis, Ioannis G.

    2013-01-01

    The subject of this work is the development and implementation of algorithms which accelerate the simulation of early stage tumor growth models. Among the different computational approaches used for the simulation of tumor progression, discrete stochastic models (e.g., cellular automata) have been widely used to describe processes occurring at the cell and subcell scales (e.g., cell-cell interactions and signaling processes). To describe macroscopic characteristics (e.g., morphology) of growing tumors, large numbers of interacting cells must be simulated. However, the high computational demands of stochastic models make the simulation of large-scale systems impractical. Alternatively, continuum models, which can describe behavior at the tumor scale, often rely on phenomenological assumptions in place of rigorous upscaling of microscopic models. This limits their predictive power. In this work, we circumvent the derivation of closed macroscopic equations for the growing cancer cell populations; instead, we construct, based on the so-called “equation-free” framework, a computational superstructure, which wraps around the individual-based cell-level simulator and accelerates the computations required for the study of the long-time behavior of systems involving many interacting cells. The microscopic model, e.g., a cellular automaton, which simulates the evolution of cancer cell populations, is executed for relatively short time intervals, at the end of which coarse-scale information is obtained. These coarse variables evolve on slower time scales than each individual cell in the population, enabling the application of forward projection schemes, which extrapolate their values at later times. This technique is referred to as coarse projective integration. Increasing the ratio of projection times to microscopic simulator execution times enhances the computational savings. Crucial accuracy issues arising for growing tumors with radial symmetry are addressed by

  5. Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations

    PubMed Central

    Bieler, Noah S.; Knowles, Tuomas P. J.; Frenkel, Daan; Vácha, Robert

    2012-01-01

    The pre-fibrillar stages of amyloid formation have been implicated in cellular toxicity, but have proved to be challenging to study directly in experiments and simulations. Rational strategies to suppress the formation of toxic amyloid oligomers require a better understanding of the mechanisms by which they are generated. We report Dynamical Monte Carlo simulations that allow us to study the early stages of amyloid formation. We use a generic, coarse-grained model of an amyloidogenic peptide that has two internal states: the first one representing the soluble random coil structure and the second one the -sheet conformation. We find that this system exhibits a propensity towards fibrillar self-assembly following the formation of a critical nucleus. Our calculations establish connections between the early nucleation events and the kinetic information available in the later stages of the aggregation process that are commonly probed in experiments. We analyze the kinetic behaviour in our simulations within the framework of the theory of classical nucleated polymerisation, and are able to connect the structural events at the early stages in amyloid growth with the resulting macroscopic observables such as the effective nucleus size. Furthermore, the free-energy landscapes that emerge from these simulations allow us to identify pertinent properties of the monomeric state that could be targeted to suppress oligomer formation. PMID:23071427

  6. Supramolecular assembly of a biomineralizing antimicrobial peptide in coarse-grained Monte Carlo simulations.

    PubMed

    Eby, D Matthew; Johnson, Glenn R; Farmer, Barry L; Pandey, Ras B

    2011-01-21

    Monte Carlo simulations are used to model the self-organizing behavior of the biomineralizing peptide KSL (KKVVFKVKFK) in the presence of phosphate. Originally identified as an antimicrobial peptide, KSL also directs the formation of biosilica through a hypothetical supramolecular template that requires phosphate for assembly. Specificity of each residue and the interactions between the peptide and phosphate are considered in a coarse-grained model. Both local and global physical quantities are calculated as the constituents execute their stochastic motion in the presence and absence of phosphate. Ordered peptide aggregates develop after simulations reach thermodynamic equilibrium, wherein phosphates form bridging ligands with lysines and are found interdigitated between peptide molecules. Results demonstrate that interactions between the lysines and phosphate drive self-organization into lower energy conformations of interconnected peptide scaffolds that resemble the supramolecular structures of polypeptide- and polyamine-mediated silica condensation systems. Furthermore, the specific phosphate-peptide organization appears to mimic the zwitterionic structure of native silaffins (scaffold proteins of diatom shells), suggesting a similar template organization for silica deposition between the in vitro KSL and silaffin systems. PMID:21072418

  7. Coarse-grained simulation study of sequence effects on DNA hybridization in a concentrated environment.

    PubMed

    Markegard, Cade B; Fu, Iris W; Reddy, K Anki; Nguyen, Hung D

    2015-02-01

    A novel coarse-grained model is developed to elucidate thermodynamics and kinetic mechanisms of DNA self-assembly. It accounts for sequence and solvent conditions to capture key experimental results such as sequence-dependent thermal property and salt-dependent persistence length of ssDNA and dsDNA. Moreover, constant-temperature simulations on two single strands of a homogeneous sequence show two main mechanisms of hybridization: a slow slithering mechanism and a one-order faster zippering mechanism. Furthermore, large-scale simulations at a high DNA strand concentration demonstrate that DNA self-assembly is a robust and enthalpically driven process in which the formation of double helices is deciphered to occur via multiple self-assembly pathways including the strand displacement mechanism. However, sequence plays an important role in shifting the majority of one pathway over the others and controlling size distribution of self-assembled aggregates. This study yields a complex picture on the role of sequence on programmable self-assembly and demonstrates a promising simulation tool that is suitable for studies in DNA nanotechnology. PMID:25581253

  8. Heat-Treatment of MgSiO Smokes of Astrophysical Interest: Possible Implications for Olivine-Pyroxene-Silica Assemblages in Chondritic Aggregate IDPs

    NASA Technical Reports Server (NTRS)

    Rietmeijer, F. J. M.; Nuth, J. A., III; Hallenbeck, S. L.

    2001-01-01

    Anhydrous silicates in coarse-grained ferromagnesiosilica principal components (PCs) formed during atmospheric entry flash-heating also constrain the astromineralogy of astrophysical dust. This is because of the unique closed-system behavior of these PCs in chondritic aggregate interplanetary dust particles (IDPs). Additional information is contained in the original extended abstract.

  9. COIN Project: Towards a zero-waste technology for concrete aggregate production in Norway

    NASA Astrophysics Data System (ADS)

    Cepuritis, Rolands; Willy Danielsen, Svein

    2014-05-01

    COIN Project: Towards a zero-waste technology for concrete aggregate production in Norway Rolands Cepuritis, Norcem/NTNU and Svein Willy Danielsen, SINTEF Aggregate production is a mining operation where no purification of the "ore" is necessary. Still it is extremely rare that an aggregate production plant is operating on the basis of zero-waste concept. This is since historically the fine crushed aggregate (particles with a size of less than 2, 4 or sometimes 8 mm) has been regarded as a by-product or waste of the more valuable coarse aggregate production. The reason is that the crushed coarse aggregates can easily replace coarse rounded natural stones in almost any concrete composition; while, the situation with the sand is different. The production of coarse aggregate normally yields fine fractions with rough surface texture, flaky or elongated particles an inadequate gradation. When such a material replaces smooth and rounded natural sand grains in a concrete mix, the result is usually poor and much more water and cement has to be used to achieve adequate concrete flow. The consequences are huge stockpiles of the crushed fine fractions that can't be sold (mass balance problems) for the aggregate producers, sustainability problems for the whole industry and environmental issues for society due to dumping and storing of the fine co-generated material. There have been attempts of utilising the material in concrete before; however, they have mostly ended up in failure. There have been attempts to adjust the crushed sand to the properties of the natural sand, which would still give a lot of waste, especially if the grading would have to be adjusted and the high amounts of fines abundantly present in the crushed sand would have to be removed. Another fundamental reason for failure has been that historically such attempts have mainly ended up in a research carried out by people (both industrial and academic) with aggregate background (= parties willing to find market

  10. Effects of oxidative modification on thermal aggregation and gel properties of soy protein by malondialdehyde.

    PubMed

    Wu, Wei; Hua, Yufei; Lin, Qinlu

    2014-03-01

    Malondialdehyde (MDA) was selected as a representative of lipid peroxidation products to investigate the effects of oxidative modification on thermal aggregation and gel properties of soy protein by lipid peroxidation products. Incubation of soy protein with increasing concentration of MDA resulted in gradual decrease of particle size and content of thermal aggregates during heat denaturation. Oxidative modification by MDA resulted in a decrease in water holding capacity, gel hardness, and gel strength of soy protein gel. An increase in coarseness and interstice of MDA modified protein gel network was accompanied by uneven distribution of interstice as MDA concentration increased. The results showed that degree of thermal aggregation of MDA-modified soy protein gradually decreased as MDA concentration increased, which contributed to a decrease in water holding capacity, gel hardness, and gel strength of MDA-modified soy protein gel. PMID:24587523

  11. Coarse-grained molecular-dynamics simulations of the self-assembly of pentablock copolymers into micelles

    NASA Astrophysics Data System (ADS)

    Chushak, Y.; Travesset, A.

    2005-12-01

    Multiblock polymers in aqueous solution, where one or several blocks are hydrophobic, exhibit a rich variety of phases and states of aggregation. In this paper, we investigate a pentablock system ABCBA, where the B block is always hydrophilic and the A and C blocks have varying degrees of hydrophobicity depending on external conditions. We report coarse-grained molecular-dynamics simulations where the solvent is included explicitly and monomers interact via a 6-9 Lennard Jones potential function. The hydrophobic interaction is modeled by tuning the parameter controlling the strength of the interaction between the hydrophobic monomers and the solvent. We investigate the structure and morphology of the micelles for two concrete situations representing changes in temperature and the pH level. The simulated system is directly relevant to a recently synthesized pentablock system consisting of a triblock Pluronic® with an added pH-sensitive end group [B. C. Anderson et al., Macromolecules 36, 1670 (2003)].

  12. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Yu, Hang; Han, Wei; Ma, Wen; Schulten, Klaus

    2015-12-01

    Parkinson's disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and 3J(HNHCα)-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.

  13. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation

    SciTech Connect

    Yu, Hang; Ma, Wen; Han, Wei; Schulten, Klaus

    2015-12-28

    Parkinson’s disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and {sup 3}J(H{sub N}H{sub C{sub α}})-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.

  14. Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations.

    PubMed

    Kraft, Johan F; Vestergaard, Mikkel; Schiøtt, Birgit; Thøgersen, Lea

    2012-05-01

    Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable to experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A. Kukol fails to maintain stable micelles, whereas the most recent CHARMM36 lipid parameters and GROMOS96 with the so-called Berger lipid parameters both succeed in this regard. PMID:26593649

  15. Algebraic Multigrid by Smoothed Aggregation for Second and Fourth Order Elliptic Problems

    NASA Technical Reports Server (NTRS)

    Vanek, Petr; Mandel, Jan; Brezina, Marian

    1996-01-01

    Multigrid methods are very efficient iterative solvers for system of algebraic equations arising from finite element and finite difference discretization of elliptic boundary value problems. The main principle of multigrid methods is to complement the local exchange of information in point-wise iterative methods by a global one utilizing several related systems, called coarse levels, with a smaller number of variables. The coarse levels are often obtained as a hierarchy of discretizations with different characteristic meshsizes, but this requires that the discretization is controlled by the iterative method. To solve linear systems produced by existing finite element software, one needs to create an artificial hierarchy of coarse problems. The principal issue is then to obtain computational complexity and approximation properties similar to those for nested meshes, using only information in the matrix of the system and as little extra information as possible. Such algebraic multigrid method that uses the system matrix only was developed by Ruge. The prolongations were based on the matrix of the system by partial solution from given values at selected coarse points. The coarse grid points were selected so that each point would be interpolated to via so-called strong connections. Our approach is based on smoothed aggregation introduced recently by Vanek. First the set of nodes is decomposed into small mutually disjoint subsets. A tentative piecewise constant interpolation (in the discrete sense) is then defined on those subsets as piecewise constant for second order problems, and piecewise linear for fourth order problems. The prolongation operator is then obtained by smoothing the output of the tentative prolongation and coarse level operators are defined variationally.

  16. Influence of recycled aggregate quality and proportioning criteria on recycled concrete properties.

    PubMed

    López-Gayarre, F; Serna, P; Domingo-Cabo, A; Serrano-López, M A; López-Colina, C

    2009-12-01

    This paper presents the results of experimental research using concrete produced by substituting part of the natural coarse aggregates with recycled aggregates from concrete demolition. The influence of the quality of the recycled aggregate (amount of declassified and source of aggregate), the percentage of replacement on the targeted quality of the concrete to be produced (strength and workability) has been evaluated. The granular structure of concrete and replacement criteria were analyzed in this study, factors which have not been analyzed in other studies. The following properties of recycled concretes were analyzed: density, absorption, compressive strength, elastic modulus, amount of occluded air, penetration of water under pressure and splitting tensile strength. A simplified test program was designed to control the costs of the testing while still producing sufficient data to develop reliable conclusions in order to make the number of tests viable whilst guaranteeing the reliability of the conclusions. Several factors were analyzed including the type of aggregate, the percentage of replacement, the type of sieve curve, the declassified content, the strength of concrete and workability of concrete and the replacement criteria. The type of aggregate and the percentage of replacement were the only factors that showed a clear influence on most of the properties. Compressive strength is clearly affected by the quality of recycled aggregates. If the water-cement ratio is kept constant and the loss of workability due to the effect of using recycled aggregate is compensated for with additives, the percentage of replacement of the recycled aggregate will not affect the compressive strength. The elastic modulus is affected by the percentage of replacement. If the percentage of replacement does not exceed 50%, the elastic modulus will only change slightly. PMID:19709870

  17. Aggregate-associated carbon and nitrogen in reclaimed sandy loam soils

    SciTech Connect

    Wick, A.F.; Stahl, P.D.; Ingram, L.J.

    2009-11-15

    Minimal research has been conducted on aggregate, C, and N in coarse-textured soils used to reclaim surface coal mine lands. Furthermore, little is known about the contribution different plant communities make to the recovery of aggregation in these soils. Two chronosequences of semiarid reclaimed sites with sandy loam soils were sampled under shrub- and grass-dominated communities. Aggregation, aggregate fractions, and associated C and N were measured. No definitive trends of increasing macroaggregates between sites were observed undershrubs; however, macro- and microaggregation was greater in the 16-yr-old (0.20 and 0.23 kg aggregate kg{sup -1} soil, respectively) than in the 5-yr-old soils (0.02 and 0.08 kg aggregate kg{sup -1} soil, respectively) under grasses. Although C and N concentrations were drastically reduced (50-75%) with mining activity between the <1-yr-old and native soils, aggregate C and N concentrations tinder shrubs and grasses were similar to each other and to the native soils in the 5-yr-old site. Sods under grass in the 16-yr-old site had lower available and aggregate-occluded C and N concentrations than the 5-yr-old site, while C and N concentrations did not change between 5- and 16-yr-old soils under shrubs. Conversely, aggregate C and N pool sizes under shrubs and grasses both increased with site age to conditions similar to those observed in the native soil. Reclaimed shrub site soils had consistently higher C concentrations in the older reclaimed sites (10 and 16 yr old) than the soils under grasses, indicating greater accumulation and retention of C and N in organic material under shrub than grass communities in semiarid reclaimed sites.

  18. Simulating Fiber Ordering and Aggregation In Shear Flow Using Dissipative Particle Dynamics

    NASA Astrophysics Data System (ADS)

    Stimatze, Justin T.

    We have developed a mesoscale simulation of fiber aggregation in shear flow using LAMMPS and its implementation of dissipative particle dynamics. Understanding fiber aggregation in shear flow and flow-induced microstructural fiber networks is critical to our interest in high-performance composite materials. Dissipative particle dynamics enables the consideration of hydrodynamic interactions between fibers through the coarse-grained simulation of the matrix fluid. Correctly simulating hydrodynamic interactions and accounting for fluid forces on the microstructure is required to correctly model the shear-induced aggregation process. We are able to determine stresses, viscosity, and fiber forces while simulating the evolution of a model fiber system undergoing shear flow. Fiber-fiber contact interactions are approximated by combinations of common pairwise forces, allowing the exploration of interaction-influenced fiber behaviors such as aggregation and bundling. We are then able to quantify aggregate structure and effective volume fraction for a range of relevant system and fiber-fiber interaction parameters. Our simulations have demonstrated several aggregate types dependent on system parameters such as shear rate, short-range attractive forces, and a resistance to relative rotation while in contact. A resistance to relative rotation at fiber-fiber contact points has been found to strongly contribute to an increased angle between neighboring aggregated fibers and therefore an increase in average aggregate volume fraction. This increase in aggregate volume fraction is strongly correlated with a significant enhancement of system viscosity, leading us to hypothesize that controlling the resistance to relative rotation during manufacturing processes is important when optimizing for desired composite material characteristics.

  19. Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence

    PubMed Central

    Nasica-Labouze, Jessica; Mousseau, Normand

    2012-01-01

    The small amyloid-forming GNNQQNY fragment of the prion sequence has been the subject of extensive experimental and numerical studies over the last few years. Using unbiased molecular dynamics with the OPEP coarse-grained potential, we focus here on the onset of aggregation in a 20-mer system. With a total of 16.9 of simulations at 280 K and 300 K, we show that the GNNQQNY aggregation follows the classical nucleation theory (CNT) in that the number of monomers in the aggregate is a very reliable descriptor of aggregation. We find that the critical nucleus size in this finite-size system is between 4 and 5 monomers at 280 K and 5 and 6 at 300 K, in overall agreement with experiment. The kinetics of growth cannot be fully accounted for by the CNT, however. For example, we observe considerable rearrangements after the nucleus is formed, as the system attempts to optimize its organization. We also clearly identify two large families of structures that are selected at the onset of aggregation demonstrating the presence of well-defined polymorphism, a signature of amyloid growth, already in the 20-mer aggregate. PMID:23209391

  20. Mucin aggregation from a rod-like meso-scale model

    NASA Astrophysics Data System (ADS)

    Moreno, Nicolas; Perilla, Jairo E.; Colina, Coray M.; Lísal, Martin

    2015-05-01

    Dissipative particle dynamics, a meso-scale particle-based model, was used to study the aggregation of mucins in aqueous solutions. Concentration, strength of the mucin-water interactions, as well as the effects of size, shape, and composition of the model molecules were studied. Model proteins were represented as rod-like objects formed by coarse-grained beads. In the first model, only one type of beads formed the mucin. It was found that all the surfaces were available to form aggregates and the conformation of the aggregates was a function of the strength of the mucin-water interaction. With this model, the number of aggregates was unaffected by the initial position of the mucins in the simulation box, except for the lowest mucin concentration. In a more refined mucin model, two kinds of beads were used in the molecule in order to represent the existence of cysteine-like terminal groups in the actual molecule. With this new scheme, aggregation took place by the interaction of the terminal groups between model molecules. The kinetic analysis of the evolution of the number of aggregates with time was also studied for both mucin models.

  1. Aggregate breakdown of nanoparticulate titania

    NASA Astrophysics Data System (ADS)

    Venugopal, Navin

    Six nanosized titanium dioxide powders synthesized from a sulfate process were investigated. The targeted end-use of this powder was for a de-NOx catalyst honeycomb monolith. Alteration of synthesis parameters had resulted principally in differences in soluble ion level and specific surface area of the powders. The goal of this investigation was to understand the role of synthesis parameters in the aggregation behavior of these powders. Investigation via scanning electron microscopy of the powders revealed three different aggregation iterations at specific length scales. Secondary and higher order aggregate strength was investigated via oscillatory stress rheometry as a means of simulating shear conditions encountered during extrusion. G' and G'' were measured as a function of the applied oscillatory stress. Oscillatory rheometry indicated a strong variation as a function of the sulfate level of the particles in the viscoelastic yield strengths. Powder yield stresses ranged from 3.0 Pa to 24.0 Pa of oscillatory stress. Compaction curves to 750 MPa found strong similarities in extrapolated yield point of stage I and II compaction for each of the powders (at approximately 500 MPa) suggesting that the variation in sulfate was greatest above the primary aggregate level. Scanning electron microscopy of samples at different states of shear in oscillatory rheometry confirmed the variation in the linear elastic region and the viscous flow regime. A technique of this investigation was to approach aggregation via a novel perspective: aggregates are distinguished as being loose open structures that are highly disordered and stochastic in nature. The methodology used was to investigate the shear stresses required to rupture the various aggregation stages encountered and investigate the attempt to realign the now free-flowing constituents comprising the aggregate into a denser configuration. Mercury porosimetry was utilized to measure the pore size of the compact resulting from

  2. Optical Properties of Fine/Coarse Mode Aerosol Mixtures

    NASA Astrophysics Data System (ADS)

    Eck, T. F.; Holben, B. N.; Siniuk, A.; Pinker, R. T.; Goloub, P.; Chen, H.; Chatenet, B.; Li, Z.; Singh, R.; Tripathi, S. N.; Dubovik, O.; Giles, D. M.; Martins, J.; Reid, J. S.; O'Neill, N. T.; Smirnov, A.

    2009-12-01

    Several regions of the earth exhibit seasonal mixtures of fine and coarse mode sized aerosol types, which are challenging to characterize from satellite remote sensing. Over land the coarse mode size aerosols (radius >1 micron) originate primarily from arid regions, which generate airborne soil dust, and the dominant fine mode sources are gases and particulates from urban/industrial emissions and from biomass burning. AERONET sun-sky radiometer almucantar retrievals from several years are analyzed for the urban sites of Beijing, China and Kanpur, India (in the Ganges floodplain) where seasonal coarse mode dust particles mix with fine mode pollution aerosol, predominately in the spring. As increasingly more absorbing fine mode pollutants are added to the dust aerosol at both sites, the single scattering albedo (SSA) of the mixtures at 675 nm through 1020 nm decrease as the fine mode fraction of AOD increases, while the 440 nm SSA is relatively constant. Additionally we compare multi-year data from Ilorin, Nigeria where desert dust from the Sahara and Sahel mix with fine mode biomass-burning aerosols. The volume size distribution retrievals from this site often shows tri-modality (third mode centered at 0.6 micron radius), which suggests a different particle source than found for most other arid region AERONET sites, which typically have bi-modal distributions. Comparison of mid-visible single scattering albedo obtained from in situ aircraft measurements during DABEX to multi-year means from the Ilorin site AERONET retrievals show close agreement (within 0.03 or less) over a wide range of Angstrom exponent (0.3 to 1.5). Observed differences in the spectral SSA as a function of fine mode fraction of the optical depth between all three sites are discussed and occur due to differences in absorption for both modes and also due to fine mode particle size dynamics.

  3. Monosized aggregates -- A new model

    SciTech Connect

    Gopal, M.

    1997-08-01

    For applications requiring colloidal particles, it is desirable that they be monosized to better control the structure and the properties. In a number of systems, the monosized particles come together to form aggregates that are also monosized. A model is presented here to explain the formation of these monosized aggregates. This is of particular importance in the fields of ceramics, catalysis, pigments, pharmacy, photographic emulsions, etc.

  4. Preparation and Physicochemical and Pharmacokinetic Characterization of Ginkgo Lactone Nanosuspensions for Antiplatelet Aggregation.

    PubMed

    Rui, Tian-Qi; Zhang, Liang; Qiao, Hong-Zhi; Huang, Ping; Qian, Shuai; Li, Jun-Song; Chen, Zhi-Peng; Fu, Ting-Ming; Di, Liu-Qing; Cai, Baochang

    2016-01-01

    The aim of this study was to investigate the potential of nanosuspensions (NSs) in improving the dissolution and absorption of poorly water-soluble ginkgo lactones (GLs), including ginkgolide A, ginkgolide B, and ginkgolide C. Liquid GL-NSs were prepared by a combined bottom-up and top-down approach with response surface methodology design, followed by freeze-drying solidification. Physicochemical characterization of the prepared freeze-dried GL-NSs was performed by photon correlation spectroscopy, scanning electron microscopy, powder X-ray diffraction, and differential scanning calorimetry. In vitro dissolution and in vivo bioavailability of ginkgolide A, ginkgolide B, and ginkgolide C in freeze-dried GL-NSs were evaluated with GLs coarse powder as control. Their inhibitory effects on platelet aggregation were also comparatively analyzed. GLs existed in an amorphous state in the prepared freeze-dried GL-NSs. The particle size, polydispersity index, zeta potential, and redispersibility index of freeze-dried GL-NSs were around 286 nm, 0.26, -25.19 mV, and 112%, respectively. The particle size reduction resulted in much more rapid and complete dissolution of ginkgolides from GL-NSs than coarse powder. Comparison with GLs coarse powder, freeze-dried GL-NSs showed a significant decreased Tmax, 2-fold higher peak concentration, and 2-fold higher area under plasma concentrations curve for 3 ginkgolides and exhibited significantly higher antiplatelet aggregation effect. PMID:26852855

  5. Statistical coarse-graining of molecular dynamics into peridynamics.

    SciTech Connect

    Silling, Stewart Andrew; Lehoucq, Richard B.

    2007-10-01

    This paper describes an elegant statistical coarse-graining of molecular dynamics at finite temperature into peridynamics, a continuum theory. Peridynamics is an efficient alternative to molecular dynamics enabling dynamics at larger length and time scales. In direct analogy with molecular dynamics, peridynamics uses a nonlocal model of force and does not employ stress/strain relationships germane to classical continuum mechanics. In contrast with classical continuum mechanics, the peridynamic representation of a system of linear springs and masses is shown to have the same dispersion relation as the original spring-mass system.

  6. Molecular Dynamics Trajectory Compression with a Coarse-Grained Model

    PubMed Central

    Cheng, Yi-Ming; Gopal, Srinivasa Murthy; Law, Sean M.; Feig, Michael

    2012-01-01

    Molecular dynamics trajectories are very data-intensive thereby limiting sharing and archival of such data. One possible solution is compression of trajectory data. Here, trajectory compression based on conversion to the coarse-grained model PRIMO is proposed. The compressed data is about one third of the original data and fast decompression is possible with an analytical reconstruction procedure from PRIMO to all-atom representations. This protocol largely preserves structural features and to a more limited extent also energetic features of the original trajectory. PMID:22025759

  7. Coarse quantization with the fast digital shearlet transform

    NASA Astrophysics Data System (ADS)

    Bodmann, Bernhard G.; Kutyniok, Gitta; Zhuang, Xiaosheng

    2011-09-01

    The fast digital shearlet transform (FDST) was recently introduced as a means to analyze natural images efficiently, owing to the fact that those are typically governed by cartoon-like structures. In this paper, we introduce and discuss a first-order hybrid sigma-delta quantization algorithm for coarsely quantizing the shearlet coefficients generated by the FDST. Radial oversampling in the frequency domain together with our choice for the quantization helps suppress the reconstruction error in a similar way as first-order sigma-delta quantization for finite frames. We provide a theoretical bound for the reconstruction error and confirm numerically that the error is in accordance with this theoretical decay.

  8. Coarse fraction of soils from building rubble (WWII)

    NASA Astrophysics Data System (ADS)

    Mekiffer, Beate; Wessolek, Gerd; Scheytt, Traugott; Bussert, Robert; Nehls, Thomas

    2010-05-01

    Soils, resulting from building rubble of WWII are wide spread in whole Europe. The parent material for pedogenesis originates from different kinds of buildings, which where destroyed of different ways. Also the kind of sorting and disposing was varying for this material. So the most important feature of soils, resulting from building rubble of WWII, is their heterogeneity. We investigated samples of soils developed from building rubble to answer the following questions: ­ What are the amounts of coarse fraction and what are their main components? ­ What are the chemical properties and what is the crystalline mineral composition of technogenic components? ­ What is the release of ions from coarse technogenic components? We sieved and hand sorted the materials, used the X-ray diffractometry and X-ray fluorescence spectroscopy and measured the ions released in 1:2-extract. In most cases, the soils have a high amount of coarse fraction (> 2mm) (median 25% w/w, N=52). Dominating components in the coarse fraction are in the order of decreasing abundance: bricks, mortar (incl. plaster and stucco), slag, ashes and unburned coals. The analyzed components show alkalescent to alkaline pH-values. 75% of the samples show low electrical conductivities of up to 141 µS/cm. Bricks mainly consist of Si oxides, followed by oxides of Al, Ca, Fe, Mg and K. X-Ray-diffractometry of bricks showed, that most common minerals are clay minerals (Kaolinit, Illit, Montmorillonit and Chlorit), Quarz, and Carbonates (Calcite and Dolomite, Siderite). Bricks contain Fe-Oxides (Hematite, Goethite), Sulphates and Sulfides (Gypsum, Pyrite, Markasite) in lower amounts. 5-20 % of the minerals are x-ray-amorphous. Mortar is characterized by a high amount of silicates (nearby 80%). The samples showed a lower percentage of Al- and Ca-compounds than bricks. Chemical composition of ashes and slag varies in wide ranges, depending on their genesis. We found mainly ashes from stove heating. They contained

  9. The power of coarse graining in biomolecular simulations

    PubMed Central

    Ingólfsson, Helgi I; Lopez, Cesar A; Uusitalo, Jaakko J; de Jong, Djurre H; Gopal, Srinivasa M; Periole, Xavier; Marrink, Siewert J

    2014-01-01

    Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large-scale biomolecular processes on time scales inaccessible to all-atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state-of-the-art examples of protein folding, membrane protein gating and self-assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling. PMID:25309628

  10. Coarse-Grained Models for Protein-Cell Membrane Interactions

    PubMed Central

    Bradley, Ryan; Radhakrishnan, Ravi

    2015-01-01

    The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes. PMID:26613047

  11. Model for amorphous aggregation processes

    NASA Astrophysics Data System (ADS)

    Stranks, Samuel D.; Ecroyd, Heath; van Sluyter, Steven; Waters, Elizabeth J.; Carver, John A.; von Smekal, Lorenz

    2009-11-01

    The amorphous aggregation of proteins is associated with many phenomena, ranging from the formation of protein wine haze to the development of cataract in the eye lens and the precipitation of recombinant proteins during their expression and purification. While much literature exists describing models for linear protein aggregation, such as amyloid fibril formation, there are few reports of models which address amorphous aggregation. Here, we propose a model to describe the amorphous aggregation of proteins which is also more widely applicable to other situations where a similar process occurs, such as in the formation of colloids and nanoclusters. As first applications of the model, we have tested it against experimental turbidimetry data of three proteins relevant to the wine industry and biochemistry, namely, thaumatin, a thaumatinlike protein, and α -lactalbumin. The model is very robust and describes amorphous experimental data to a high degree of accuracy. Details about the aggregation process, such as shape parameters of the aggregates and rate constants, can also be extracted.

  12. Glycation precedes lens crystallin aggregation

    SciTech Connect

    Swamy, M.S.; Perry, R.E.; Abraham, E.C.

    1987-05-01

    Non-enzymatic glycosylation (glycation) seems to have the potential to alter the structure of crystallins and make them susceptible to thiol oxidation leading to disulfide-linked high molecular weight (HMW) aggregate formation. They used streptozotocin diabetic rats during precataract and cataract stages and long-term cell-free glycation of bovine lens crystallins to study the relationship between glycation and lens crystallin aggregation. HMW aggregates and other protein components of the water-soluble (WS) and urea-soluble (US) fractions were separated by molecular sieve high performance liquid chromatography. Glycation was estimated by both (/sup 3/H)NaBH/sub 4/ reduction and phenylboronate agarose affinity chromatography. Levels of total glycated protein (GP) in the US fractions were about 2-fold higher than in the WS fractions and there was a linear increase in GP in both WS and US fractions. This increase was parallelled by a corresponding increase in HMW aggregates. Total GP extracted by the affinity method from the US fraction showed a predominance of HMW aggregates and vice versa. Cell-free glycation studies with bovine crystallins confirmed the results of the animals studies. Increasing glycation caused a corresponding increase in protein insolubilization and the insoluble fraction thus formed also contained more glycated protein. It appears that lens protein glycation, HMW aggregate formation, and protein insolubilization are interrelated.

  13. Modifiers of mutant huntingtin aggregation

    PubMed Central

    Teuling, Eva; Bourgonje, Annika; Veenje, Sven; Thijssen, Karen; de Boer, Jelle; van der Velde, Joeri; Swertz, Morris; Nollen, Ellen

    2011-01-01

    Protein aggregation is a common hallmark of a number of age-related neurodegenerative diseases, including Alzheimer’s, Parkinson’s, and polyglutamine-expansion disorders such as Huntington’s disease, but how aggregation-prone proteins lead to pathology is not known. Using a genome-wide RNAi screen in a C. elegans-model for polyglutamine aggregation, we previously identified 186 genes that suppress aggregation. Using an RNAi screen for human orthologs of these genes, we here present 26 human genes that suppress aggregation of mutant huntingtin in a human cell line. Among these are genes that have not been previously linked to mutant huntingtin aggregation. They include those encoding eukaryotic translation initiation, elongation and translation factors, and genes that have been previously associated with other neurodegenerative diseases, like the ATP-ase family gene 3-like 2 (AFG3L2) and ubiquitin-like modifier activating enzyme 1 (UBA1). Unravelling the role of these genes will broaden our understanding of the pathogenesis of Huntington’s disease. PMID:21915392

  14. Kinetic model for erythrocyte aggregation.

    PubMed

    Bertoluzzo, S M; Bollini, A; Rasia, M; Raynal, A

    1999-01-01

    It is well known that light transmission through blood is the most widely utilized method for the study of erythrocyte aggregation. The curves obtained had been considered empirically as exponential functions. In consequence, the process becomes characterized by an only parameter that varies with all the process factors without discrimination. In the present paper a mathematical model for RBC aggregation process is deduced in accordance with von Smoluchowski's theory about the kinetics of colloidal particles agglomeration. The equation fitted the experimental pattern of the RBC suspension optical transmittance closely and contained two parameters that estimate the most important characteristics of the aggregation process separately, i.e., (1) average size of rouleaux at equilibrium and (2) aggregation rate. The evaluation of the method was assessed by some factors affecting erythrocyte aggregation, such as temperature, plasma dilutions, Dextran 500, Dextran 70 and PVP 360, at different media concentrations, cellular membrane alteration by the alkylating agent TCEA, and decrease of medium osmolarity. Results were interpreted considering the process characteristics estimated by the parameters, and there were also compared with similar studies carried out by other authors with other methods. This analysis allowed us to conclude that the equation proposed is reliable and useful to study erythrocyte aggregation. PMID:10660481

  15. Ash Aggregates in Proximal Settings

    NASA Astrophysics Data System (ADS)

    Porritt, L. A.; Russell, K.

    2012-12-01

    Ash aggregates are thought to have formed within and been deposited by the eruption column and plume and dilute density currents and their associated ash clouds. Moist, turbulent ash clouds are considered critical to ash aggregate formation by facilitating both collision and adhesion of particles. Consequently, they are most commonly found in distal deposits. Proximal deposits containing ash aggregates are less commonly observed but do occur. Here we describe two occurrences of vent proximal ash aggregate-rich deposits; the first within a kimberlite pipe where coated ash pellets and accretionary lapilli are found within the intra-vent sequence; and the second in a glaciovolcanic setting where cored pellets (armoured lapilli) occur within <1 km of the vent. The deposits within the A418 pipe, Diavik Diamond Mine, Canada, are the residual deposits within the conduit and vent of the volcano and are characterised by an abundance of ash aggregates. Coated ash pellets are dominant but are followed in abundance by ash pellets, accretionary lapilli and rare cored pellets. The coated ash pellets typically range from 1 - 5 mm in diameter and have core to rim ratios of approximately 10:1. The formation and preservation of these aggregates elucidates the style and nature of the explosive phase of kimberlite eruption at A418 (and other pipes?). First, these pyroclasts dictate the intensity of the kimberlite eruption; it must be energetic enough to cause intense fragmentation of the kimberlite to produce a substantial volume of very fine ash (<62 μm). Secondly, the ash aggregates indicate the involvement of moisture coupled with the presence of dilute expanded eruption clouds. The structure and distribution of these deposits throughout the kimberlite conduit demand that aggregation and deposition operate entirely within the confines of the vent; this indicates that aggregation is a rapid process. Ash aggregates within glaciovolcanic sequences are also rarely documented. The

  16. Crystal aggregation in kidney stones; a polymer aggregation problem?

    NASA Astrophysics Data System (ADS)

    Wesson, J.; Beshensky, A.; Viswanathan, P.; Zachowicz, W.; Kleinman, J.

    2008-03-01

    Kidney stones most frequently form as aggregates of calcium oxalate monohydrate (COM) crystals with organic layers between them, and the organic layers contain principally proteins. The pathway leading to the formation of these crystal aggregates in affected people has not been identified, but stone forming patients are thought to have a defect in the structure or distribution of urinary proteins, which normally protect against stone formation. We have developed two polyelectrolyte models that will induce COM crystal aggregation in vitro, and both are consistent with possible urinary protein compositions. The first model was based on mixing polyanionic and polycationic proteins, in portions such that the combined protein charge is near zero. The second model was based on reducing the charge density on partially charged polyanionic proteins, specifically Tamm-Horsfall protein, the second most abundant protein in urine. Both models demonstrated polymer phase separation at solution conditions where COM crystal aggregation was observed. Correlation with data from other bulk crystallization measurements suggest that the anionic side chains form critical binding interactions with COM surfaces that are necessary along with the phase separation process to induce COM crystal aggregation.

  17. Coarse bedload routing and dispersion through tributary confluences

    NASA Astrophysics Data System (ADS)

    Imhoff, K. S.; Wilcox, A. C.

    2015-12-01

    Sediment routing fundamentally influences channel morphology and propagation of disturbances. However, the transport and storage of bedload particles in headwater channel confluences, which may be significant nodes of the channel network in terms of sediment routing, morphology, and habitat, is poorly understood. To characterize routing processes through confluences of headwater channels, we investigate how sediment routing patterns through headwater confluences compare to those described in low-gradient gravel bed river systems, and how confluences affect the dispersive behavior of coarse bedload particles compared to non-confluence reaches. We address these questions with a field tracer experiment using passive-integrated transponder and radio-frequency identification technology in the East Fork Bitterroot River basin, Montana, USA. Within the confluence zone, transport occurs along scour hole margins in narrow, efficient transport corridors that mirror those observed in finer-grained experiments and field studies. Coarse particles entering confluences experience reduced depositional probabilities, in contrast to the size-selective transport observed in a control reach. Stochastic transport modeling, tail analysis, and use of a dimensionless impulse (I*) suggest that transport distance and variance growth are enhanced through confluences for a given flow strength. We suggest that confluences absent of disturbances enhance sediment transport and dispersive growth through headwater networks.

  18. Effective surface coverage of coarse-grained soft matter.

    PubMed

    Craven, Galen T; Popov, Alexander V; Hernandez, Rigoberto

    2014-12-11

    The surface coverage of coarse-grained macromolecules bound to a solid substrate is not simply proportional to the two-dimensional number density because macromolecules can overlap. As a function of the overlap probability δ, we have developed analytical formulas and computational models capable of characterizing this nonlinear relationship. For simplicity, we ignore site-site interactions that would be induced by length-scale mismatches between binding sites and the radius of gyration of the incident coarse-grained macromolecular species. The interactions between macromolecules are modeled with a finite bounded potential that allows multiple macromolecules to occupy the same binding site. The softness of the bounded potential is thereby reduced to the single parameter δ. Through variation of this parameter, completely hard (δ = 0) and completely soft (δ = 1) behavior can be bridged. For soft macromolecular interactions (δ > 0), multiple occupancy reduces the fraction of sites ϕ occupied on the substrate. We derive the exact transition probability between sequential configurations and use this probability to predict ϕ and the distribution of occupied sites. Due to the complexity of the exact ϕ expressions and their analytical intractability at the thermodynamic limit, we apply a simplified mean-field (MF) expression for ϕ. The MF model is found to be in excellent agreement with the exact result. Both the exact and MF models are applied to an example dynamical system with multibody interactions governed by a stochastic bounded potential. Both models show agreement with results measured from simulation. PMID:25059882

  19. A coarse-grained model of microtubule self-assembly

    NASA Astrophysics Data System (ADS)

    Regmi, Chola; Cheng, Shengfeng

    Microtubules play critical roles in cell structures and functions. They also serve as a model system to stimulate the next-generation smart, dynamic materials. A deep understanding of their self-assembly process and biomechanical properties will not only help elucidate how microtubules perform biological functions, but also lead to exciting insight on how microtubule dynamics can be altered or even controlled for specific purposes such as suppressing the division of cancer cells. Combining all-atom molecular dynamics (MD) simulations and the essential dynamics coarse-graining method, we construct a coarse-grained (CG) model of the tubulin protein, which is the building block of microtubules. In the CG model a tubulin dimer is represented as an elastic network of CG sites, the locations of which are determined by examining the protein dynamics of the tubulin and identifying the essential dynamic domains. Atomistic MD modeling is employed to directly compute the tubulin bond energies in the surface lattice of a microtubule, which are used to parameterize the interactions between CG building blocks. The CG model is then used to study the self-assembly pathways, kinetics, dynamics, and nanomechanics of microtubules.

  20. Minimizing memory as an objective for coarse-graining

    NASA Astrophysics Data System (ADS)

    Guttenberg, Nicholas; Dama, James F.; Saunders, Marissa G.; Voth, Gregory A.; Weare, Jonathan; Dinner, Aaron R.

    2013-03-01

    Coarse-graining a molecular model is the process of integrating over degrees of freedom to obtain a reduced representation. This process typically involves two separate but related steps, selection of the coordinates comprising the reduced system and modeling their interactions. Both the coordinate selection and the modeling procedure present challenges. Here, we focus on the former. Typically, one seeks to integrate over the fast degrees of freedom and retain the slow degrees of freedom. Failure to separate timescales results in memory. With this motivation, we introduce a heuristic measure of memory and show that it can be used to compare competing coordinate selections for a given modeling procedure. We numerically explore the utility of this heuristic for three systems of increasing complexity. The first example is a four-particle linear model, which is exactly solvable. The second example is a sixteen-particle nonlinear model; this system has interactions that are characteristic of molecular force fields but is still sufficiently simple to permit exhaustive numerical treatment. The third example is an atomic-resolution representation of a protein, the class of models most often treated by relevant coarse-graining approaches; we specifically study an actin monomer. In all three cases, we find that the heuristic suggests coordinate selections that are physically intuitive and reflect molecular structure. The memory heuristic can thus serve as an objective codification of expert knowledge and a guide to sites within a model that requires further attention.

  1. COARSE-GRAINED MODELING OF PROTEIN UNFOLDING DYNAMICS*

    PubMed Central

    DENG, MINGGE

    2014-01-01

    We present a new dynamic elastic network model (DENM) that describes the unfolding process of a force-loaded protein. The protein interaction network and its potentials are constructed based on information of its native-state structure obtained from the Protein Data Bank, with network nodes positioned at the Cα coordinates of the protein backbone. Specifically, to mimic the unfolding process, i.e., to simulate the process of overcoming the local energy barrier on the free energy landscape with force loading, the noncovalent protein network bonds (i.e., hydrogen bonds, salt bridges, hydrophobic contacts, etc.) are broken one-by-one with a certain probability, while the strong covalent bonds along the backbone (i.e., peptide bonds, disulfide bonds, etc.) are kept intact. The jumping event from local energy minima (bonds breaking rate) are chosen according to Kramer’s theory and the Bell model. Moreover, we exploit the self-similar structure of proteins at different scales to design an effective coarse-graining procedure for DENM with optimal parameter selection. The robustness of DENM is validated by coarse-grained molecular dynamics (MD) simulation against atomistic MD simulation of force-extension processes of the Fibrinogen and Titin Immunoglobulin proteins. We observe that the native structure of the proteins determines the total unfolding dynamics (including large deviations) and not just the fluctuations around the native state. PMID:25400515

  2. Coarse-to-fine wavelet-based airport detection

    NASA Astrophysics Data System (ADS)

    Li, Cheng; Wang, Shuigen; Pang, Zhaofeng; Zhao, Baojun

    2015-10-01

    Airport detection on optical remote sensing images has attracted great interest in the applications of military optics scout and traffic control. However, most of the popular techniques for airport detection from optical remote sensing images have three weaknesses: 1) Due to the characteristics of optical images, the detection results are often affected by imaging conditions, like weather situation and imaging distortion; and 2) optical images contain comprehensive information of targets, so that it is difficult for extracting robust features (e.g., intensity and textural information) to represent airport area; 3) the high resolution results in large data volume, which makes real-time processing limited. Most of the previous works mainly focus on solving one of those problems, and thus, the previous methods cannot achieve the balance of performance and complexity. In this paper, we propose a novel coarse-to-fine airport detection framework to solve aforementioned three issues using wavelet coefficients. The framework includes two stages: 1) an efficient wavelet-based feature extraction is adopted for multi-scale textural feature representation, and support vector machine(SVM) is exploited for classifying and coarsely deciding airport candidate region; and then 2) refined line segment detection is used to obtain runway and landing field of airport. Finally, airport recognition is achieved by applying the fine runway positioning to the candidate regions. Experimental results show that the proposed approach outperforms the existing algorithms in terms of detection accuracy and processing efficiency.

  3. Effective mobility of dislocations from systematic coarse-graining

    NASA Astrophysics Data System (ADS)

    Kooiman, M.; Hütter, M.; Geers, MGD

    2015-06-01

    The dynamics of large amounts of dislocations governs the plastic response of crystalline materials. In this contribution we discuss the relation between the mobility of discrete dislocations and the resulting flow rule for coarse-grained dislocation densities. The mobilities used in literature on these levels are quite different, for example in terms of their intrinsic the stress dependence. To establish the relation across the scales, we have derived the macroscopic evolution equations of dislocation densities from the equations of motion of individual dislocations by means of systematic coarse-graining. From this, we can identify a memory kernel relating the driving force and the flux of dislocations. This kernel can be considered as an effective macroscopic mobility with two contributions; a direct contribution related to the overdamped motion of individual dislocations, and an emergent contribution that arises from time correlations of fluctuations in the Peach-Koehler force. Scaling analysis shows that the latter contribution is dominant for dislocations in metals at room temperature. We also discuss several concerns related to the separation of timescales.

  4. Coarse-mesh diffusion synthetic acceleration in slab geometry

    SciTech Connect

    Kim, K.S.; Palmer, T.S.

    2000-07-01

    It has long been known that the success of a diffusion synthetic acceleration (DSA) scheme is very sensitive to the consistency between the discretization of the transport and diffusion acceleration equations. Acceleration schemes involving inconsistent discretizations have been successful, but no prescription is available that determines a priori an allowable degree of inconsistency. It is notable, however, that all current DSA schemes involve diffusion equations discretized on the spatial mesh used to solve the transport equations. Often the solution of a large number of low-order equations is an expensive part of the transport simulation. This motivates the desire to find stable and rapidly convergent acceleration schemes that are discretized on a mesh that is coarse relative to the transport mesh. The authors present here results showing that the low-order diffusion equation can be solved on a mesh coarser (by a factor of 2) than that used for the slab geometry transport equation. Their results show that coarse-mesh DSA is unconditionally stable and is as rapidly convergent as a DSA method discretized on the transport mesh. They have used Adams and Martin's modified four-step acceleration method (M4S) applied to the linear discontinuous (LD) finite element transport equations in slab geometry. To evaluate their procedure, they have performed a Fourier analysis to calculate theoretical spectral radii. They compare this analysis with convergence behavior observed in an implementation code for several model problems.

  5. Deformation Behaviour of Coarse Grain Alumina under Shock Loading

    NASA Astrophysics Data System (ADS)

    Gupta, Satish

    2013-06-01

    To develop better understanding of the shock wave induced deformation behavior of coarse grain alumina ceramics, and for measurement of its Hugoniot Elastic Limit (HEL), in-situ and recovery gas gun experiments have been carried out on coarse grain alumina (grain size ~ 10 μm), prepared in the form of discs (>99.9% TMD) by pressure-less sintering of alpha alumina powder at 1583 K. The HEL value of 1.9 GPa has been determined from the kink in the pressure history recorded using piezoresistance gauge and also from the free surface velocity history of the sample shocked to 9 GPa. The nano-indentation measurements on the alumina samples shocked to 6.5 GPa showed hardness value 15% lower than 21.3 GPa for unshocked alumina, and strong Indentation Size Effect (ISE); the hardness value was still lower and the ISE was stronger for the sample shocked to 12 GPa. The XRD measurements showed reduced particle size and increased microstrains in the shocked alumina fragments. SEM, FESEM and TEM measurements on shock treated samples showed presence of grain localized micro- and nano-scale deformations, micro-cleavages, grain-boundary microcracks, extensive shear induced deformations, and localized micro-fractures, etc. These observations led to the development of a qualitative model for the damage initiation and its subsequent growth mechanisms in shocked alumina. The work performed in collaboration with K.D. Joshi of BARC and A.K. Mukhopadhyay of CGCRI.

  6. A quantitative coarse-grain model for lipid bilayers.

    PubMed

    Orsi, Mario; Haubertin, David Y; Sanderson, Wendy E; Essex, Jonathan W

    2008-01-24

    A simplified particle-based computer model for hydrated phospholipid bilayers has been developed and applied to quantitatively predict the major physical features of fluid-phase biomembranes. Compared with available coarse-grain methods, three novel aspects are introduced. First, the main electrostatic features of the system are incorporated explicitly via charges and dipoles. Second, water is accurately (yet efficiently) described, on an individual level, by the soft sticky dipole model. Third, hydrocarbon tails are modeled using the anisotropic Gay-Berne potential. Simulations are conducted by rigid-body molecular dynamics. Our technique proves 2 orders of magnitude less demanding of computational resources than traditional atomic-level methodology. Self-assembled bilayers quantitatively reproduce experimental observables such as electron density, compressibility moduli, dipole potential, lipid diffusion, and water permeability. The lateral pressure profile has been calculated, along with the elastic curvature constants of the Helfrich expression for the membrane bending energy; results are consistent with experimental estimates and atomic-level simulation data. Several of the results presented have been obtained for the first time using a coarse-grain method. Our model is also directly compatible with atomic-level force fields, allowing mixed systems to be simulated in a multiscale fashion. PMID:18085766

  7. An exactly solvable coarse-grained model for species diversity

    NASA Astrophysics Data System (ADS)

    Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

    2012-07-01

    We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology.

  8. Simulating the entropic collapse of coarse-grained chromosomes.

    PubMed

    Shendruk, Tyler N; Bertrand, Martin; de Haan, Hendrick W; Harden, James L; Slater, Gary W

    2015-02-17

    Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continuous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition. PMID:25692586

  9. Million atom DFT calculations using coarse graining and petascale computing

    NASA Astrophysics Data System (ADS)

    Nicholson, Don; Odbadrakh, Kh.; Samolyuk, G. D.; Stoller, R. E.; Zhang, X. G.; Stocks, G. M.

    2014-03-01

    Researchers performing classical Molecular Dynamics (MD) on defect structures often find it necessary to use millions of atoms in their models. It would be useful to perform density functional calculations on these large configurations in order to observe electron-based properties such as local charge and spin and the Helmann-Feynman forces on the atoms. The great number of atoms usually requires that a subset be ``carved'' from the configuration and terminated in a less that satisfactory manner, e.g. free space or inappropriate periodic boundary conditions. Coarse graining based on the Locally Self-consistent Multiple Scattering method (LSMS) and petascale computing can circumvent this problem by treating the whole system but dividing the atoms into two groups. In Coarse Grained LSMS (CG-LSMS) one group of atoms has its charge and scattering determined prescriptively based on neighboring atoms while the remaining group of atoms have their charge and scattering determined according to DFT as implemented in the LSMS. The method will be demonstrated for a one-million-atom model of a displacement cascade in Fe for which 24,130 atoms are treated with full DFT and the remaining atoms are treated prescriptively. Work supported as part of Center for Defect Physics, an Energy Frontier Research Center funded by the U.S. DOE, Office of Science, Basic Energy Sciences, used Oak Ridge Leadership Computing Facility, Oak Ridge National Lab, of DOE Office of Science.

  10. Transport of fine sediment over a coarse, immobile riverbed

    USGS Publications Warehouse

    Grams, Paul E.; Wilcock, Peter R.

    2014-01-01

    Sediment transport in cobble-boulder rivers consists mostly of fine sediment moving over a coarse, immobile bed. Transport rate depends on several interrelated factors: boundary shear stress, the grain size and volume of fine sediment, and the configuration of fine sediment into interstitial deposits and bed forms. Existing models do not incorporate all of these factors. Approaches that partition stress face a daunting challenge because most of the boundary shear is exerted on immobile grains. We present an alternative approach that divides the bed into sand patches and interstitial deposits and is well constrained by two clear end-member cases: full sand cover and absence of sand. Entrainment from sand patches is a function of their aerial coverage. Entrainment from interstices among immobile grains is a function of sand elevation relative to the size of the immobile grains. The bed-sand coverage function is used to predict the ratio of the rate of entrainment from a partially covered bed to the rate of entrainment from a completely sand-covered bed, which is determined using a standard sand transport model. We implement the bed-sand coverage function in a morphodynamic routing model and test it against observations of sand bed elevation and suspended sand concentration for conditions of nonuniform fine sediment transport in a large flume with steady uniform flow over immobile hemispheres. The results suggest that this approach may provide a simple and robust method for predicting the transport and migration of fine sediment through rivers with coarse, immobile beds.

  11. Simulating the Entropic Collapse of Coarse-Grained Chromosomes

    PubMed Central

    Shendruk, Tyler N.; Bertrand, Martin; de Haan, Hendrick W.; Harden, James L.; Slater, Gary W.

    2015-01-01

    Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continuous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition. PMID:25692586

  12. Land Cover of Northern Eurasia: Comparison and Assessment of Coarse Resolution Maps

    NASA Astrophysics Data System (ADS)

    Krankina, O. N.; Pflugmacher, D.; Cohen, W.; Kennedy, R.; Nelson, P.; Loboda, T.

    2007-12-01

    Consistent measurements of land cover are critical for addressing a range of important science questions, from quantifying the effects of vegetation on the carbon, energy, and water cycles, to understanding the social and economic causes and consequences of land-use and land-cover change. While multiple moderate and coarse- resolution land-cover products have been developed, they disagree significantly. Resolving discrepancies among maps is particularly challenging for boreal and temperate Northern Eurasia, where validation sites are sparse and processes of ecosystem disturbance and land-cover change are widespread. To identify specific needs and possibilities for improved mapping of land cover across boreal and temperate Northern Eurasia, we compared the performance of three recent land-cover products based on different sensors: MODIS (Global Land Cover Collection 4), AVHRR (DISCover v. 2.0), and SPOT VEGETATION (GLC2000 for Northern Eurasia v. 4.0). First, we examined the level of agreement among these data sets across the entire region. On a qualitative level, the assessment of general patterns indicates the highest degree of disagreement in transitional zones at the northern and southern fringes of boreal forest, in mountainous regions, and in areas of extensive wetlands, agricultural development, and urban land use. The quantitative analysis measured the level of disagreement between land-cover classes aggregated according to dominant type of vegetation (trees, shrubs, herbaceous, bare land, permanent snow/ice). Secondly, validation of these products was performed at two test sites where Landsat-based classifications were developed based on FAO Land Cover Classification System. Fractional land cover was calculated for each 1x1 km pixel and used to construct fractional error matrices. Most errors were associated with "mixed" coarse-resolution pixels (i.e. those having nearly equal percentage of multiple class types), while errors in "pure" (single class) pixels

  13. Fractal Aggregates in Tennis Ball Systems

    ERIC Educational Resources Information Center

    Sabin, J.; Bandin, M.; Prieto, G.; Sarmiento, F.

    2009-01-01

    We present a new practical exercise to explain the mechanisms of aggregation of some colloids which are otherwise not easy to understand. We have used tennis balls to simulate, in a visual way, the aggregation of colloids under reaction-limited colloid aggregation (RLCA) and diffusion-limited colloid aggregation (DLCA) regimes. We have used the…

  14. Zwitterionic lipid assemblies: Molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field

    PubMed Central

    Shinoda, Wataru; DeVane, Russell; Klein, Michael L.

    2010-01-01

    A new coarse-grained (CG) intermolecular force field is presented for a series of zwitterionic lipids. The model is an extension of our previous work on nonionic surfactants and is designed to reproduce experimental surface/interfacial properties as well as distribution functions from all-atom molecular dynamics (MD) simulations. Using simple functional forms, the force field parameters are optimized for multiple lipid molecules, simultaneously. The resulting CG lipid bilayers have reasonable molecular areas, chain order parameters, and elastic properties. The computed surface pressure vs. area (π-A) curve for a DPPC monolayer demonstrates a significant improvement over the previous CG models. The DPPC monolayer has a longer persistence length than a PEG lipid monolayer, exhibiting a long-lived curved monolayer surface under negative tension. The bud ejected from an oversaturated DPPC monolayer has a large bicelle-like structure, which is different from the micellar bud formed from an oversaturated PEG lipid monolayer. We have successfully observed vesicle formation during CG-MD simulations, starting from an aggregate of DMPC molecules. Depending on the aggregate size, the lipid assembly spontaneously transforms into a closed vesicle or a bicelle. None of the various intermediate structures between these extremes seem to be stable. An attempt to observe fusion of two vesicles through the application of an external adhesion force was not successful. The present CG force field also supports stable multi-lamellar DMPC vesicles. PMID:20438090

  15. Aggregated Recommendation through Random Forests

    PubMed Central

    2014-01-01

    Aggregated recommendation refers to the process of suggesting one kind of items to a group of users. Compared to user-oriented or item-oriented approaches, it is more general and, therefore, more appropriate for cold-start recommendation. In this paper, we propose a random forest approach to create aggregated recommender systems. The approach is used to predict the rating of a group of users to a kind of items. In the preprocessing stage, we merge user, item, and rating information to construct an aggregated decision table, where rating information serves as the decision attribute. We also model the data conversion process corresponding to the new user, new item, and both new problems. In the training stage, a forest is built for the aggregated training set, where each leaf is assigned a distribution of discrete rating. In the testing stage, we present four predicting approaches to compute evaluation values based on the distribution of each tree. Experiments results on the well-known MovieLens dataset show that the aggregated approach maintains an acceptable level of accuracy. PMID:25180204

  16. Aggregated recommendation through random forests.

    PubMed

    Zhang, Heng-Ru; Min, Fan; He, Xu

    2014-01-01

    Aggregated recommendation refers to the process of suggesting one kind of items to a group of users. Compared to user-oriented or item-oriented approaches, it is more general and, therefore, more appropriate for cold-start recommendation. In this paper, we propose a random forest approach to create aggregated recommender systems. The approach is used to predict the rating of a group of users to a kind of items. In the preprocessing stage, we merge user, item, and rating information to construct an aggregated decision table, where rating information serves as the decision attribute. We also model the data conversion process corresponding to the new user, new item, and both new problems. In the training stage, a forest is built for the aggregated training set, where each leaf is assigned a distribution of discrete rating. In the testing stage, we present four predicting approaches to compute evaluation values based on the distribution of each tree. Experiments results on the well-known MovieLens dataset show that the aggregated approach maintains an acceptable level of accuracy. PMID:25180204

  17. Scaling behavior and local structure of ion aggregates in single-ion conductors.

    PubMed

    Lu, Keran; Rudzinski, Joseph F; Noid, W G; Milner, Scott T; Maranas, Janna K

    2014-02-21

    Single-ion conductors are attractive electrolyte materials because of their inherent safety and ease of processing. Most ions in a sodium-neutralized PEO sulfonated-isophthalate ionomer electrolyte exist as one dimensional chains, restricted in dimensionality by the steric hindrance of the attached polymer. Because the ions are slow to reconfigure, atomistic MD simulations of this material are unable to adequately sample equilibrium ion structures. We apply a novel coarse-graining scheme using a generalized-YBG procedure in which the polymer backbone is completely removed and implicitly represented by the effective potentials of the remaining ions. The ion-only coarse-grained simulation allows for substantial sampling of equilibrium aggregate configurations. We extend the wormlike micelle theory to model ion chain equilibrium. Our aggregates are random walks which become more positively charged with increasing size. Defects occur on the string-like structure in the form of “dust” and “knots,” which form due to cation coordination with open sites along the string. The presence of these defects suggest that cation hopping along open third-coordination sites could be an important mechanism of charge transport using ion aggregates. PMID:24983107

  18. Aggregation operations for multiaspect fuzzy soft sets

    NASA Astrophysics Data System (ADS)

    Sulaiman, Nor Hashimah; Mohamad, Daud

    2015-10-01

    Multiaspect fuzzy soft set (MAFSS) is one of the generalized forms of fuzzy soft sets. In this paper, we introduce two types of aggregation operations for MAFSSs, namely the weighted arithmetic mean (WAM)-based MAFSS aggregation, and the ordered weighted aggregation (OWA)-based MAFSS aggregation. The applicability of the two MAFSS-aggregation operations is illustrated with numerical examples in group decision making.

  19. A coarse grained stochastic particle interacting system for tropical convection

    NASA Astrophysics Data System (ADS)

    Khouider, B.

    2012-12-01

    Climate models (GCMs) fail to represent adequately the variability associated with organized convection in the tropics. This deficiency is believed to hinder medium and long range weather forecasts, over weeks to months. GCMs use very complex sub-grid models, known as cumulus parameterizations, to represent the effects of clouds and convection as well as other unresolved processes. Cumulus parameterizations are intrinsically deterministic and are typically based on the quasi-equilibrium theory, which assumes that convection instantaneously consumes the atmospheric instability produced by radiation. In this talk, I will discuss a stochastic model for organized tropical convection based on a particle interacting system defined on a microscopic lattice. An order parameter is assumed to take the values 0,1,2,3 at a any given lattice site according to whether it is a clear site or it is occupied by a cloud of a one of the three types: congestus, deep, or stratiform, following intuitive rules motivated by recent satellite observations and various field campaigns conducted over the Indian Ocean and Western Pacific. The microscopic Markov process is coarse-grained systematically to obtain a multidimensional birth-death process with immigration, following earlier work done by Katsoulakis, Majda, and Vlachos (JCP 2003) for the case of the Ising model where the order parameter takes the values 0 and 1. The coarse grained birth-death process is a stochastic model, intermediate between the microscopic lattice model and the deterministic mean field limit, that is used to represent the sub-grid scale variability of the underlying physical process (here the cloud cover) with a negligible computational overhead and yet permits both local interactions between lattice sites and two-way interactions between the cloud cover and the large-scale climate dynamics. The new systematic coarse-graining, developed here for the multivalued order parameter, provides a unifying framework

  20. Use of plastic waste (poly-ethylene terephthalate) in asphalt concrete mixture as aggregate replacement.

    PubMed

    Hassani, Abolfazl; Ganjidoust, Hossein; Maghanaki, Amir Abedin

    2005-08-01

    One of the environmental issues in most regions of Iran is the large number of bottles made from poly-ethylene terephthalate (PET) deposited in domestic wastes and landfills. Due to the high volume of these bottles, more than 1 million m3 landfill space is needed for disposal every year. The purpose of this experimental study was to investigate the possibility of using PET waste in asphalt concrete mixes as aggregate replacement (Plastiphalt) to reduce the environmental effects of PET disposal. For this purpose the mechanical properties of plastiphalt mixes were compared with control samples. This study focused on the parameters of Marshall stability, flow, Marshall quotient (stability-to-flow ratio) and density. The waste PET used in this study was in the form of granules of about 3 mm diameter which would replace (by volume) a portion of the mineral coarse aggregates of an equal size (2.36-4.75 mm). In all prepared mixes the determined 6.6% optimum bitumen content was used. In this investigation, five different percentages of coarse aggregate replacement were used. The results showed that the aggregate replacement of 20% by volume with PET granules would result in a reduction of 2.8% in bulk compacted mix density. The value of flow in the plastiphalt mix was lower than that of the control samples. The results also showed that when PET was used as partial aggregate replacement, the corresponding Marshall stability and Marshall quotient were almost the same as for the control samples. According to most of specification requirement, these results introduce an asphalt mix that has properties that makes it suitable for practical use and furthermore, the recycling of PET for asphalt concrete roads helps alleviate an environmental problem and saves energy. PMID:16200982

  1. Impact load-induced micro-structural damage and micro-structure associated mechanical response of concrete made with different surface roughness and porosity aggregates

    SciTech Connect

    Erdem, Savas Dawson, Andrew Robert; Thom, Nicholas Howard

    2012-02-15

    The relationship between the nature of micro damage under impact loading and changes in mechanical behavior associated with different microstructures is studied for concretes made with two different coarse aggregates having significant differences mainly in roughness and porosity - sintered fly ash and uncrushed gravel. A range of techniques including X-ray diffraction, digital image analysis, mercury porosimetry, X-ray computed tomography, laser surface profilometry and scanning electron microscopy were used to characterize the aggregates and micro-structures. The concrete prepared with lightweight aggregates was stronger in compression than the gravel aggregate concrete due to enhanced hydration as a result of internal curing. In the lightweight concrete, it was deduced that an inhomogeneous micro-structure led to strain incompatibilities and consequent localized stress concentrations in the mix, leading to accelerated failure. The pore structure, compressibility, and surface texture of the aggregates are of paramount importance for the micro-cracking growth.

  2. Evaporation effects in elastocapillary aggregation

    NASA Astrophysics Data System (ADS)

    Vella, Dominic; Hadjittofis, Andreas; Singh, Kiran; Lister, John

    2015-11-01

    We consider the effect of evaporation on the aggregation of a number of elastic objects due to a liquid's surface tension. In particular, we consider an array of spring-block elements in which the gaps between blocks are filled by thin liquid films that evaporate during the course of an experiment. Using lubrication theory to account for the fluid flow within the gaps, we study the dynamics of aggregation. We find that a non-zero evaporation rate causes the elements to aggregate more quickly and, indeed, to contact within finite time. However, we also show that the number of elements within each cluster decreases as the evaporation rate increases. We explain these results quantitatively by comparison with the corresponding two-body problem and discuss their relevance for controlling pattern formation in carbon nanotube forests.

  3. Molecular Aggregation in Disodium Cromoglycate

    NASA Astrophysics Data System (ADS)

    Singh, Gautam; Agra-Kooijman, D.; Collings, P. J.; Kumar, Satyendra

    2012-02-01

    Details of molecular aggregation in the mesophases of the anti-asthmatic drug disodium cromoglycate (DSCG) have been studied using x-ray synchrotron scattering. The results show two reflections, one at wide angles corresponding to π-π stacking (3.32 å) of molecules, and the other at small angles which is perpendicular to the direction of molecular stacking and corresponds to the distance between the molecular aggregates. The latter varies from 35 - 41 å in the nematic (N) phase and 27 -- 32 å in the columnar (M) phase. The temperature evolution of the stack height, positional order correlations in the lateral direction, and orientation order parameter were determined in the N, M, and biphasic regions. The structure of the N and M phases and the nature of the molecular aggregation, together with their dependence on temperature and concentration, will be presented.

  4. Global kinetic analysis of seeded BSA aggregation.

    PubMed

    Sahin, Ziya; Demir, Yusuf Kemal; Kayser, Veysel

    2016-04-30

    Accelerated aggregation studies were conducted around the melting temperature (Tm) to elucidate the kinetics of seeded BSA aggregation. Aggregation was tracked by SEC-HPLC and intrinsic fluorescence spectroscopy. Time evolution of monomer, dimer and soluble aggregate concentrations were globally analysed to reliably deduce mechanistic details pertinent to the process. Results showed that BSA aggregated irreversibly through both sequential monomer addition and aggregate-aggregate interactions. Sequential monomer addition proceeded only via non-native monomers, starting to occur only by 1-2°C below the Tm. Aggregate-aggregate interactions were the dominant mechanism below the Tm due to an initial presence of small aggregates that acted as seeds. Aggregate-aggregate interactions were significant also above the Tm, particularly at later stages of aggregation when sequential monomer addition seemed to cease, leading in some cases to insoluble aggregate formation. The adherence (or non-thereof) of the mechanisms to Arrhenius kinetics were discussed alongside possible implications of seeding for biopharmaceutical shelf-life and spectroscopic data interpretation, the latter of which was found to often be overlooked in BSA aggregation studies. PMID:26970282

  5. Environmentalism and natural aggregate mining

    USGS Publications Warehouse

    Drew, L.J.; Langer, W.H.; Sachs, J.S.

    2002-01-01

    Sustaining a developed economy and expanding a developing one require the use of large volumes of natural aggregate. Almost all human activity (commercial, recreational, or leisure) is transacted in or on facilities constructed from natural aggregate. In our urban and suburban worlds, we are almost totally dependent on supplies of water collected behind dams and transported through aqueducts made from concrete. Natural aggregate is essential to the facilities that produce energy-hydroelectric dams and coal-fired powerplants. Ironically, the utility created for mankind by the use of natural aggregate is rarely compared favorably with the environmental impacts of mining it. Instead, the empty quarries and pits are seen as large negative environmental consequences. At the root of this disassociation is the philosophy of environmentalism, which flavors our perceptions of the excavation, processing, and distribution of natural aggregate. The two end-member ideas in this philosophy are ecocentrism and anthropocentrism. Ecocentrism takes the position that the natural world is a organism whose arteries are the rivers-their flow must not be altered. The soil is another vital organ and must not be covered with concrete and asphalt. The motto of the ecocentrist is "man must live more lightly on the land." The anthropocentrist wants clean water and air and an uncluttered landscape for human use. Mining is allowed and even encouraged, but dust and noise from quarry and pit operations must be minimized. The large volume of truck traffic is viewed as a real menace to human life and should be regulated and isolated. The environmental problems that the producers of natural aggregate (crushed stone and sand and gravel) face today are mostly difficult social and political concerns associated with the large holes dug in the ground and the large volume of heavy truck traffic associated with quarry and pit operations. These concerns have increased in recent years as society's demand for

  6. Effects of Concentration and Temperature on DNA Hybridization by Two Closely Related Sequences via Large-Scale Coarse-Grained Simulations.

    PubMed

    Markegard, Cade B; Gallivan, Cameron P; Cheng, Darrell D; Nguyen, Hung D

    2016-08-18

    A newly developed coarse-grained model called BioModi is utilized to elucidate the effects of temperature and concentration on DNA hybridization in self-assembly. Large-scale simulations demonstrate that complementary strands of either the tetrablock sequence or randomized sequence with equivalent number of cytosine or guanine nucleotides can form completely hybridized double helices. Even though the end states are the same for the two sequences, there exist multiple kinetic pathways that are populated with a wider range of transient aggregates of different sizes in the system of random sequences compared to that of the tetrablock sequence. The ability of these aggregates to undergo the strand displacement mechanism to form only double helices depends upon the temperature and DNA concentration. On one hand, low temperatures and high concentrations drive the formation and enhance stability of large aggregating species. On the other hand, high temperatures destabilize base-pair interactions and large aggregates. There exists an optimal range of moderate temperatures and low concentrations that allow minimization of large aggregate formation and maximization of fully hybridized dimers. Such investigation on structural dynamics of aggregating species by two closely related sequences during the self-assembly process demonstrates the importance of sequence design in avoiding the formation of metastable species. Finally, from kinetic modeling of self-assembly dynamics, the activation energy for the formation of double helices was found to be in agreement with experimental results. The framework developed in this work can be applied to the future design of DNA nanostructures in both fields of structural DNA nanotechnology and dynamic DNA nanotechnology wherein equilibrium end states and nonequilibrium dynamics are equally important requiring investigation in cooperation. PMID:27447850

  7. Coarse-fine residual gravity cancellation system with magnetic levitation

    NASA Technical Reports Server (NTRS)

    Salcudean, S. E.; Davis, H.; Chen, C. T.; Goertz, D. E.; Tryggvason, B. V.

    1992-01-01

    Aircraft flight along parabolic trajectories have been proposed and executed in order to achieve low cost, near free fall conditions of moderate duration. This paper describes a six degree of freedom experiment isolation system designed to cancel out residual accelerations due to mechanical vibrations and errors in aircraft trajectory. The isolation system consists of a fine motion magnetic levitator whose stator is transported by a conventional coarse motion stage. The levitator uses wide gap voice coil actuators and has the dual purpose of isolating the experiment platform from aircraft vibrations and actively cancelling residual accelerations through feedback control. The course motion stage tracks the levitated platform in order to keep the levitator's coils centered within their matching magnetic gaps. Aspects of system design, an analysis of the proposed control strategy and simulation results are presented. Feasibility experiments are also discussed.

  8. Optimised fine and coarse parallelism for sequence homology search.

    PubMed

    Meng, Xiandong; Chaudhary, Vipin

    2006-01-01

    New biological experimental techniques are continuing to generate large amounts of data using DNA, RNA, human genome and protein sequences. The quantity and quality of data from these experiments makes analyses of their results very time-consuming, expensive and impractical. Searching on DNA and protein databases using sequence comparison algorithms has become one of the most powerful techniques to better understand the functionality of particular DNA, RNA, genome, or protein sequence. This paper presents a technique to effectively combine fine and coarse grain parallelism using general-purpose processors for sequence homology database searches. The results show that the classic Smith-Waterman sequence alignment algorithm achieves super linear performance with proper scheduling and multi-level parallel computing at no additional cost. PMID:18048183

  9. The Apollo 15 coarse fines (4-10 mm)

    NASA Technical Reports Server (NTRS)

    Ryder, Graham; Sherman, Sarah Bean

    1989-01-01

    A new catalog of the Apollo 15 coarse fines particles is presented. Powell's macroscopic descriptions, resulting from his 1972 particle by particle binocular examination of all of the Apollo 15 4 to 10 mm fines samples, are retained. His groupings are also retained, but petrographic, chemical, and other data from later analyses are incorporated into this catalog to better characterize individual particles and describe the groups. A large number of particles have no characterization beyond that done by Powell. Complete descriptions of the particles and all known references are provided. The catalog is intended for anyone interested in the rock types collected by Dave Scott and Jim Irwin in the Hadley-Appenine region, and particularly for researchers requiring sample allocations.

  10. Investigating the impact of representation upon coarse-grained models

    NASA Astrophysics Data System (ADS)

    Foley, Thomas; Shell, M. Scott; Noid, William

    The first step in building a coarse-grained (CG) model is choosing a representation or `mapping' of the original system at a reduced resolution. In practice, the mapping is often chosen on the basis of `physical intuition.' Consequently this crucial step would greatly benefit from the development of systematic and principled methodologies. Accordingly, we have studied the relationship between the mapping and the resulting CG model. As a starting point, we have analytically derived, as a function of the CG mapping, the exact many-body potential of mean force (PMF) for the simple Gaussian Network Model (GNM) of protein fluctuations. We use this as a simple model for investigating the effect of the CG mapping upon the information loss and quality of the CG model. Moreover, by considering the GNM's for different proteins, we investigate the significance of high resolution structural features for the quality of the CG model. We acknowledge support from the NSF, Alfred P. Sloan Foundation, and KITP.

  11. A Coarse-Grained Model for Simulating Chitosan Hydrogels

    NASA Astrophysics Data System (ADS)

    Xu, Hongcheng; Matysiak, Silvina

    Hydrogels are biologically-derived materials composed of water-filled cross-linking polymer chains. It has widely been used as biodegradable material and has many applications in medical devices. The chitosan hydrogel is stimuli-responsive for undergoing pH-sensitive self-assembly process, allowing programmable tuning of the chitosan deposition through electric pulse. To explore the self-assembly mechanism of chitosan hydroge, we have developed an explicit-solvent coarse-grained chitosan model that has roots in the MARTINI force field, and the pH change is modeled by protonating chitosan chains using the Henderson-Hasselbalch equation. The mechanism of hydrogel network formation will be presented. The self-assembled polymer network qualitatively reproduce many experimental observables such as the pH-dependent strain-stress curve, bulk moduli, and structure factor. Our model is also capable of simulating other similar polyelectrolyte polymer systems.

  12. Supramolecular polymerization: a coarse grained molecular dynamics study.

    PubMed

    Bejagam, Karteek K; Balasubramanian, Sundaram

    2015-04-30

    A coarse-grained (CG) force field to model the self-assembly of benzene-1,3,5-tricarboxamide (BTA) class of compounds in nonpolar solvents has been developed. The model includes an intrinsic point dipole embedded on one of the CG beads so as to impart a macrodipole moment to the oligomer, one of its characteristic feature. Chemical specificity has been preserved by benchmarking against results, including dimerization and solvation free energies, obtained from an all-atom representation. Starting from a well-dispersed configuration in n-nonane, BTA molecules self-assemble to form one-dimensional stacks. Free energy (FE) changes for the various manner in which short oligomers can exchange between the assembled and the dispersed states have been calculated. These calculations show BTA to self-assemble via a downhill cooperative mechanism with a nucleus size of three. PMID:25853485

  13. Moderated regression analysis and Likert scales: too coarse for comfort.

    PubMed

    Russell, C J; Bobko, P

    1992-06-01

    One of the most commonly accepted models of relationships among three variables in applied industrial and organizational psychology is the simple moderator effect. However, many authors have expressed concern over the general lack of empirical support for interaction effects reported in the literature. We demonstrate in the current sample that use of a continuous, dependent-response scale instead of a discrete, Likert-type scale, causes moderated regression analysis effect sizes to increase an average of 93%. We suggest that use of relatively coarse Likert scales to measure fine dependent responses causes information loss that, although varying widely across subjects, greatly reduces the probability of detecting true interaction effects. Specific recommendations for alternate research strategies are made. PMID:1601825

  14. Coarse-Grained Modeling of Mucus Barrier Properties

    PubMed Central

    Gniewek, Pawel; Kolinski, Andrzej

    2012-01-01

    We designed a simple coarse-grained model of the glycocalyx layer, or adhesive mucus layer (AML), covered by mucus gel (luminal mucus layer) using a polymer lattice model and stochastic sampling (replica exchange Monte Carlo) for canonical ensemble simulations. We assumed that mucin MUC16 is responsible for the structural properties of the AML. Other mucins that are much smaller in size and less relevant for layer structure formation were not included. We further assumed that the system was in quasi-equilibrium. For systems with surface coverage and concentrations of model mucins mimicking physiological conditions, we determined the equilibrium distribution of inert nanoparticles within the mucus layers using an efficient replica exchange Monte Carlo sampling procedure. The results show that the two mucus layers penetrate each other only marginally, and the bilayer imposes a strong barrier for nanoparticles, with the AML layer playing a crucial role in the mucus barrier. PMID:22339855

  15. The spatial variation of vegetation changes at very coarse scales

    NASA Technical Reports Server (NTRS)

    Townshend, John R. G.; Justice, Christopher O.

    1990-01-01

    Previous analysis (Townshend and Justice 1988) is extended to examine the spatial variations in images of the normalized difference vegetation index (NDVI) of seven areas. These images were derived by subtracting corresponding pixel values from pairs of registered MSS images. The changes depicted by these derived images were analyzed by scale variance analysis for pixel sizes between 4 km and 64 km. It is shown that for some areas substantial changes are detectable at these very coarse scales, although there is less contrast between the areas than at finer spatial resolutions below 1 km. In all the areas the total spatial variability of the images is contributed at a wide variety of spatial scales.

  16. Coarse-grained theory of a realistic tetrahedral liquid model

    NASA Astrophysics Data System (ADS)

    Procaccia, I.; Regev, I.

    2012-02-01

    Tetrahedral liquids such as water and silica-melt show unusual thermodynamic behavior such as a density maximum and an increase in specific heat when cooled to low temperatures. Previous work had shown that Monte Carlo and mean-field solutions of a lattice model can exhibit these anomalous properties with or without a phase transition, depending on the values of the different terms in the Hamiltonian. Here we use a somewhat different approach, where we start from a very popular empirical model of tetrahedral liquids —the Stillinger-Weber model— and construct a coarse-grained theory which directly quantifies the local structure of the liquid as a function of volume and temperature. We compare the theory to molecular-dynamics simulations and show that the theory can rationalize the simulation results and the anomalous behavior.

  17. Fine and coarse dust separation with polarization lidar

    NASA Astrophysics Data System (ADS)

    Mamouri, R. E.; Ansmann, A.

    2014-05-01

    The polarization-lidar photometer networking (POLIPHON) method for separating dust and non-dust aerosol backscatter and extinction, volume, and mass concentration is extended to allow for a height-resolved separation of fine-mode and coarse-mode dust properties in addition. The method is applied to a period with complex aerosol layering of fine-mode background dust from Turkey and Arabian desert dust from Syria. The observation was performed at the combined European Aerosol Research Lidar Network (EARLINET) and Aerosol Robotic Network (AERONET) site of Limassol (34.7° N, 33° E), Cyprus, in September 2011. The dust profiling methodology and case studies are presented. Consistency between the column-integrated optical properties obtained with sun/sky photometer and the respective results derived by means of the new lidar-based method corroborate the applicability of the extended POLIPHON version.

  18. Fine and coarse dust separation with polarization lidar

    NASA Astrophysics Data System (ADS)

    Mamouri, R. E.; Ansmann, A.

    2014-11-01

    The polarization-lidar photometer networking (POLIPHON) method for separating dust and non-dust aerosol backscatter and extinction, volume, and mass concentration is extended to allow for a height-resolved separation of fine-mode and coarse-mode dust properties in addition. The method is applied to a period with complex aerosol layering of fine-mode background dust from Turkey and Arabian desert dust from Syria. The observation was performed at the combined European Aerosol Research Lidar Network (EARLINET) and Aerosol Robotic Network (AERONET) site of Limassol (34.7° N, 33° E), Cyprus, in September 2011. The dust profiling methodology and case studies are presented. Consistency between the column-integrated optical properties obtained with sun/sky photometer and the respective results derived by means of the new lidar-based method corroborate the applicability of the extended POLIPHON version.

  19. Coarse grained modeling of transport properties in monoclonal antibody solution

    NASA Astrophysics Data System (ADS)

    Swan, James; Wang, Gang

    Monoclonal antibodies and their derivatives represent the fastest growing segment of the bio pharmaceutical industry. For many applications such as novel cancer therapies, high concentration, sub-cutaneous injections of these protein solutions are desired. However, depending on the peptide sequence within the antibody, such high concentration formulations can be too viscous to inject via human derived force alone. Understanding how heterogenous charge distribution and hydrophobicity within the antibodies leads to high viscosities is crucial to their future application. In this talk, we explore a coarse grained computational model of therapeutically relevant monoclonal antibodies that accounts for electrostatic, dispersion and hydrodynamic interactions between suspended antibodies to predict assembly and transport properties in concentrated antibody solutions. We explain the high viscosities observed in many experimental studies of the same biologics.

  20. Coarse-grained kinetic equations for quantum systems

    NASA Astrophysics Data System (ADS)

    Petrov, E. G.

    2013-01-01

    The nonequilibrium density matrix method is employed to derive a master equation for the averaged state populations of an open quantum system subjected to an external high frequency stochastic field. It is shown that if the characteristic time τstoch of the stochastic process is much lower than the characteristic time τsteady of the establishment of the system steady state populations, then on the time scale Δ t ˜ τsteady, the evolution of the system populations can be described by the coarse-grained kinetic equations with the averaged transition rates. As an example, the exact averaging is carried out for the dichotomous Markov process of the kangaroo type.

  1. Polysaccharide-Protein Complexes in a Coarse-Grained Model.

    PubMed

    Poma, Adolfo B; Chwastyk, Mateusz; Cieplak, Marek

    2015-09-10

    We construct two variants of coarse-grained models of three hexaoses: one based on the centers of mass of the monomers and the other associated with the C4 atoms. The latter is found to be better defined and more suitable for studying interactions with proteins described within α-C based models. We determine the corresponding effective stiffness constants through all-atom simulations and two statistical methods. One method is the Boltzmann inversion (BI) and the other, named energy-based (EB), involves direct monitoring of energies as a function of the variables that define the stiffness potentials. The two methods are generally consistent in their account of the stiffness. We find that the elastic constants differ between the hexaoses and are noticeably different from those determined for the crystalline cellulose Iβ. The nonbonded couplings through hydrogen bonds between different sugar molecules are modeled by the Lennard-Jones potentials and are found to be stronger than the hydrogen bonds in proteins. We observe that the EB method agrees with other theoretical and experimental determinations of the nonbonded parameters much better than BI. We then consider the hexaose-Man5B catalytic complexes and determine the contact energies between their the C4-α-C atoms. These interactions are found to be stronger than the proteinic hydrogen bonds: about four times as strong for cellohexaose and two times for mannohexaose. The fluctuational dynamics of the coarse-grained complexes are found to be compatible with previous all-atom studies by Bernardi et al. PMID:26291477

  2. Mesoscopic coarse-grained simulations of lysozyme adsorption.

    PubMed

    Yu, Gaobo; Liu, Jie; Zhou, Jian

    2014-05-01

    Coarse-grained simulations are adopted to study the adsorption behavior of lysozyme on different (hydrophobic, neutral hydrophilic, zwitterionic, negatively charged, and positively charged) surfaces at the mesoscopic microsecond time scale (1.2 μs). Simulation results indicate the following: (i) the conformation change of lysozyme on the hydrophobic surface is bigger than any other studied surfaces; (ii) the active sites of lysozyme are faced to the hydrophobic surface with a "top end-on" orientation, while they are exposed to the liquid phase on the hydrophilic surface with a "back-on" orientation; (iii) the neutral hydrophilic surface can induce the adsorption of lysozyme, while the nonspecific protein adsorption can be resisted by the zwitterionic surface; (iv) when the solution ionic strength is low, lysozyme can anchor on the negatively charged surface easily but cannot adsorb on the positively charged surface; (v) when the solution ionic strength is high, the positively charged lysozyme can also adsorb on the like-charged surface; (vi) the major positive potential center of lysozyme, especially the residue ARG128, plays a vital role in leading the adsorption of lysozyme on charged surfaces; (vii) when the ionic strength is high, a counterion layer is formed above the positively charged surface, which is the key factor why lysozyme can adsorb on a like-charged surface. The coarse-grained method based on the MARTINI force field for proteins and the BMW water model could provide an efficient way to understand protein interfacial adsorption behavior at a greater length scale and time scale. PMID:24785197

  3. Coarse-grained model for colloidal protein interactions, B(22), and protein cluster formation.

    PubMed

    Blanco, Marco A; Sahin, Erinc; Robinson, Anne S; Roberts, Christopher J

    2013-12-19

    Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semiquantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as the osmotic second virial coefficient (B22). Based on earlier work (Grüenberger et al., J. Phys. Chem. B 2013, 117, 763), this CG model treats proteins as rigid bodies composed of one bead per amino acid, with each amino acid having specific parameters for its size, hydrophobicity, and charge. The net interactions are a combination of steric repulsions, short-range attractions, and screened long-range charge-charge interactions. Model parametrization was done by fitting simulation results against experimental value of B22 as a function of solution ionic strength for α-chymotrypsinogen A and γD-Crystallin (gD-Crys). The CG model is applied to characterize the pairwise interactions and dimerization of gD-Crys and the dependence on temperature, protein concentration, and ionic strength. The results illustrate that at experimentally relevant conditions where stable dimers do not form, the entropic contributions are predominant in the free-energy of protein cluster formation and colloidal protein interactions, arguing against interpretations that treat B22 primarily from energetic considerations alone. Additionally, the results suggest that electrostatic interactions help to modulate the population of the different stable configurations for protein nearest-neighbor pairs, while short-range attractions determine the relative orientations of proteins within these configurations. Finally, simulation results are combined with Principal Component Analysis to identify those amino

  4. Effect of surrogate aggregates on the thermal conductivity of concrete at ambient and elevated temperatures.

    PubMed

    Yun, Tae Sup; Jeong, Yeon Jong; Youm, Kwang-Soo

    2014-01-01

    The accurate assessment of the thermal conductivity of concretes is an important part of building design in terms of thermal efficiency and thermal performance of materials at various temperatures. We present an experimental assessment of the thermal conductivity of five thermally insulated concrete specimens made using lightweight aggregates and glass bubbles in place of normal aggregates. Four different measurement methods are used to assess the reliability of the thermal data and to evaluate the effects of the various sensor types. The concrete specimens are also assessed at every 100 °C during heating to ~800 °C. Normal concrete is shown to have a thermal conductivity of ~2.25 W m(-1) K(-1). The surrogate aggregates effectively reduce the conductivity to ~1.25 W m(-1) K(-1) at room temperature. The aggregate size is shown not to affect thermal conduction: fine and coarse aggregates each lead to similar results. Surface contact methods of assessment tend to underestimate thermal conductivity, presumably owing to high thermal resistance between the transducers and the specimens. Thermogravimetric analysis shows that the stages of mass loss of the cement paste correspond to the evolution of thermal conductivity upon heating. PMID:24696666

  5. Effect of Aggregation on the Mechanical Properties of Ionomers from MD Simulations

    NASA Astrophysics Data System (ADS)

    Sampath, Janani; Hall, Lisa M.

    Ionomers are polymers with a small fraction of charged monomers; these bound ions, along with free counterions, tend to aggregate together strongly in the absence of solvent. Ionic aggregates can act like temporary cross-links, giving rise to interesting mechanical properties. We perform coarse-grained molecular dynamics simulations of ionomers with various spacings of charges along the chain, representing experimental precisely spaced, neutralized poly(ethylene-co-acrylic acid) materials. We calculate aggregate morphology, dynamics, and scattering profiles and study the systems during uniaxial tensile strain to understand how aggregate structure changes under deformation and affects mechanical properties. Anisotropic structure factors (parallel and perpendicular to the direction of pull) and visualization shows that the aggregates align, in qualitative agreement with experimental findings. Stress-strain curves at different strain rates are also obtained. A modification of the model to account for unneutralized acid groups by adjusting their Lennard-Jones interaction strengths with each other and with ionic groups will also be discussed. This material is based upon work supported by the National Science Foundation under Grant 1463103.

  6. Effect of Surrogate Aggregates on the Thermal Conductivity of Concrete at Ambient and Elevated Temperatures

    PubMed Central

    Yun, Tae Sup; Jeong, Yeon Jong; Youm, Kwang-Soo

    2014-01-01

    The accurate assessment of the thermal conductivity of concretes is an important part of building design in terms of thermal efficiency and thermal performance of materials at various temperatures. We present an experimental assessment of the thermal conductivity of five thermally insulated concrete specimens made using lightweight aggregates and glass bubbles in place of normal aggregates. Four different measurement methods are used to assess the reliability of the thermal data and to evaluate the effects of the various sensor types. The concrete specimens are also assessed at every 100°C during heating to ~800°C. Normal concrete is shown to have a thermal conductivity of ~2.25 W m−1 K−1. The surrogate aggregates effectively reduce the conductivity to ~1.25 W m−1 K−1 at room temperature. The aggregate size is shown not to affect thermal conduction: fine and coarse aggregates each lead to similar results. Surface contact methods of assessment tend to underestimate thermal conductivity, presumably owing to high thermal resistance between the transducers and the specimens. Thermogravimetric analysis shows that the stages of mass loss of the cement paste correspond to the evolution of thermal conductivity upon heating. PMID:24696666

  7. Coarse-grained computer simulation of dynamics in thylakoid membranes: methods and opportunities

    PubMed Central

    Schneider, Anna R.; Geissler, Phillip L.

    2013-01-01

    Coarse-grained simulation is a powerful and well-established suite of computational methods for studying structure and dynamics in nanoscale biophysical systems. As our understanding of the plant photosynthetic apparatus has become increasingly nuanced, opportunities have arisen for coarse-grained simulation to complement experiment by testing hypotheses and making predictions. Here, we give an overview of best practices in coarse-grained simulation, with a focus on techniques and results that are applicable to the plant thylakoid membrane–protein system. We also discuss current research topics for which coarse-grained simulation has the potential to play a key role in advancing the field. PMID:24478781

  8. Importance of Coarse Woody Debris to Avian Communities in Loblolly Pine Forests

    SciTech Connect

    Lohr, S.M.; Gauthreaux, S.A.; Kilgo, J.C.

    2001-06-14

    Investigates the importance of standing and down coarse woody debris to bird communities in loblolly pine forests, researchers compared breeding and nonbreeding responses of birds among two coarse woody debris removal and control treatments. Quantification of vegetation layers to determine their effects on the experimental outcome coarse woody debris removal had no effect on the nonbreeding bird community. Most breeding and nonbreeding species used habitats with sparse midstory and well-developed understory, where as sparse canopy cover and dense midstory were important to some nonbreeding species. Snag and down coarse woody debris practices that maintain a dense understory, sparse midstory and canopy will create favorable breeding habitat.

  9. Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA

    PubMed Central

    Mashayak, S. Y.; Jochum, Mara N.; Koschke, Konstantin; Aluru, N. R.; Rühle, Victor; Junghans, Christoph

    2015-01-01

    We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations. In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process. PMID:26192992

  10. Relative entropy and optimization-driven coarse-graining methods in VOTCA

    SciTech Connect

    Mashayak, S. Y.; Jochum, Mara N.; Koschke, Konstantin; Aluru, N. R.; Rühle, Victor; Junghans, Christoph; Huang, Xuhui

    2015-07-20

    We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations.We have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.

  11. Classical predictability and coarse-grained evolution of the quantum baker's map

    SciTech Connect

    Scherer, Artur; Soklakov, Andrei N.; Schack, Ruediger

    2006-06-15

    We investigate how classical predictability of the coarse-grained evolution of the quantum baker's map depends on the character of the coarse-graining. Our analysis extends earlier work by Brun and Hartle [Phys. Rev. D 60, 123503 (1999)] to the case of a chaotic map. To quantify predictability, we compare the rate of entropy increase for a family of coarse-grainings in the decoherent histories formalism. We find that the rate of entropy increase is dominated by the number of scales characterizing the coarse-graining.

  12. RAGG - R EPISODIC AGGREGATION PACKAGE

    EPA Science Inventory

    The RAGG package is an R implementation of the CMAQ episodic model aggregation method developed by Constella Group and the Environmental Protection Agency. RAGG is a tool to provide climatological seasonal and annual deposition of sulphur and nitrogen for multimedia management. ...

  13. An Aggregation Advisor for Ligand Discovery.

    PubMed

    Irwin, John J; Duan, Da; Torosyan, Hayarpi; Doak, Allison K; Ziebart, Kristin T; Sterling, Teague; Tumanian, Gurgen; Shoichet, Brian K

    2015-09-10

    Colloidal aggregation of organic molecules is the dominant mechanism for artifactual inhibition of proteins, and controls against it are widely deployed. Notwithstanding an increasingly detailed understanding of this phenomenon, a method to reliably predict aggregation has remained elusive. Correspondingly, active molecules that act via aggregation continue to be found in early discovery campaigns and remain common in the literature. Over the past decade, over 12 thousand aggregating organic molecules have been identified, potentially enabling a precedent-based approach to match known aggregators with new molecules that may be expected to aggregate and lead to artifacts. We investigate an approach that uses lipophilicity, affinity, and similarity to known aggregators to advise on the likelihood that a candidate compound is an aggregator. In prospective experimental testing, five of seven new molecules with Tanimoto coefficients (Tc's) between 0.95 and 0.99 to known aggregators aggregated at relevant concentrations. Ten of 19 with Tc's between 0.94 and 0.90 and three of seven with Tc's between 0.89 and 0.85 also aggregated. Another three of the predicted compounds aggregated at higher concentrations. This method finds that 61 827 or 5.1% of the ligands acting in the 0.1 to 10 μM range in the medicinal chemistry literature are at least 85% similar to a known aggregator with these physical properties and may aggregate at relevant concentrations. Intriguingly, only 0.73% of all drug-like commercially available compounds resemble the known aggregators, suggesting that colloidal aggregators are enriched in the literature. As a percentage of the literature, aggregator-like compounds have increased 9-fold since 1995, partly reflecting the advent of high-throughput and virtual screens against molecular targets. Emerging from this study is an aggregator advisor database and tool ( http://advisor.bkslab.org ), free to the community, that may help distinguish between

  14. Hydrodynamic effects on β-amyloid (16-22) peptide aggregation

    NASA Astrophysics Data System (ADS)

    Chiricotto, Mara; Melchionna, Simone; Derreumaux, Philippe; Sterpone, Fabio

    2016-07-01

    Computer simulations based on simplified representations are routinely used to explore the early steps of amyloid aggregation. However, when protein models with implicit solvent are employed, these simulations miss the effect of solvent induced correlations on the aggregation kinetics and lifetimes of metastable states. In this work, we apply the multi-scale Lattice Boltzmann Molecular Dynamics technique (LBMD) to investigate the initial aggregation phases of the amyloid Aβ16-22 peptide. LBMD includes naturally hydrodynamic interactions (HIs) via a kinetic on-lattice representation of the fluid kinetics. The peptides are represented by the flexible OPEP coarse-grained force field. First, we have tuned the essential parameters that control the coupling between the molecular and fluid evolutions in order to reproduce the experimental diffusivity of elementary species. The method is then deployed to investigate the effect of HIs on the aggregation of 100 and 1000 Aβ16-22 peptides. We show that HIs clearly impact the aggregation process and the fluctuations of the oligomer sizes by favouring the fusion and exchange dynamics of oligomers between aggregates. HIs also guide the growth of the leading largest cluster. For the 100 Aβ16-22 peptide system, the simulation of ˜300 ns allowed us to observe the transition from ellipsoidal assemblies to an elongated and slightly twisted aggregate involving almost the totality of the peptides. For the 1000 Aβ16-22 peptides, a system of unprecedented size at quasi-atomistic resolution, we were able to explore a branched disordered fibril-like structure that has never been described by other computer simulations, but has been observed experimentally.

  15. Impact of climate aggregation over different scales on regional NPP modelling

    NASA Astrophysics Data System (ADS)

    Kuhnert, Matthias

    2016-04-01

    Model input data aggregation methods and data aggregation across spatial scales affect various model outputs, e.g. Net Primary Productivity (NPP). The scale at which data is collected is of great importance. In ecosystem modelling studies we often see soil and climate data collected at coarse scale being used in models to predict ecosystem responses e.g. NPP in dependency of these parameters at finer scale. Outputs of these models are impacted by the way the data is aggregated or dis-aggregated to the spatial scale. Up to know there are very few studies which quantified the impact of scaling on the simulation results. In this study, we quantify the impact of climate data aggregation using five different resolutions, to simulate NPP by 11 different crop and biogeochemical models for the same study area. The aggregation effect is investigated for wheat and maize cropping systems in the state of North Rhine-Westphalia, Germany. The simulation results are analysed for NPP averaged over growing seasons of a 30 year period at different spatial resolutions as well as for annual NPP during growing season. While there is only a minor impact of input data aggregation on NPP on 30 year averages, the annual data show differences in NPP up to 9.4 % and 13.6 % between the different resolutions for wheat and maize, respectively. The scale effect differ between the models and shows higher impacts for extreme years. This is tested by selecting years with extreme dry conditions based on a drought index, which showed stronger scale effects of up to 12.8 % and 15.5 % for wheat and maize, respectively.

  16. Aggregation-induced reversal of transport distances of soil organic matter: are our balances correct?

    NASA Astrophysics Data System (ADS)

    Hu, Yaxian; Kuhn, Nikolaus

    2014-05-01

    The effect of soil erosion on global carbon cycling, especially as a source or sink of green-house gases (GHGs), is the subject of intense debate. The controversy arises mostly from the lack of information on the fate of eroded soil organic carbon (SOC) as it moves from the site of erosion to the site of longer-term deposition. This requires improved understanding the transport distances of eroded SOC, which is principally related to the settling velocities of sediment fractions that carry the eroded SOC. For aggregated soils, settling velocities are affected by their actual aggregate size rather than the mineral grain size distribution. Aggregate stability is, in turn, strongly influenced by soil organic matter. This study aims at identifying the effect of aggregation on the transport distances of eroded SOC and its susceptibility to mineralization after transport and deposition. A rainfall simulation was carried out on a silty loam soil. The eroded sediments were fractionated by a settling tube apparatus into six different size classes according to their settling velocities and likely transport distances. Weight, SOC concentration and instantaneous respiration rates of the fractions of the six classes were measured. Our results show that: 1) 41% of the eroded SOC was transported with coarse aggregates that would be likely re-distributed across landscapes; 2) erosion was prone to accelerate the mineralization of eroded organic carbon immediately after erosion, compared to undisturbed aggregates; 3) erosion might make a higher contribution to atmospheric CO2 than the estimation made without considering the effects of aggregation and extra SOC mineralization during transport.

  17. Hydrodynamic effects on β-amyloid (16-22) peptide aggregation.

    PubMed

    Chiricotto, Mara; Melchionna, Simone; Derreumaux, Philippe; Sterpone, Fabio

    2016-07-21

    Computer simulations based on simplified representations are routinely used to explore the early steps of amyloid aggregation. However, when protein models with implicit solvent are employed, these simulations miss the effect of solvent induced correlations on the aggregation kinetics and lifetimes of metastable states. In this work, we apply the multi-scale Lattice Boltzmann Molecular Dynamics technique (LBMD) to investigate the initial aggregation phases of the amyloid Aβ16-22 peptide. LBMD includes naturally hydrodynamic interactions (HIs) via a kinetic on-lattice representation of the fluid kinetics. The peptides are represented by the flexible OPEP coarse-grained force field. First, we have tuned the essential parameters that control the coupling between the molecular and fluid evolutions in order to reproduce the experimental diffusivity of elementary species. The method is then deployed to investigate the effect of HIs on the aggregation of 100 and 1000 Aβ16-22 peptides. We show that HIs clearly impact the aggregation process and the fluctuations of the oligomer sizes by favouring the fusion and exchange dynamics of oligomers between aggregates. HIs also guide the growth of the leading largest cluster. For the 100 Aβ16-22 peptide system, the simulation of ∼300 ns allowed us to observe the transition from ellipsoidal assemblies to an elongated and slightly twisted aggregate involving almost the totality of the peptides. For the 1000 Aβ16-22 peptides, a system of unprecedented size at quasi-atomistic resolution, we were able to explore a branched disordered fibril-like structure that has never been described by other computer simulations, but has been observed experimentally. PMID:27448906

  18. Coarse mode aerosol measurement using a Low Turbulence Inlet

    NASA Astrophysics Data System (ADS)

    Brooke, J.; Bart, M.; Trembath, J.; McQuaid, J. B.; Brooks, B. J.; Osborne, S.

    2012-04-01

    The Sahara desert is a major natural source of global mineral dust emissions (Forster et al., 2007) through the mobilisation and lifting of dust particles into the atmosphere from dust storms. A significant fraction of this dust is in the aerosol coarse mode (Weinzierl et al., 2009). It is highlighted of the difficulty in making accurate and reliable measurements from an aircraft platform, particularly that of coarse mode aerosol (Wendisch et al., 2004). To achieve the measurement of a representative aerosol sample an aerosol inlet, on an aircraft, is required for the delivery of the sample to the instruments making the measurements. Inlet design can modify aerosol size distribution through either underestimating due to aerosol losses or overestimation due to enhancements. The Low Turbulence Inlet (LTI) was designed to improve inlet efficiency. This is achieved by reducing turbulence flow within the tip of the inlet, reducing impaction of particles to the walls of the inlet (Wilson et al., 2004). The LTI further maintains isokinetic sampling flow (free stream velocity, U0 and sampling velocity, U are equal to 1). Dust aerosol over the Sahara desert provides an excellent environment to test and quantify the capabilities of the LTI on the FAAM BAe 146, whilst enabling in-situ dust measurement. The LTI was operated during the Fennec field campaign in June 2011 with 11 flights during the campaign over Mauritania and Mali. We are using the LTI to provide critical information on the sampling characteristics of the inlet used by nearly all aerosol instruments inside the aircraft (AMS, Nephelometer, PSAP, and CCN). Inlet experiments were performed with identical Optical Particle Counters (OPC) connected to the rosemount and LTI with size distribution for each inlet measured and Rosemount enhancements determined. Rosemount inlet enhancements were determined to be 2 to 4 times for particles up to 2.5 µm. A key parameter in aerosol measurement is size distribution, in which

  19. A coarse to fine minutiae-based latent palmprint matching.

    PubMed

    Liu, Eryun; Jain, Anil K; Tian, Jie

    2013-10-01

    With the availability of live-scan palmprint technology, high resolution palmprint recognition has started to receive significant attention in forensics and law enforcement. In forensic applications, latent palmprints provide critical evidence as it is estimated that about 30 percent of the latents recovered at crime scenes are those of palms. Most of the available high-resolution palmprint matching algorithms essentially follow the minutiae-based fingerprint matching strategy. Considering the large number of minutiae (about 1,000 minutiae in a full palmprint compared to about 100 minutiae in a rolled fingerprint) and large area of foreground region in full palmprints, novel strategies need to be developed for efficient and robust latent palmprint matching. In this paper, a coarse to fine matching strategy based on minutiae clustering and minutiae match propagation is designed specifically for palmprint matching. To deal with the large number of minutiae, a local feature-based minutiae clustering algorithm is designed to cluster minutiae into several groups such that minutiae belonging to the same group have similar local characteristics. The coarse matching is then performed within each cluster to establish initial minutiae correspondences between two palmprints. Starting with each initial correspondence, a minutiae match propagation algorithm searches for mated minutiae in the full palmprint. The proposed palmprint matching algorithm has been evaluated on a latent-to-full palmprint database consisting of 446 latents and 12,489 background full prints. The matching results show a rank-1 identification accuracy of 79.4 percent, which is significantly higher than the 60.8 percent identification accuracy of a state-of-the-art latent palmprint matching algorithm on the same latent database. The average computation time of our algorithm for a single latent-to-full match is about 141 ms for genuine match and 50 ms for impostor match, on a Windows XP desktop system with 2

  20. Coarse graining the distribution function of cold dark matter - II

    NASA Astrophysics Data System (ADS)

    Henriksen, R. N.

    2004-12-01

    We study analytically the coarse- and fine-grained distribution function (DF) established by the self-similar infall of collisionless matter. We find this function explicitly for isotropic and spherically symmetric systems in terms of cosmological initial conditions. The coarse-grained function is structureless and steady but the familiar phase-space sheet substructure is recovered in the fine-grained limit. By breaking the self-similarity of the halo infall we are able to argue for a central density flattening. In addition there will be an edge steepening. The best-fitting analytic density function is likely to be provided by a high-order polytrope fit smoothly to an outer power law of index -3 for isolated systems. There may be a transition to a -4 power law in the outer regions of tidally truncated systems. As we find that the central flattening is progressive in time, dynamically young systems such as galaxy clusters may well possess a Navarro, Frenk and White type density profile, while primordial dwarf galaxies, for example, are expected to have cores. This progressive flattening is expected to end either in the non-singular isothermal sphere, or in the non-singular metastable polytropic cores; as the DFs associated with each of these arise naturally in the bulk halo during the infall. We suggest, based on previous studies of the evolution of de-stabilized polytropes, that a collisionless system may pass through a family of polytropes of increasing order, finally approaching the limit of the non-singular isothermal sphere, if the `violent' collective relaxation is frequently re-excited by `merger' events. Thus central dominant (cD) galaxies, and indeed all bright galaxies that have grown in this fashion, should be in polytropic states. Our results suggest that no physics beyond that of wave-particle scattering is necessary to explain the nature of dark matter density profiles. However, this may be assisted by the scattering of particles from the centre of the

  1. Internal curing with lightweight aggregate produced from biomass-derived waste

    SciTech Connect

    Lura, Pietro; Wyrzykowski, Mateusz; Tang, Clarence; Lehmann, Eberhard

    2014-05-01

    Shrinkage of concrete may lead to cracking and ultimately to a reduction of the service life of concrete structures. Among known methods for shrinkage mitigation, internal curing with porous aggregates was successfully utilized in the last couple of decades for decreasing autogenous and drying shrinkage. In this paper, the internal curing performance of pre-saturated lightweight aggregates produced from biomass-derived waste (bio-LWA) was studied. In the first part of this paper, the microstructure of the bio-LWA is investigated, with special focus on their pore structure and on their water absorption and desorption behavior. The bio-LWA has large porosity and coarse pore structure, which allows them to release the entrained water at early age and counteract self-desiccation and autogenous shrinkage. In the second part, the efficiency of internal curing in mortars incorporating the bio-LWA is examined by neutron tomography, internal relative humidity and autogenous deformation measurements.

  2. Aggregation of metallochlorophylls - Examination by spectroscopy

    NASA Technical Reports Server (NTRS)

    Boucher, L. J.; Katz, J. J.

    1969-01-01

    Nuclear magnetic resonance measurements determine which metallochlorophylls, besides magnesium-containing chlorophylls, possess coordination aggregation properties. Infrared spectroscopy reveals that only zinc pheophytin and zinc methyl pheophorbide showed significant coordination aggregation, whereas divalent nickel and copper did not.

  3. Oligomeric baroeffect and gas aggregation states

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1992-01-01

    The baroeffect is analyzed to include a gas that aggregates into higher-order polymers or oligomers. The resulting pressure change is found to vary independently of the molecular weight of the gas components and to depend only on the aggregation or oligomeric order of the gas. With increasing aggregation, diffusive slip velocities are found to increase. The calculations are extended to include general counterdiffusion of two distinct aggregation states (k-, j-mer) for the gas, and the pressure change is derived as a function that is independent of both molecular weight and the absolute aggregation. The only parameter that determines the baroeffect is the ratio of aggregated states, beta = k/j. For gases that reversibly aggregate, possible oscillatory behavior and complex dynamics for pressure are discussed. Gas aggregation may play a role for low-temperature crystal-growth conditions in which vapor concentrations of one (or more) species are high.

  4. The decomposition of fine and coarse roots: their global patterns and controlling factors

    PubMed Central

    Zhang, Xinyue; Wang, Wei

    2015-01-01

    Fine root decomposition represents a large carbon (C) cost to plants, and serves as a potential soil C source, as well as a substantial proportion of net primary productivity. Coarse roots differ markedly from fine roots in morphology, nutrient concentrations, functions, and decomposition mechanisms. Still poorly understood is whether a consistent global pattern exists between the decomposition of fine (<2 mm root diameter) and coarse (≥2 mm) roots. A comprehensive terrestrial root decomposition dataset, including 530 observations from 71 sampling sites, was thus used to compare global patterns of decomposition of fine and coarse roots. Fine roots decomposed significantly faster than coarse roots in middle latitude areas, but their decomposition in low latitude regions was not significantly different from that of coarse roots. Coarse root decomposition showed more dependence on climate, especially mean annual temperature (MAT), than did fine roots. Initial litter lignin content was the most important predictor of fine root decomposition, while lignin to nitrogen ratios, MAT, and mean annual precipitation were the most important predictors of coarse root decomposition. Our study emphasizes the necessity of separating fine roots and coarse roots when predicting the response of belowground C release to future climate changes. PMID:25942391

  5. The decomposition of fine and coarse roots: their global patterns and controlling factors

    NASA Astrophysics Data System (ADS)

    Zhang, Xinyue; Wang, Wei

    2015-05-01

    Fine root decomposition represents a large carbon (C) cost to plants, and serves as a potential soil C source, as well as a substantial proportion of net primary productivity. Coarse roots differ markedly from fine roots in morphology, nutrient concentrations, functions, and decomposition mechanisms. Still poorly understood is whether a consistent global pattern exists between the decomposition of fine (<2 mm root diameter) and coarse (≥2 mm) roots. A comprehensive terrestrial root decomposition dataset, including 530 observations from 71 sampling sites, was thus used to compare global patterns of decomposition of fine and coarse roots. Fine roots decomposed significantly faster than coarse roots in middle latitude areas, but their decomposition in low latitude regions was not significantly different from that of coarse roots. Coarse root decomposition showed more dependence on climate, especially mean annual temperature (MAT), than did fine roots. Initial litter lignin content was the most important predictor of fine root decomposition, while lignin to nitrogen ratios, MAT, and mean annual precipitation were the most important predictors of coarse root decomposition. Our study emphasizes the necessity of separating fine roots and coarse roots when predicting the response of belowground C release to future climate changes.

  6. DEVELOPMENT AND EVALUATION OF A CONTINUOUS COARSE (PM10-PM2.5) PARTICLE MONITOR

    EPA Science Inventory

    In this paper, we describe the development and laboratory and field evaluation of a continuous coarse (2.5-10 um) particle mass (PM) monitor that can provide reliable measurements of the coarse mass (CM) concentrations in time intervals as short as 5-10 min. The operating princ...

  7. Chemical Characterization of Coarse Particulate Matter in the Desert Southwest - Pinal County Arizona, USA

    EPA Science Inventory

    The Desert Southwest Coarse Particulate Matter Study was undertaken of ambient concentrations and the composition of fine and coarse particles in rural, arid environments. Sampling was conducted in Pinal County, Arizona between February 2009 and February 2010. The goals of this ...

  8. Geochemical studies of backfill aggregates, lake sediment cores and the Hueco Bolson Aquifer

    NASA Astrophysics Data System (ADS)

    Thapalia, Anita

    This dissertation comprises of three different researches that focuses on the application of geochemistry from aggregates, lake sediment cores and Hueco Bolson Aquifer. Each study is independent and presented in the publication format. The first chapter is already published and the second chapter is in revision phase. Overall, three studies measure the large scale (field) as well as bench scale (lab) water-rock interactions influenced by the climatic and anthropogenic factors spans from the field of environmental geology to civil engineering. The first chapter of this dissertation addresses the chemical evaluation of coarse aggregates from six different quarries in Texas. The goal of this work is to find out the best geochemical methods for assessing the corrosion potential of coarse aggregates prior to their use in mechanically stabilized earth walls. Electrochemical parameters help to define the corrosion potential of aggregates following two different leaching protocols. Testing the coarse and fine aggregates demonstrate the chemical difference due to size-related kinetic leaching effects. Field fines also show different chemistry than the bulk rock indicating the weathering impact on carbonate rocks. The second chapter investigates zinc (Zn) isotopic signatures from eight lake sediment cores collected both from pristine lakes and those impacted by urban anthropogenic contamination. Zinc from the natural weathering of rocks and anthropogenic atmospheric pollutants are transported to these lakes and the signatures are recorded in the sediments. Isotopic analysis of core samples provides the signature of anthropogenic contamination sources. Dated sediment core and isotopic analysis can identify Zn inputs that are correlated to the landuse and population change of the watersheds. Comparison of isotopic data from both pristine and urban lake sediment core also serves as an analog in other lake sediment cores in the world. The third chapter studies on Hueco Bolson

  9. Protein aggregation in salt solutions

    PubMed Central

    Kastelic, Miha; Kalyuzhnyi, Yurij V.; Hribar-Lee, Barbara; Dill, Ken A.; Vlachy, Vojko

    2015-01-01

    Protein aggregation is broadly important in diseases and in formulations of biological drugs. Here, we develop a theoretical model for reversible protein–protein aggregation in salt solutions. We treat proteins as hard spheres having square-well-energy binding sites, using Wertheim’s thermodynamic perturbation theory. The necessary condition required for such modeling to be realistic is that proteins in solution during the experiment remain in their compact form. Within this limitation our model gives accurate liquid–liquid coexistence curves for lysozyme and γ IIIa-crystallin solutions in respective buffers. It provides good fits to the cloud-point curves of lysozyme in buffer–salt mixtures as a function of the type and concentration of salt. It than predicts full coexistence curves, osmotic compressibilities, and second virial coefficients under such conditions. This treatment may also be relevant to protein crystallization. PMID:25964322

  10. Perspective: Coarse-grained models for biomolecular systems

    NASA Astrophysics Data System (ADS)

    Noid, W. G.

    2013-09-01

    By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.

  11. Coarse-Grained Molecular Models of Water: A Review

    PubMed Central

    Hadley, Kevin R.; McCabe, Clare

    2012-01-01

    Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems that involve large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger timesteps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biological importance that are beyond the reach of atomistic simulation, necessitating a computationally efficient and accurate CG model for water. In this review, we discuss the methods used for developing CG water models and the relative advantages and disadvantages of the resulting models. In general, CG water models differ with regards to how many waters each CG group or bead represents, whether analytical or tabular potentials have been used to describe the interactions, and how the model incorporates electrostatic interactions. Finally, how the models are parameterized depends on their application, so, while some are fitted to experimental properties such as surface tension and density, others are fitted to radial distribution functions extracted from atomistic simulations. PMID:22904601

  12. Fine and coarse components in surface sediments from Bikini Lagoon

    SciTech Connect

    Noshkin, V. E., LLNL

    1997-01-01

    In 1979, 21 years after the moratorium on nuclear testing in the Marshall Islands, surface sediment samples (to depths of 2 and 4 cm) were collected from 87 locations in the lagoon of Bikini Atoll, one of the two sites in the Marshall Islands used by the United States to test nuclear devices from 1946 through 1958. The main purpose for the collections was to map the distribution of long-lived man-made radionuclides associated with the bottom material. In addition the samples were processed to estimate the fraction of fine and coarse components to show, by comparison, what modifications occurred in the composition since the sediments were first described in samples collected before testing in 1946. Nuclear testing produced more finely divided material that is now found in the surface sediment layer over large areas of the lagoon and especially in regions of the lagoon and reef adjacent to test sites. The 5 cratering events alone at Bikini Atoll redistributed sufficient material to account for the higher inventory of fine material found over the surface 4 cm of the sediment of the lagoon. Although the fraction of fine material in the bottom sediments was altered by the nuclear events, the combined processes of formation, transport and deposition were not sufficiently dynamic to greatly change the general geographical features of the major sedimentary components over most of the lagoon floor.

  13. Coarse-grained potentials of single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Zhao, Junhua; Jiang, Jin-Wu; Wang, Lifeng; Guo, Wanlin; Rabczuk, Timon

    2014-11-01

    We develop the coarse-grained (CG) potentials of single-walled carbon nanotubes (SWCNTs) in CNT bundles and buckypaper for the study of the static and dynamic behaviors. The explicit expressions of the CG stretching, bending and torsion potentials for the nanotubes are obtained by the stick-spiral and the beam models, respectively. The non-bonded CG potentials between two different CG beads are derived from analytical results based on the cohesive energy between two parallel and crossing SWCNTs from the van der Waals interactions. We show that the CG model is applicable to large deformations of complex CNT systems by combining the bonded potentials with non-bonded potentials. Checking against full atom molecular dynamics calculations and our analytical results shows that the present CG potentials have high accuracy. The established CG potentials are used to study the mechanical properties of the CNT bundles and buckypaper efficiently at minor computational cost, which shows great potential for the design of micro- and nanomechanical devices and systems.

  14. Anatomy of an Allende coarse-grained inclusion

    NASA Astrophysics Data System (ADS)

    El Gorsey, A.; Armstrong, J. T.; Wasserburg, G. J.

    1985-11-01

    The petrology, mineralogy, and mineral chemistry of a coarse-grained calcium-aluminum-rich inclusion from Allende are studied. The inclusion consists of a spinel-fassaite-melilite core surrounded by a melilite mantle. The zoning, chemical variation between crystals, and concentration of molecules in the melilite and fassaite of the spinel-free island, spinel-rich area, and melilite mantle are examined. The possible formation of the inclusion by gas-solid condensation, crystallization from a homogeneous refractory silicate melt, and evaporative loss due to distillation is analyzed. These processes, however, do not explain the textural relations and mineral chemistries of the spinel-free island, spinel-rich areas, and melilite mantle. The formation of the inclusion by spinel-free islands forming by crystallization from a spinel deficient liquid, the capture of solid clasts and Fremdlinge in a more refractory spinel-saturated liquid, and formation of the outer melilite veneer mantle from two refractory liquid layers is proposed.

  15. Coarse grained molecular simulations of melting kinetics of DPPC vesicles

    NASA Astrophysics Data System (ADS)

    Bolling-Patel, Lara A.; Kindt, James T.

    2015-03-01

    Phase transitions in unilamellar vesicles are of particular interest as the increase in permeability of lipid bilayers around the main phase transition temperature makes them candidates for drug encapsulation and temperature-responsive delivery. We study the transition between the gel and fluid phases of a unilamellar vesicle of MARTINI coarse grain DPPC lipids with a diameter of 40 nm following temperature jumps from 280 K to temperatures near the transition temperature of 295 K. At 290 K and 295 K vesicles show single exponential melting kinetics in qualitative agreement with the early stages of melting measured in IR temperature-jump experiments. These trajectories exhibit partial melting over 500 ns, accompanied by a decrease in the number of gel domains from 8 domains in the initial faceted structure to 5 and 3 respectively. Melting at 295 K results in a shape change to an asymmetric structure that appears to be transforming into an oblate solid. Complete melting is seen for temperature jumps to 300 K and 310 K, in which cases vesicles undergo shape transitions into prolate dumbbell shapes. The shape changes that accompany the phase transition indicate that the phase transition kinetics are correlated to changes in curvature. NSF CHE-1213904.

  16. Improving the treatment of coarse-grain electrostatics: CVCEL.

    PubMed

    Ceres, N; Lavery, R

    2015-12-28

    We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding. PMID:26723603

  17. Coarse-grained molecular simulations of allosteric cooperativity

    NASA Astrophysics Data System (ADS)

    Nandigrami, Prithviraj; Portman, John J.

    2016-03-01

    Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca2+ ions to each domain of Calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein's conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding are treated implicitly within the grand canonical ensemble. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energies to the open and closed ensembles accurately describes the simulated binding thermodynamics. The simulations predict that the two domains of CaM have distinct binding affinity and cooperativity. In particular, the C-terminal domain binds Ca2+ with higher affinity and greater cooperativity than the N-terminal domain. From a structural point of view, the affinity of an individual binding loop depends sensitively on the loop's structural compatibility with the ligand in the bound ensemble, as well as the conformational flexibility of the binding site in the unbound ensemble.

  18. Complete Eulerian-mean tracer equation for coarse resolution OGCMs

    NASA Astrophysics Data System (ADS)

    Dubovikov, M. S.; Canuto, V. M.

    2006-06-01

    McDougall and McIntosh showed that the adiabatic mesoscale mixing is represented incompletely in the tracer Eulerian-averaged equation (EAE) of coarse resolution OGCMs. We show that completing EAE requires an adequate decomposition of the mesoscale tracer flux which is achieved by means of transforming mesoscale fields to isopycnal coordinates (IC) where mesoscale dynamics has the simplest form. The transformation results in splitting Fτ into two components and : the former is determined by buoyancy mesoscale dynamics only and has a trivial kinematic dependence on the mean tracer field, the latter is determined by mesoscale tracer dynamics. Thus, the problem of modelling (parameterizing) Fτ in ZC is divided in two stages which can be termed kinematic and dynamic. The kinematic stage consists in adequate decomposing Fτ, and the result is expressed in terms of mesoscale fields. The dynamic stage consists in applying a specific dynamic mesoscale model to parameterize the components of Fτ. In this article, we show that some components of Fτ are missing in ZC-OGCMs tracer equation and that their contribution is of the same order of magnitude as the mesoscale contribution itself. We also show that Fτ has components across mean isopycnals and that their existence is consistent with the adiabatic approximation which requires vanishing all fluxes across isopycnal surfaces. As for practical results, we derive the complete equation for the large scale tracer in ZC-OGCMs and present the parameterization of the terms which have been missing thus far.

  19. Nanodomained Nickel Unite Nanocrystal Strength with Coarse-Grain Ductility

    PubMed Central

    Wu, Xiaolei; Yuan, Fuping; Yang, Muxin; Jiang, Ping; Zhang, Chuanxin; Chen, Liu; Wei, Yueguang; Ma, Evan

    2015-01-01

    Conventional metals are routinely hardened by grain refinement or by cold working with the expense of their ductility. Recent nanostructuring strategies have attempted to evade this strength versus ductility trade-off, but the paradox persists. It has never been possible to combine the strength reachable in nanocrystalline metals with the large uniform tensile elongation characteristic of coarse-grained metals. Here a defect engineering strategy on the nanoscale is architected to approach this ultimate combination. For Nickel, spread-out nanoscale domains (average 7 nm in diameter) were produced during electrodeposition, occupying only ~2.4% of the total volume. Yet the resulting Ni achieves a yield strength approaching 1.3 GPa, on par with the strength for nanocrystalline Ni with uniform grains. Simultaneously, the material exhibits a uniform elongation as large as ~30%, at the same level of ductile face-centered-cubic metals. Electron microscopy observations and molecular dynamics simulations demonstrate that the nanoscale domains effectively block dislocations, akin to the role of precipitates for Orowan hardening. In the meantime, the abundant domain boundaries provide dislocation sources and trapping sites of running dislocations for dislocation multiplication, and the ample space in the grain interior allows dislocation storage; a pronounced strain-hardening rate is therefore sustained to enable large uniform elongation. PMID:26122728

  20. High-efficiency flotation of coarse and fine coal

    SciTech Connect

    Atkinson, B.W.; Conway, C.J.; Jameson, G.J.

    1995-10-01

    The flotation of coal in the fine and coarse particle size ranges presents particular problems. Fine or ultra-fine coal less than 100 microns presents a challenge to conventional flotation machines because the rate of capture of the coal particles can be very low, so longer residence times are needed. Also, conventional mechanical cells are not normally designed with froth properties in mind. Froth drainage may be inadequate, leading to excessive entrainment of ash. The upper limit of flotation of coal is normally put at about 500 {micro}m (30 mesh). It appears that, in mechanical cells, coarser particles tend to be torn away from bubbles in the turbulent environment created by the impeller. In this paper, results are presented from plant trials of a high-intensity flotation column of novel design, namely the Jameson cell. Extensive trials have been conducted on coal slurries with a top size of around 1 mm. Size-by size analysis shows that it is possible to achieve high yields of low ash product over the whole particle size range.

  1. Improving the treatment of coarse-grain electrostatics: CVCEL

    SciTech Connect

    Ceres, N.; Lavery, R.

    2015-12-28

    We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding.

  2. Safety Ellipse Motion with Coarse Sun Angle Optimization

    NASA Technical Reports Server (NTRS)

    Naasz, Bo

    2005-01-01

    The Hubble Space Telescope Robotic Servicing and De-orbit Mission (HRSDM) was t o be performed by the unmanned Hubble Robotic Vehicle (HRV) consisting of a Deorbit Module (DM), responsible for the ultimate disposal of Hubble Space Telescope (HST) at the end of science operations, and an Ejection Module (EM), responsible for robotically servicing the HST to extend its useful operational lifetime. HRSDM consisted of eight distinct phases, including: launch, pursuit, proximity operations, capture, servicing, EM jettison and disposal, science operations, and deorbit. The scope of this paper is limited to the Proximity Operations phase of HRSDM. It introduces a relative motion strategy useful for Autonomous Rendezvous and Docking (AR&D) or Formation Flying missions where safe circumnavigation trajectories, or close proximity operations (tens or hundreds of meters) are required for extended periods of time. Parameters and algorithms used to model the relative motion of HRV with respect to HST during the Proximity Operations phase of the HRSDM are described. Specifically, the Safety Ellipse (SE) concept, convenient parameters for describing SE motion, and a concept for initializing SE motion around a target vehicle to coarsely optimize sun and relative navigation sensor angles are presented. The effects of solar incidence angle variations on sun angle optimization, and the effects of orbital perturbations and navigation uncertainty on long term SE motion are discussed.

  3. Penetration strength of coarse granular materials from DEM simulations

    NASA Astrophysics Data System (ADS)

    Quezada, Juan Carlos; Saussine, Gilles; Breul, Pierre; Radjai, Farhang

    2013-06-01

    Field tests are widely used for soil characterization in geotechnical applications in spite of implementation difficulties. The light penetrometer test is a well-known testing tool for fine soils, but the physical interpretation of the output data in the case of coarse granular materials is far less evident. In fact, the data are considerably more sensitive to various parameters such as fabric structure, particles shape or the applied impact energy. In order to achieve a better understanding of the underlying phenomena, we performed a numerical study by means contact dynamics DEM simulations. We consider the penetration of a moving tip into a sample composed of irregular grain shapes and we analyze the influence of the driving velocity and applied energy on the penetration strength. We find that the latter grows with both the penetration rate and energy. Force fluctuations on the tip involve a jamming-unjamming process. The typology of contact network and inter-granular friction play a major role in the fluctuations and measured values of the cone penetration strength.

  4. Personal coarse particulate matter exposures in an adult cohort

    NASA Astrophysics Data System (ADS)

    Williams, Ron; Case, Martin; Yeatts, Karin; Chen, Fu-Lin; Scott, James; Svendsen, Erik; Devlin, Robert

    Volunteers associated with the North Carolina Adult Asthma and Environment Study (NCAAES) participated in an investigation of personal daily exposures to coarse and fine particulate matter size fractions (PM 10-2.5, PM 2.5). Data from these personal measurements were then compared to community-based measures that might typically represent surrogate measurements of exposure often used in epidemiological assessments. To determine personal exposures to various particulate matter (PM) size fractions, a recently evaluated personal PM monitor capable of direct PM 10-2.5 size fraction collection was used. Participants living in the central region of North Carolina and enrolled in the NCAAES were asked to wear the monitor attached to a supporting backpack for 24-h collection periods. These volunteers were monitored for 2 to 4 days with subsequent gravimetric analysis of their PM samples. Personal PM 10-2.5 mass concentrations were observed to be highly variable and ranged from 7.6 to 40.2 μg/m 3 over an 8-month period. The median for this measurement from all participants (50th percentile) was 13.7 μg/m 3. A coefficient of determination ( r2) of 0.02 was established for community-based PM 10-2.5 mass concentrations versus personal exposures. Similar coefficients established for PM 2.5 mass revealed only a modest improvement in agreement ( r2 = 0.12). Data from the exposure findings are reported here.

  5. Fuzzy logic and coarse coding using programmable logic devices

    NASA Astrophysics Data System (ADS)

    Brooks, Geoffrey

    2009-05-01

    Naturally-occurring sensory signal processing algorithms, such as those that inspired fuzzy-logic control, can be integrated into non-naturally-occurring high-performance technology, such as programmable logic devices, to realize novel bio-inspired designs. Research is underway concerning an investigation into using field programmable logic devices (FPLD's) to implement fuzzy logic sensory processing. A discussion is provided concerning the commonality between bio-inspired fuzzy logic algorithms and coarse coding that is prevalent in naturally-occurring sensory systems. Undergraduate design projects using fuzzy logic for an obstacle-avoidance robot has been accomplished at our institution and other places; numerous other successful fuzzy logic applications can be found as well. The long-term goal is to leverage such biomimetic algorithms for future applications. This paper outlines a design approach for implementing fuzzy-logic algorithms into reconfigurable computing devices. This paper is presented in an effort to connect with others who may be interested in collaboration as well as to establish a starting point for future research.

  6. Coarse-grained force field; general folding theory

    PubMed Central

    Liwo, Adam; He, Yi; Scheraga, Harold A.

    2012-01-01

    We review the coarse-grained UNited RESidue (UNRES) force field for the simulations of protein structure and dynamics, which is being developed in our laboratory over the last several years. UNRES is a physics-based force field, the prototype of which is defined as a potential of mean force of polypeptide chains in water, where all the degrees of freedom except the coordinates of α-carbon atoms and side-chain centers have been integrated out. We describe the initial implementation of UNRES to protein-structure prediction formulated as a search for the global minimum of the potential-energy function and its subsequent molecular dynamics and extensions of molecular-dynamics implementation, which enabled us to study protein-folding pathways and thermodynamics, as well as to reformulate the protein-structure prediction problem as a search for the conformational ensemble with the lowest free energy at temperatures below the folding-transition temperature. Applications of UNRES to study biological problems are also described. PMID:21643583

  7. Coarse-grained, foldable, physical model of the polypeptide chain

    PubMed Central

    Chakraborty, Promita; Zuckermann, Ronald N.

    2013-01-01

    Although nonflexible, scaled molecular models like Pauling–Corey’s and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and α-carbon units, connected by mechanical bonds (corresponding to φ and ψ) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human–computer interface. PMID:23898168

  8. Subsurface flow mixing in coarse, braided river deposits

    NASA Astrophysics Data System (ADS)

    Huber, Emanuel; Huggenberger, Peter

    2016-05-01

    Coarse, braided river deposits show a large hydraulic heterogeneity on the metre scale. One of the main depositional elements found in such deposits is a trough structure filled with layers of bimodal gravel and open-framework gravel, the latter being highly permeable. However, the impact of such trough fills on subsurface flow and advective mixing has not drawn much attention. A geologically realistic model of trough fills is proposed and fitted to a limited number of ground-penetrating radar records surveyed on the river bed of the Tagliamento River (northeast Italy). A steady-state, saturated subsurface flow simulation is performed on the small-scale, high-resolution, synthetic model (size: 75 m × 80 m × 9 m). Advective mixing (i.e. streamline intertwining) is visualised and quantified based on particle tracking. The results indicate strong advective mixing as well as a large flow deviation induced by the asymmetry of the trough fills with regard to the main flow direction. The flow deviation induces a partial, large-scale rotational effect. These findings depict possible advective mixing found in natural environments and can guide the interpretation of ecological processes such as in the hyporheic zone.

  9. Entrainment of coarse grains using a discrete particle model

    SciTech Connect

    Valyrakis, Manousos; Arnold, Roger B. Jr.

    2014-10-06

    Conventional bedload transport models and incipient motion theories relying on a time-averaged boundary shear stress are incapable of accounting for the effects of fluctuating near-bed velocity in turbulent flow and are therefore prone to significant errors. Impulse, the product of an instantaneous force magnitude and its duration, has been recently proposed as an appropriate criterion for quantifying the effects of flow turbulence in removing coarse grains from the bed surface. Here, a discrete particle model (DPM) is used to examine the effects of impulse, representing a single idealized turbulent event, on particle entrainment. The results are classified according to the degree of grain movement into the following categories: motion prior to entrainment, initial dislodgement, and energetic displacement. The results indicate that in all three cases the degree of particle motion depends on both the force magnitude and the duration of its application and suggest that the effects of turbulence must be adequately accounted for in order to develop a more accurate method of determining incipient motion. DPM is capable of simulating the dynamics of grain entrainment and is an appropriate tool for further study of the fundamental mechanisms of sediment transport.

  10. Ambient fine and coarse particle suppression of alveolar macrophage functions.

    PubMed

    Kleinman, M T; Sioutas, C; Chang, M C; Boere, A J F; Cassee, F R

    2003-02-01

    Alveolar macrophages (AM) are part of the innate immunological defense system and are among the first cells to respond to the effects of inhaled particles. Study of macrophage responses to particles is, therefore, relevant to understanding the mechanisms by which inhaled particles can adversely affect health. Size-fractionated ambient particles were collected at traffic-dominated sites in The Netherlands using a mobile high volume slit impactor system. AM were obtained by bronchoalveolar lavage from adult as well as aged rats and were incubated with for 4 h with collected particles at concentrations of 25-1000 pg per cell. Free radical generation by AM was measured with and without stimulation of AM with phorbol myristate acetate (PMA). There were dose-dependent decreases in macrophage production of superoxide radicals as measured by the chemiluminescent method. Coarse particles were more toxic than were fine particles. Suppression of free radical production did not seem to be related to the presence of bioavailable iron or to endotoxin associated with the particles. There were no statistically significant differences related to age or strain of the rats tested. We conclude that in vitro tests using AM is a useful and rapid method for delineating differences in toxicity between environmental samples of size fractionated ambient particles. PMID:12523957

  11. Coarse-grained description of cosmic structure from Szekeres models

    NASA Astrophysics Data System (ADS)

    Sussman, Roberto A.; Delgado Gaspar, I.; Hidalgo, Juan Carlos

    2016-03-01

    We show that the full dynamical freedom of the well known Szekeres models allows for the description of elaborated 3-dimensional networks of cold dark matter structures (over-densities and/or density voids) undergoing ``pancake'' collapse. By reducing Einstein's field equations to a set of evolution equations, which themselves reduce in the linear limit to evolution equations for linear perturbations, we determine the dynamics of such structures, with the spatial comoving location of each structure uniquely specified by standard early Universe initial conditions. By means of a representative example we examine in detail the density contrast, the Hubble flow and peculiar velocities of structures that evolved, from linear initial data at the last scattering surface, to fully non-linear 10-20 Mpc scale configurations today. To motivate further research, we provide a qualitative discussion on the connection of Szekeres models with linear perturbations and the pancake collapse of the Zeldovich approximation. This type of structure modelling provides a coarse grained—but fully relativistic non-linear and non-perturbative —description of evolving large scale cosmic structures before their virialisation, and as such it has an enormous potential for applications in cosmological research.

  12. On a Primal Coarse Projective Integration Method for Multiscale Simulations

    NASA Astrophysics Data System (ADS)

    Skoric, Milos; Ishiguro, Seiji; Maluckov, Sandra

    2006-10-01

    A novel simulation framework called Equation-Free Projective Integration (EFPI) was recently applied to nonlinear plasmas by M. Shay [1] to study propagation and steepening of a 1D ion sound (IS) with a PIC code as a microscopic simulator. To initialize, macro plasma variables are ``lifted'' to a fine micro-representation. PIC code is stepped forward for a short time, and the results are ``restricted'' or smoothed back to macro space. By extrapolation, time derivative is estimated and projected with a large step; the process is repeated. As a simple alternative, we propose a sort of a primal EPFI scheme to simulate nonlinear plasmas including kinetic effects. The micro-simulator is a standard 1D ES PIC code. Ions are assumed inherently coarse grained or ``smoothed'' and tracked to extrapolate in time and project. The potential is averaged over the electron plasma period to extrapolate and project. No adiabatic approximation for electrons is used [2], instead, self-consistently find the non-uniform electron distribution from the Poisson equation and ion density. Preliminary results for nonlinear IS as well as for the IS double layer paradigm are presented and some limitations on the EPFI discussed. [1] M. Shay, J. Drake, W. Dorland, J. of Comp. Phys (APS DPP 2005) [2] G. Stanchev, A. Maluckov et al., in EPS Fusion (Rome, 2006).

  13. Coarse-Grained Model for Water Involving a Virtual Site.

    PubMed

    Deng, Mingsen; Shen, Hujun

    2016-02-01

    In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones. PMID:26747089

  14. Nanodomained Nickel Unite Nanocrystal Strength with Coarse-Grain Ductility

    NASA Astrophysics Data System (ADS)

    Wu, Xiaolei; Yuan, Fuping; Yang, Muxin; Jiang, Ping; Zhang, Chuanxin; Chen, Liu; Wei, Yueguang; Ma, Evan

    2015-06-01

    Conventional metals are routinely hardened by grain refinement or by cold working with the expense of their ductility. Recent nanostructuring strategies have attempted to evade this strength versus ductility trade-off, but the paradox persists. It has never been possible to combine the strength reachable in nanocrystalline metals with the large uniform tensile elongation characteristic of coarse-grained metals. Here a defect engineering strategy on the nanoscale is architected to approach this ultimate combination. For Nickel, spread-out nanoscale domains (average 7 nm in diameter) were produced during electrodeposition, occupying only ~2.4% of the total volume. Yet the resulting Ni achieves a yield strength approaching 1.3 GPa, on par with the strength for nanocrystalline Ni with uniform grains. Simultaneously, the material exhibits a uniform elongation as large as ~30%, at the same level of ductile face-centered-cubic metals. Electron microscopy observations and molecular dynamics simulations demonstrate that the nanoscale domains effectively block dislocations, akin to the role of precipitates for Orowan hardening. In the meantime, the abundant domain boundaries provide dislocation sources and trapping sites of running dislocations for dislocation multiplication, and the ample space in the grain interior allows dislocation storage; a pronounced strain-hardening rate is therefore sustained to enable large uniform elongation.

  15. Cellulose microfibril formation within a coarse grained molecular dynamics

    NASA Astrophysics Data System (ADS)

    Nili, Abdolmadjid; Shklyaev, Oleg; Crespi, Vincent; Zhao, Zhen; Zhong, Linghao; CLSF Collaboration

    2014-03-01

    Cellulose in biomass is mostly in the form of crystalline microfibrils composed of 18 to 36 parallel chains of polymerized glucose monomers. A single chain is produced by cellular machinery (CesA) located on the preliminary cell wall membrane. Information about the nucleation stage can address important questions about intermediate region between cell wall and the fully formed crystalline microfibrils. Very little is known about the transition from isolated chains to protofibrils up to a full microfibril, in contrast to a large body of studies on both CesA and the final crystalline microfibril. In addition to major experimental challenges in studying this transient regime, the length and time scales of microfibril nucleation are inaccessible to atomistic molecular dynamics. We have developed a novel coarse grained model for cellulose microfibrils which accounts for anisotropic interchain interactions. The model allows us to study nucleation, kinetics, and growth of cellulose chains/protofibrils/microfibrils. This work is supported by the US Department of Energy, Office of Basic Energy Sciences as part of The Center for LignoCellulose Structure and Formation, an Energy Frontier Research Center.

  16. Aggregated Authentication (AMAC) Using Universal Hash Functions

    NASA Astrophysics Data System (ADS)

    Znaidi, Wassim; Minier, Marine; Lauradoux, Cédric

    Aggregation is a very important issue to reduce the energy consumption in Wireless Sensors Networks (WSNs). There is currently a lack of cryptographic primitives for authentication of aggregated data. The theoretical background for Aggregated Message Authentication Codes (AMACs) has been proposed by Chan and Castelluccia at ISIT 08.

  17. Mineral resource of the month: aggregates

    USGS Publications Warehouse

    Willett, Jason C.

    2012-01-01

    Crushed stone and construction sand and gravel, the two major types of natural aggregates, are among the most abundant and accessible natural resources on the planet. The earliest civilizations used aggregates for various purposes, mainly construction. Today aggregates provide the basic raw materials for the foundation of modern society.

  18. 28 CFR 2.5 - Sentence aggregation.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Sentence aggregation. 2.5 Section 2.5 Judicial Administration DEPARTMENT OF JUSTICE PAROLE, RELEASE, SUPERVISION AND RECOMMITMENT OF PRISONERS... aggregation. When multiple sentences are aggregated by the Bureau of Prisons pursuant to 18 U.S.C. 4161...

  19. Cytotoxic effects of aggregated nanomaterials.

    PubMed

    Soto, Karla; Garza, K M; Murr, L E

    2007-05-01

    This study deals with cytotoxicity assays performed on an array of commercially manufactured inorganic nanoparticulate materials, including Ag, TiO(2), Fe(2)O(3), Al(2)O(3), ZrO(2), Si(3)N(4), naturally occurring mineral chrysotile asbestos and carbonaceous nanoparticulate materials such as multiwall carbon nanotube aggregates and black carbon aggregates. The nanomaterials were characterized by TEM, as the primary particles, aggregates or long fiber dimensions ranged from 2nm to 20microm. Cytotoxicological assays of these nanomaterials were performed utilizing a murine alveolar macrophage cell line and human macrophage and epithelial lung cell lines as comparators. The nanoparticulate materials exhibited varying degrees of cytoxicity for all cell lines and the general trends were similar for both the murine and human macrophage cell lines. These findings suggest that representative cytotoxic responses for humans might be obtained by nanoparticulate exposures to simple murine macrophage cell line assays. Moreover, these results illustrate the utility in performing rapid in vitro assays for cytotoxicity assessments of nanoparticulate materials as a general inquiry of potential respiratory health risks in humans. PMID:17275430

  20. Aggregation of Heterogeneously Charged Colloids.

    PubMed

    Dempster, Joshua M; Olvera de la Cruz, Monica

    2016-06-28

    Patchy colloids are attractive as programmable building blocks for metamaterials. Inverse patchy colloids, in which a charged surface is decorated with patches of the opposite charge, are additionally noteworthy as models for heterogeneously charged biological materials such as proteins. We study the phases and aggregation behavior of a single charged patch in an oppositely charged colloid with a single-site model. This single-patch inverse patchy colloid model shows a large number of phases when varying patch size. For large patch sizes we find ferroelectric crystals, while small patch sizes produce cross-linked gels. Intermediate values produce monodisperse clusters and unusual worm structures that preserve finite ratios of area to volume. The polarization observed at large patch sizes is robust under extreme disorder in patch size and shape. We examine phase-temperature dependence and coexistence curves and find that large patch sizes produce polarized liquids, in contrast to mean-field predictions. Finally, we introduce small numbers of unpatched charged colloids. These can either suppress or encourage aggregation depending on their concentration and the size of the patches on the patched colloids. These effects can be exploited to control aggregation and to measure effective patch size. PMID:27253725

  1. Aggregation and Aggregate Carbon in a Forested Southeastern Coastal Plain Spodosol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil aggregation is influenced by the soil environment and is a factor in soil carbon sequestration. Sandy Coastal Plain soils often do not have the clay to promote aggregation nor have been considered soils with high levels of aggregation. This study was conducted to examine the aggregate morpholog...

  2. Cathodoluminescence microscopy and petrographic image analysis of aggregates in concrete pavements affected by alkali-silica reaction

    SciTech Connect

    Stastna, A.; Sachlova, S.; Pertold, Z.; Prikryl, R.; Leichmann, J.

    2012-03-15

    Various microscopic techniques (cathodoluminescence, polarizing and electron microscopy) were combined with image analysis with the aim to determine a) the modal composition and degradation features within concrete, and b) the petrographic characteristics and the geological types (rocks, and their provenance) of the aggregates. Concrete samples were taken from five different portions of Highway Nos. D1, D11, and D5 (the Czech Republic). Coarse and fine aggregates were found to be primarily composed of volcanic, plutonic, metamorphic and sedimentary rocks, as well as of quartz and feldspar aggregates of variable origins. The alkali-silica reaction was observed to be the main degradation mechanism, based upon the presence of microcracks and alkali-silica gels in the concrete. Use of cathodoluminescence enabled the identification of the source materials of the quartz aggregates, based upon their CL characteristics (i.e., color, intensity, microfractures, deformation, and zoning), which is difficult to distinguish only employing polarizing and electron microscopy. - Highlights: Black-Right-Pointing-Pointer ASR in concrete pavements on the Highways Nos. D1, D5 and D11 (Czech Republic). Black-Right-Pointing-Pointer Cathodoluminescence was combined with various microscopic techniques and image analysis. Black-Right-Pointing-Pointer ASR was attributed to aggregates. Black-Right-Pointing-Pointer Source materials of aggregates were identified based on cathodoluminescence characteristics. Black-Right-Pointing-Pointer Quartz comes from different volcanic, plutonic and metamorphic parent rocks.

  3. Effects of cholesterol on pore formation in lipid bilayers induced by human islet amyloid polypeptide fragments: A coarse-grained molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Xu, Weixin; Wei, Guanghong; Su, Haibin; Nordenskiöld, Lars; Mu, Yuguang

    2011-11-01

    Disruption of the cellular membrane by the amyloidogenic peptide, islet amyloid polypeptide (IAPP), has been considered as one of the mechanisms of β-cell death during type 2 diabetes. The N-terminal region (residues 1-19) of the human version of IAPP is suggested to be primarily responsible for the membrane-disrupting effect of the full-length hIAPP peptide. However, the detailed assembly mode of hIAPP1-19 with membrane remains unclear. To gain insight into the interactions of hIAPP1-19 oligomer with the model membrane, we have employed coarse-grained molecular dynamics self-assembly simulations to study the aggregation of hIAPP1-19 fragments in the binary lipid made of zwitterionic dipalmitoylphosphatidylcholine (DPPC) and anionic dipalmitoylphosphatidylserine (DPPS) in the presence and absence of different levels of cholesterol content. The membrane-destabilizing effect of hIAPP1-19 is found to be modulated by the presence of cholesterol. In the absence of cholesterol, hIAPP1-19 aggregates prefer to locate inside the bilayer, forming pore-like assemblies. While in the presence of cholesterol molecules, the lipid bilayer becomes more ordered and stiff, and the hIAPP1-19 aggregates are dominantly positioned at the bilayer-water interface. The action of cholesterol may suggest a possible way to maintain the membrane integrity by small molecule interference.

  4. Transitional grain-size-sensitive flow of milky quartz aggregates

    NASA Astrophysics Data System (ADS)

    Fukuda, J. I.; Holyoke, C. W., III; Kronenberg, A. K.

    2014-12-01

    Fine-grained (~15 μm) milky quartz aggregates exhibit reversible flow strengths in triaxial compression experiments conducted at T = 800-900oC, Pc = 1.5 GPa when strain rates are sequentially decreased (typically from 10-3.5 to 10-4.5 and 10-5.5 s-1), and then returned to the original rate (10-3.5 s-1), while samples that experience grain growth at 1000oC (to 35 μm) over the same sequence of strain rates exhibit an irreversible increase in strength. Polycrystalline quartz aggregates have been synthesized from natural milky quartz powders (ground to 5 μm) by HIP methods at T = 1000oC, Pc = 1.5 GPa and t = 24 hours, resulting in dense, fine-grained aggregates of uniform water content of ~4000 ppm (H/106Si), as indicated by a broad OH absorption band at 3400 cm-1. In experiments performed at 800o and 900oC, grain sizes of the samples are essentially constant over the duration of each experiment, though grain shapes change significantly, and undulatory extinction and deformation lamellae indicate that much of the sample shortening (to 50%) is accomplished, over the four strain-rate steps, by dislocation creep. Differential stresses measured at T = 800oC decrease from 160 to 30 MPa as strain rate is reduced from 10-4.6 to 10-5.5 s-1, and a stress of 140 MPa is measured when strain rate is returned to 10-4.5 s-1. Samples deformed at 1000o and 1100oC experience normal grain growth, with grain boundary energy-driven grain-coarsening textures superposed by undulatory extinction and deformation lamellae. Differential stresses measured at 1000oC and strain rates of 10-3.6, 10-4.6, and 10-5.5 s-1 are 185, 80, and 80 MPa, respectively, while an increased flow stress of 260 MPa is measured (following ~28 hours of prior high temperature deformation and grain growth) when strain rate is returned to 10-3.6 s-1. While all samples exhibit lattice preferred orientations, the stress exponent n inferred for the fine-grained 800oC sample is 1.5 and the stress exponent of the coarse

  5. [AGGREGATION OF METABOLICALLY DEPLETED HUMAN ERYTHROCYTES].

    PubMed

    Sheremet'ev, Yu A; Popovicheva, A N; Rogozin, M M; Levin, G Ya

    2016-01-01

    An aggregation of erythrocytes in autologous plasma after blood storage for 14 days at 4 °C was studied using photometry and light microscopy. The decrease of ATP content, the formation of echinocytes and spheroechinocytes, the decrease of rouleaux form of erythrocyte aggregation were observed during the storage. On the other hand the aggregates of echinocytes were formed in the stored blood. The addition of plasma from the fresh blood didn't restore the normal discocytic shape and aggregation of erythrocytes in the stored blood. The possible mechanisms of erythrocytes and echinocytes aggregation are discussed. PMID:27220249

  6. [Lysophosphatidic acid and human erythrocyte aggregation].

    PubMed

    Sheremet'ev, Iu A; Popovicheva, A N; Levin, G Ia

    2014-01-01

    The effects of lysophosphatidic acid on the morphology and aggregation of human erythrocytes has been studied. Morphology of erythrocytes and their aggregates were studied by light microscopy. It has been shown that lysophosphatidic acid changes the shape of red blood cells: diskocyte become echinocytes. Aggregation of red blood cells (rouleaux) was significantly reduced in autoplasma. At the same time there is a strong aggregation of echinocytes. This was accompanied by the formation of microvesicles. Adding normal plasma to echinocytes restores shape and aggregation of red blood cells consisting of "rouleaux". A possible mechanism of action of lysophosphatidic acid on erythrocytes is discussed. PMID:25509147

  7. Experimental testing of hot mix asphalt mixture made of recycled aggregates.

    PubMed

    Rafi, Muhammad Masood; Qadir, Adnan; Siddiqui, Salman Hameed

    2011-12-01

    The migration of population towards big cities generates rapid construction activities. These activities not only put pressure on natural resources but also produce construction, renovation and demolition waste. There is an urgent need to find out ways to handle this waste owing to growing environmental concerns. This can reduce pressure on natural resources as well. This paper presents the results of experimental studies which were carried out on hot mix asphalt mixture samples. These samples were manufactured by adding recycled aggregates (RA) with natural crushed stone aggregates (CSA). Three levels of addition of RA were considered in the presented studies. RA were obtained from both the concrete waste of construction, renovation and demolition activities and reclaimed asphalt pavement. Separate samples were manufactured with the coarse and fine aggregate fractions of both types of RA. Samples made with CSA were used as control specimens. The samples were prepared and tested using the Marshall method. The performance of the samples was investigated in terms of density-void and stability/flow analysis and was compared with the performance criteria as given by National Highway Authority for wearing course material in Pakistan. Based on this data optimum asphalt contents were determined. All the samples made by adding up to 50% RA conform to the specification requirements of wearing course material as given by National Highway Authority in terms of optimum asphalt contents, voids in mineral aggregates and stability/flow. A statistical analysis of variation of these samples confirmed that addition is also possible statistically. PMID:20483876

  8. Lipid extraction mediates aggregation of carbon nanospheres in pulmonary surfactant monolayers.

    PubMed

    Yue, Tongtao; Xu, Yan; Li, Shixin; Zhang, Xianren; Huang, Fang

    2016-07-28

    Increasing evidence indicates that carbon nanoparticles (CNPs), which mainly originate from incomplete combustion of fossil fuels, have an adverse impact on the respiratory system. Recent in vivo experiments have shown that the pulmonary toxicity of CNPs is attributed to their aggregation in pulmonary surfactant monolayers (PSMs) while the underlying mechanism of aggregation remains unclear. Here, by performing coarse grained molecular dynamics simulations, we demonstrate for the first time that the aggregation of carbon nanospheres (CNSs) in PSMs is in fact size-dependent and mediated by lipid extractions. Upon CNS deposition, neighbouring lipid molecules are extracted from PSMs to cover CNSs from the top side. The extracted lipids induce clustering of CNSs to maximize the CNS-lipid interaction, by forming inverse micelles to wrap the aggregated CNSs cooperatively. The formed CNS clusters perturb the molecule structure of the PSM and thus affect its biofunction on respiration. Our simulations show that during the expiration process, CNSs form clusters that perturb the mechanical properties of the PSM in a manner depending on the CNS size. With deep inspiration, a high concentration of large CNSs may induce PSM rupture and thus have a potential impact on its biophysical properties. PMID:27353041

  9. Coarse-pored ceramic supports for pyrolysis catalysts

    SciTech Connect

    Potapova, L.L.; Cherches, B.Kh.; Egiazarov, Yu.G.

    1988-03-20

    One promising trend in improvement of pyrolysis of hydrocarbon feedstocks is the use of heterogeneous catalysts in the process. The industrial use of highly effective catalysts would result in substantially increased product yields and in decrease of energy consumption in comparison with the requirements of drastic thermal processes. The aims of the present work were to obtain a mechanically strong coarse-pored ceramic support for pyrolysis catalysts and to study the influence of various factors on formation of its structure. The support material was made from an industrial ceramic mass of the following composition (%): koalin 30, plastic refractory clay 21, quartz 32, pegmatite 17. Various additives were used for formation of a porous structure: noncombustible highly porous (pumice, claydite), partially combustible (shungite), and completely combustible (SKT) activated carbon). The authors results show that 15 mass % of SKT carbon (particle size 0.1-0.2 mm) and 1-2 mass % of sodium trimetaphosphate should be added to the ceramic mass. The crushing strength of the resultant support samples reaches 550-630 kg/cm/sup 2/, with 34-35% porosity. Under the optimal conditions of pyrolysis of a straight-run gasoline fraction the catalyst obtained by deposition of 12 mass % of In/sub 2/O/sub 3/ and 4% K/sub 2/O on the synthesized support gives a yield of 39-41 mass % of ethylene and 61-62 mass % of unsaturated C/sub 2/-C/sub 4/ hydrocarbons, with 88-90 mass % gasification.

  10. Coarse-grained DNA modeling: Hybridization and ionic effects

    NASA Astrophysics Data System (ADS)

    Hinckley, Daniel M.

    Deoxyribonucleic acid (DNA) is a biopolymer of enormous significance in living systems. The utility of DNA in such systems is derived from the programmable nature of DNA and its unique mechanical properties. Recently, material scientists have harnessed these properties in order to create systems that spontaneous self-assemble on the nanoscale. Both biologists and material scientists are hindered by an incomplete understanding of the physical interactions that together govern DNA's behavior. Computer simulations, especially those at the coarse-grained (CG) level, can potentially complete this understanding by resolving details indiscernible with current experimental techniques. In this thesis, we advance the state-of-the-art of DNA CG simulations by first reviewing the relevant theory and the evolution of CG DNA models since their inception. Then we present 3SPN.2, an improved CG model for DNA that should provide new insights into biological and nanotechnological systems which incorporate DNA. We perform forward flux sampling simulations in order to examine the effect of sequence, oligomer length, and ionic strength on DNA oligomer hybridization. Due to the limitations inherent in continuum treatments of electrostatic interactions in biological systems, we generate a CG model of biological ions for use with 3SPN.2 and other CG models. Lastly, we illustrate the potential of 3SPN.2 and CG ions by using the models in simulations of viral capsid packaging experiments. The models and results described in this thesis will be useful in future modeling efforts that seek to identify the fundamental physics that govern behavior such as nucleosome positioning, DNA hybridization, and DNA nanoassembly.

  11. Impact Cratering on Small Asteroids and into Coarse Regoliths

    NASA Astrophysics Data System (ADS)

    Durda, D. D.

    2012-12-01

    Impact cratering on the smallest asteroids can result in crater and other associated impact scar morphologies that we do not usually see exhibited in imagery of larger main-belt asteroids and airless moons. The NEAR-Shoemaker spacecraft at (433) Eros and the Hayabusa spacecraft at (25143) Itokawa showed the surfaces of these near-Earth asteroids to be relatively depleted in smaller craters. 'Armoring' of the surface by the presence of boulders larger than the size of the projectiles needed to form the missing craters has been proposed as one possible contributing factor in the observed depletion. Indeed, a number of bright spots observed on the surfaces of some boulders on Itokawa appear to have a size distribution consistent with small projectiles and have been interpreted as impact scars - an extreme end member example of the armoring hypothesis. Several research teams have conducted a number of laboratory impact experiments focusing on the range of morphological expression of craters formed in coarse regoliths where the impacting projectiles are comparable in size to the regolith grains. The results of these experiments suggest that craters become less well defined and more irregular in shape as soon as the regolith target grains are larger than the projectiles. I will give an overview of the range of visual appearance of impact features on small asteroids, review the results of some previous laboratory experiments relevant to the armoring hypothesis, and present results of our own new impact experiments conducted at the Ames Vertical Gun Range to examine the range of morphological expression of impacts onto blocks on and in the regolith of small airless bodies.

  12. Development and application of coarse-grained models for lipids

    NASA Astrophysics Data System (ADS)

    Cui, Qiang

    2013-03-01

    I'll discuss a number of topics that represent our efforts in developing reliable molecular models for describing chemical and physical processes involving biomembranes. This is an exciting yet challenging research area because of the multiple length and time scales that are present in the relevant problems. Accordingly, we attempt to (1) understand the value and limitation of popular coarse-grained (CG) models for lipid membranes with either a particle or continuum representation; (2) develop new CG models that are appropriate for the particular problem of interest. As specific examples, I'll discuss (1) a comparison of atomistic, MARTINI (a particle based CG model) and continuum descriptions of a membrane fusion pore; (2) the development of a modified MARTINI model (BMW-MARTINI) that features a reliable description of membrane/water interfacial electrostatics and its application to cell-penetration peptides and membrane-bending proteins. Motivated specifically by the recent studies of Wong and co-workers, we compare the self-assembly behaviors of lipids with cationic peptides that include either Arg residues or a combination of Lys and hydrophobic residues; in particular, we attempt to reveal factors that stabilize the cubic ``double diamond'' Pn3m phase over the inverted hexagonal HII phase. For example, to explicitly test the importance of the bidentate hydrogen-bonding capability of Arg to the stabilization of negative Gaussian curvature, we also compare results using variants of the BMW-MARTINI model that treat the side chain of Arg with different levels of details. Collectively, the results suggest that both the bidentate feature of Arg and the overall electrostatic properties of cationic peptides are important to the self-assembly behavior of these peptides with lipids. The results are expected to have general implications to the mechanism of peptides and proteins that stimulate pore formation in biomembranes. Work in collaboration with Zhe Wu, Leili Zhang

  13. Critical parameters for coarse coal underground slurry haulage systems

    SciTech Connect

    Maynard, D.P.

    1981-02-15

    This report describes the basic parameters which directly influence the behavior of a coal slurry pipeline transportation system and determine the limitations of the system performance. The purpose of this technology assessment is to provide an identification and understanding of the critical factors which must be given consideration in the design and evaluation of such a slurry haulage system intended for use in an underground coal mine. The slurry haulage system will be utilized to satisfy the transportation requirements of conveying, in a pipeline, the coal mined by a continuous mining machine to a storage location near the mine entrance or to a coal preparation plant located on the surface. Coal-water slurries, particularly those consisting of homogeneous suspensions of small particles, frequently behave as non-Newtonian, Bingham-plastic fluids. For successful operation, slurry transport systems should be designed to operate in the turbulent flow regime and at a flow rate at least 30% greater than the deposition velocity. The deposition velocity is defined as the slurry flow rate at which the solid particles tend to settle in the pipe. Due to the importance of accurately determining the deposition velocity and the uncertainties of current methods for predicting the deposition velocity of coarse particle slurries, it is recommended that experimental efforts be performed as a part of the system design. The capacity of the haulage system should be compatible with the mine's projected coal output in order to avoid operational delays and the necessity for in-mine coal storage. The slurry pumps must generate sufficient discharge pressure to overcome the resultant friction losses in horizontal and vertical pipe sections and to satisfy the slurry hoisting requirements.

  14. Microwave extinction characteristics of nanoparticle aggregates

    NASA Astrophysics Data System (ADS)

    Wu, Y. P.; Cheng, J. X.; Liu, X. X.; Wang, H. X.; Zhao, F. T.; Wen, W. W.

    2016-07-01

    Structure of nanoparticle aggregates plays an important role in microwave extinction capacity. The diffusion-limited aggregation model (DLA) for fractal growth is utilized to explore the possible structures of nanoparticle aggregates by computer simulation. Based on the discrete dipole approximation (DDA) method, the microwave extinction performance by different nano-carborundum aggregates is numerically analyzed. The effects of the particle quantity, original diameter, fractal structure, as well as orientation on microwave extinction are investigated, and also the extinction characteristics of aggregates are compared with the spherical nanoparticle in the same volume. Numerical results give out that proper aggregation of nanoparticle is beneficial to microwave extinction capacity, and the microwave extinction cross section by aggregated granules is better than that of the spherical solid one in the same volume.

  15. Simulation of J-aggregate microcavity photoluminescence

    NASA Astrophysics Data System (ADS)

    Michetti, Paolo; La Rocca, Giuseppe C.

    2008-05-01

    We have developed a model in order to account for the photoexcitation dynamics of J-aggregate films and strongly coupled J-aggregate microcavities. The J aggregates are described as a disordered Frenkel exciton system in which relaxation occurs due to the presence of a thermal bath of molecular vibrations. The correspondence between the photophysics in J-aggregate films and that in J-aggregate microcavities is obtained by introducing a model polariton wave function mixing cavity photon modes and J-aggregate super-radiant excitons. With the same description of the material properties, we have calculated both absorption and luminescence spectra for the J-aggregate film and the photoluminescence of strongly coupled organic microcavities. The model is able to account for the fast relaxation dynamics in organic microcavities following nonresonant pumping and explains the temperature dependence of the ratio between the upper polariton and the lower polariton luminescence.

  16. 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.

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

    DOE PAGESBeta

    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. Physicochemical properties and ability to generate free radicals of ambient coarse, fine, and ultrafine particles in the atmosphere of Xuanwei, China, an area of high lung cancer incidence

    NASA Astrophysics Data System (ADS)

    Lu, Senlin; Yi, Fei; Hao, Xiaojie; Yu, Shang; Ren, Jingjing; Wu, Minghong; Jialiang, Feng; Yonemochi, Shinich; Wang, Qingyue

    2014-11-01

    The link between the high incidence of lung cancer and harmful pollutants emitted by local coal combustion in Xuanwei, Yunnan province, China, has been a focus of study since the 1980s. However, the mechanisms responsible for the high lung cancer rate remain unclear, necessitating further study. Since a close relationship between ambient air particle pollution and respiratory diseases exists, we sampled size-resolved ambient particles from the atmosphere of Xuanwei. In our indoor experiment, cutting-edge methods, including scanning electron microscopy coupled with energy dispersive X-ray detection (SEM/EDX), particle-induced X-ray emission (PIXE), electronic paramagnetic resonance (EPR) and the cell-free DCFH-DA assay, were employed to investigate the physicochemical properties, the potential to generate free radicals and the oxidative potential of ambient coarse (diameter, 1.8-10 μm), fine (diameter, 0.1-1.8 μm), and ultrafine (diameter, <0.1 μm) particles. We found the total mass concentrations of the size-resolved particles collected in spring were higher than that in early winter. Mass percentage of fine particles accounted for 68% and 61% of the total particulate mass in spring and in early winter samples, respectively, indicating that fine particles were the major component of the Xuanwei ambient particulate matters. On the other hand, the results of SEM/EDX analysis showed that the coarse particles were dominated by minerals, the fine particles by soot aggregates and fly ashes, and the ultrafine particles by soot particles and unidentified particles. Our PIXE results revealed that crustal elements (Ca, Ti Si, Fe) were mainly distributed in coarse particles, while trace metals (Cr, Mn, Ni, Cu, Zn, Pb) dominated in the fine particle fraction, and S, a typical element emitted by coal combustion, mainly resided in fine particles collected from the winter atmosphere. EPR results indicated that the magnitude of free radical intensity caused by size

  19. Characteristics and origin of coarse gold in Late Pleistocene sediments of the Cariboo placer mining district, British Columbia, Canada

    NASA Astrophysics Data System (ADS)

    Eyles, N.

    1995-02-01

    The Cariboo placer mining district (1000 km 2) sited in the Interior Plateau of central British Columbia, Canada, is the premier placer gold mining district of the Province. Gold is recovered from three Late Pleistocene sedimentary facies: postglacial fluvial gravels (< 10 Ka), Late Wisconsin till (ca. 25-10 Ka), and "older" fluvial gravels (>25 Ka). This study reports the morphology (size, roundness, sphericity) of 1636 gold grains, ranging in size from 0.25 to 17 mm, recovered from 19 placer mines. Older gravels contain the smallest gold grains (mean grani size 1.53 mm), grains of intermediate size occur in till (2.23 mm) and the coarsest gold occurs in postglacial gravels (2.34 mm) with a mean of 1.93 mm for the mining district as a whole. The most common grain shapes are sub-rounded, discoidal (14.73% of the grain population), sub-angular, discoidal (10.88%), and sub-rounded, sub-discoidal (9.59%); the most angular grains occur in postglacial gravels. In-situ growth of coarse, angular grains is indicated by a "composite" grain structure, consisting of aggregates of gold particles welded together by high-grade (Ag = < 2%) filamentous gold; in-situ coarsening may be reliant on organic complexing agents produced below a dense forest cover. An evolutionary sequence of grain form, from angular aggregates to rounded "pumpkin seed" grains, is suggested. Rounded grains commonly show a crystalline structure which may result from the cold hammering of gold during transport; fracturing along crystal boundaries is common. Gold grains may undergo cycles of coarsening, rounding, diagenesis and breakup in response to repeated recycling through Pleistocene sedimentary environments.

  20. First-principle approach to rescale the dynamics of simulated coarse-grained macromolecular liquids

    NASA Astrophysics Data System (ADS)

    Lyubimov, I.; Guenza, M. G.

    2011-09-01

    We present a detailed derivation and testing of our approach to rescale the dynamics of mesoscale simulations of coarse-grained polymer melts (I. Y. Lyubimov, J. McCarty, A. Clark, and M. G. Guenza, J. Chem. Phys.JCPSA60021-960610.1063/1.3450301 132, 224903 (2010)). Starting from the first-principle Liouville equation and applying the Mori-Zwanzig projection operator technique, we derive the generalized Langevin equations (GLEs) for the coarse-grained representations of the liquid. The chosen slow variables in the projection operators define the length scale of coarse graining. Each polymer is represented at two levels of coarse graining: monomeric as a bead-and-spring model and molecular as a soft colloid. In the long-time regime where the center-of-mass follows Brownian motion and the internal dynamics is completely relaxed, the two descriptions must be equivalent. By enforcing this formal relation we derive from the GLEs the analytical rescaling factors to be applied to dynamical data in the coarse-grained representation to recover the monomeric description. Change in entropy and change in friction are the two corrections to be accounted for to compensate the effects of coarse graining on the polymer dynamics. The solution of the memory functions in the coarse-grained representations provides the dynamical rescaling of the friction coefficient. The calculation of the internal degrees of freedom provides the correction of the change in entropy due to coarse graining. The resulting rescaling formalism is a function of the coarse-grained model and thermodynamic parameters of the system simulated. The rescaled dynamics obtained from mesoscale simulations of polyethylene, represented as soft-colloidal particles, by applying our rescaling approach shows a good agreement with data of translational diffusion measured experimentally and from simulations. The proposed method is used to predict self-diffusion coefficients of new polyethylene samples.

  1. Comparison of the transport of the aggregates of nanoscale zerovalent iron under vertical and horizontal flow.

    PubMed

    Li, Jing; Ghoshal, Subhasis

    2016-02-01

    Direct injection of nanoscale zerovalent iron (NZVI) particles is being considered for remediation of contaminated sites. However, the transport characteristics of NZVI under horizontal flow conditions are not fully understood. In this study, NZVI particles were stabilized with carboxymethyl cellulose (CMC) and injected in vertical and horizontal columns to compare the effects of the flow direction on the transport. Columns were packed with sand of mean grain diameters of 180, 340 or 1140 µm (referred to as fine, intermediate and coarse sand, respectively), and were injected with CMC-NZVI suspensions of 0.3, 1 or 3 g Fe L(-1). Experimental breakthrough curves showed that with the coarse and intermediate sands, the steady-state effluent concentration in the horizontal column were up to 84% lower than those in the vertical column regardless of the initial NZVI concentration. However, in the fine sand the differences were insignificant, except at the highest NZVI particle concentration. Additionally, in the horizontally-oriented columns containing the coarse or intermediated sand, NZVI aggregates particles were non-uniformly distributed in the cross-section of the columns and there higher deposition in the bottom-half of the cross-section due to gravity effects. These deposition patterns can be accounted for, in part, by the gravitational settling of the large aggregates of NZVI, especially at high NZVI concentrations. A particle trajectory analysis in three dimensions demonstrated that under horizontal flow, gravity forces resulted in lower deposition of NZVI on the bottom-half of a single collector, as particles approaching the bottom-half of the collector were deflected by gravity to collectors below. PMID:26498094

  2. Inhomogeneous diffusion-limited aggregation

    NASA Technical Reports Server (NTRS)

    Selinger, Robin Blumberg; Nittmann, Johann; Stanley, H. E.

    1989-01-01

    It is demonstrated here that inhomogeneous diffusion-limited aggregation (DLA) model can be used to simulate viscous fingering in a medium with inhomogeneous permeability and homogeneous porosity. The medium consists of a pipe-pore square-lattice network in which all pores have equal volume and the pipes have negligible volume. It is shown that fluctuations in a DLA-based growth process may be tuned by noise reduction, and that fluctuations in the velocity of the moving interface are multiplicative in form.

  3. Majorization approach to entropic uncertainty relations for coarse-grained observables

    NASA Astrophysics Data System (ADS)

    Rudnicki, Łukasz

    2015-03-01

    We improve the entropic uncertainty relations for position and momentum coarse-grained measurements. We derive the continuous, coarse-grained counterparts of the discrete uncertainty relations based on the concept of majorization. The entropic inequalities obtained involve two Rényi entropies of the same order, and thus go beyond the standard scenario with conjugated parameters. In a special case describing the sum of two Shannon entropies, the majorization-based bounds significantly outperform the currently known results in the regime of larger coarse graining, and might thus be useful for entanglement detection in continuous variables.

  4. Coarse fragmental material of the littoral zones on the Murmansk and Carelian coasts

    NASA Astrophysics Data System (ADS)

    Mityaev, M. V.; Gerasimova, M. V.

    2010-04-01

    A three-year study of the abrasion of coarse fragmental material on the Murmansk coast has been carried out. According to the researchers, the average rate of the abrasion of the coarse-fragmental material of granitoid composition on the Murmansk coast has been determined. It was revealed that the rate of the destruction of the blocks increases from the lower littoral zone to the upper one. The estimation of the quantity of sedimentary material coming to the sedimentation basin as a result of the abrasion of coarse-fragmental material has been carried out.

  5. Investigating the mechanisms leading to protein aggregation

    NASA Astrophysics Data System (ADS)

    McNamara, Ruth; McManus, Jennifer J.

    2014-03-01

    The formation of protein aggregates is a feature of several diseases and is a problem during the manufacture of biopharmaceutical and protein based food products. During processing, stability may become compromised leading to the condensation of proteins to form non-native aggregates. The aim of this work is to induce aggregation on model proteins by the imposition of a particular stress to evaluate the extent of aggregation and to assess the degree of structural change to the protein. Aggregation of two proteins, lysozyme and bovine serum albumin has been induced by several mechanisms. Using various techniques (electrophoresis, HPLC, spectroscopic analysis, and microscopic techniques) both the level of aggregation extent of protein unfolding has been investigated for a range of solution conditions. Our results show that the amount of aggregation depends strongly on the mechanism by which non-native aggregation proceeds, and within each mechanism, solution conditions are an important factor. With the exception of aggregation by self-association (which is concentration dependent), the appearance of aggregation is driven by structural changes induced by the applied stress (heat, chemical denaturant, oxidation or contact with a surface). Author would like to acknowledge support from Science Foundation Ireland (SFI), National University of Maynooth John and Pat Hume Scholarship.

  6. Applications of aggregation theory to sustainability assessment

    DOE PAGESBeta

    Pollesch, N.; Dale, V. H.

    2015-04-01

    In order to aid in transition towards operations that promote sustainability goals, researchers and stakeholders use sustainability assessments. Although assessments take various forms, many utilize diverse sets of indicators that can number anywhere from two to over 2000. Indices, composite indicators, or aggregate values are used to simplify high dimensional and complex data sets and to clarify assessment results. Although the choice of aggregation function is a key component in the development of the assessment, there are few examples to be found in literature to guide appropriate aggregation function selection. This paper develops a connection between the mathematical study ofmore » aggregation functions and sustainability assessment in order to aid in providing criteria for aggregation function selection. Relevant mathematical properties of aggregation functions are presented and interpreted. Lastly, we provide cases of these properties and their relation to previous sustainability assessment research. Examples show that mathematical aggregation properties can be used to address the topics of compensatory behavior and weak versus strong sustainability, aggregation of data under varying units of measurements, multiple site multiple indicator aggregation, and the determination of error bounds in aggregate output for normalized and non-normalized indicator measures.« less

  7. Applications of aggregation theory to sustainability assessment

    SciTech Connect

    Pollesch, N.; Dale, V. H.

    2015-04-01

    In order to aid in transition towards operations that promote sustainability goals, researchers and stakeholders use sustainability assessments. Although assessments take various forms, many utilize diverse sets of indicators that can number anywhere from two to over 2000. Indices, composite indicators, or aggregate values are used to simplify high dimensional and complex data sets and to clarify assessment results. Although the choice of aggregation function is a key component in the development of the assessment, there are few examples to be found in literature to guide appropriate aggregation function selection. This paper develops a connection between the mathematical study of aggregation functions and sustainability assessment in order to aid in providing criteria for aggregation function selection. Relevant mathematical properties of aggregation functions are presented and interpreted. Lastly, we provide cases of these properties and their relation to previous sustainability assessment research. Examples show that mathematical aggregation properties can be used to address the topics of compensatory behavior and weak versus strong sustainability, aggregation of data under varying units of measurements, multiple site multiple indicator aggregation, and the determination of error bounds in aggregate output for normalized and non-normalized indicator measures.

  8. A review of volcanic ash aggregation

    NASA Astrophysics Data System (ADS)

    Brown, R. J.; Bonadonna, C.; Durant, A. J.

    2012-01-01

    Most volcanic ash particles with diameters <63 μm settle from eruption clouds as particle aggregates that cumulatively have larger sizes, lower densities, and higher terminal fall velocities than individual constituent particles. Particle aggregation reduces the atmospheric residence time of fine ash, which results in a proportional increase in fine ash fallout within 10-100 s km from the volcano and a reduction in airborne fine ash mass concentrations 1000 s km from the volcano. Aggregate characteristics vary with distance from the volcano: proximal aggregates are typically larger (up to cm size) with concentric structures, while distal aggregates are typically smaller (sub-millimetre size). Particles comprising ash aggregates are bound through hydro-bonds (liquid and ice water) and electrostatic forces, and the rate of particle aggregation correlates with cloud liquid water availability. Eruption source parameters (including initial particle size distribution, erupted mass, eruption column height, cloud water content and temperature) and the eruption plume temperature lapse rate, coupled with the environmental parameters, determines the type and spatiotemporal distribution of aggregates. Field studies, lab experiments and modelling investigations have already provided important insights on the process of particle aggregation. However, new integrated observations that combine remote sensing studies of ash clouds with field measurement and sampling, and lab experiments are required to fill current gaps in knowledge surrounding the theory of ash aggregate formation.

  9. Role of Multicellular Aggregates in Biofilm Formation

    PubMed Central

    Kragh, Kasper N.; Hutchison, Jaime B.; Melaugh, Gavin; Rodesney, Chris; Roberts, Aled E. L.; Irie, Yasuhiko; Jensen, Peter Ø.; Diggle, Stephen P.; Allen, Rosalind J.

    2016-01-01

    ABSTRACT In traditional models of in vitro biofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of experimental and computational approaches to determine the relative fitness of single cells and preformed aggregates during early development of Pseudomonas aeruginosa biofilms. We find that the relative fitness of aggregates depends markedly on the density of surrounding single cells, i.e., the level of competition for growth resources. When competition between aggregates and single cells is low, an aggregate has a growth disadvantage because the aggregate interior has poor access to growth resources. However, if competition is high, aggregates exhibit higher fitness, because extending vertically above the surface gives cells at the top of aggregates better access to growth resources. Other advantages of seeding by aggregates, such as earlier switching to a biofilm-like phenotype and enhanced resilience toward antibiotics and immune response, may add to this ecological benefit. Our findings suggest that current models of biofilm formation should be reconsidered to incorporate the role of aggregates in biofilm initiation. PMID:27006463

  10. Preferential Transport of Coarse Sediment in Steep Channels

    NASA Astrophysics Data System (ADS)

    Moody, J. A.

    2002-12-01

    Wildfires can change a source-limited system to a transport-limited system especially in steep mountainous terrain where the erosion threshold has been lowered by a wildfire. Such a situation occurred in the Buffalo and Spring Creek watersheds after the 1996 Buffalo Creek Fire, when 1 to 3 m of sediment was deposited in two relatively steep main channels (channel slope equal to 0.02 and 0.04 respectively) after an intense rainstorm of about 110 mm/hour. The bed material was a mixture of coarse grain sizes in both channels. The median size class in Buffalo Creek was 2-4 mm and in Spring Creek it was 4-8 mm. Bedload transport samples were collected in the field using a US BLH-84 sampler for discharge ranging from 0.0036 to 5.2 m3/s. The particle-size distributions for the bedload samples were analyzed to investigate sediment mobility. For each size class, a ratio was calculated equal to the percent of sediment transported divided by the percent of sediment available for transport. The percent available for transport was determined by recalculating the particle-size distribution of the bed material by excluding those sizes that did not move. The average ratio for the median-size class was 1.00 (13 samples) for Buffalo Creek and 0.94 (12 samples) for Spring Creek. In the Buffalo Creek channel, the average ratio for sizes larger than the median size (greater than 2-4 mm) was less than 1.00. Whereas in the Spring Creek channel, the data indicate a preferential transport of sizes larger than the median size with the ratio ranging from 0.86 to 2.22 and averaging 1.42 for the 8-16 mm size class and from 0.37 to 3.86 and averaging 1.28 for the 16-32 mm size class. Possible causes for the difference between Buffalo and Spring Creeks are: 1) the smaller value of the relative roughness (particle diameter/flow depth) in Buffalo Creek, 2) the less steep bed slope in Buffalo Creek, and 3) the difference in the sediment-size distribution

  11. Protein aggregates in Huntington's disease.

    PubMed

    Arrasate, Montserrat; Finkbeiner, Steven

    2012-11-01

    Huntington's disease (HD) is an incurable neurodegenerative disease characterized by abnormal motor movements, personality changes, and early death. HD is caused by a mutation in the IT-15 gene that expands abnormally the number of CAG nucleotide repeats. As a result, the translated protein huntingtin contains disease-causing expansions of glutamines (polyQ) that make it prone to misfold and aggregate. While the gene and mutations that cause HD are known, the mechanisms underlying HD pathogenesis are not. Here we will review the state of knowledge of HD, focusing especially on a hallmark pathological feature-intracellular aggregates of mutant Htt called inclusion bodies (IBs). We will describe the role of IBs in the disease. We speculate that IB formation could be just one component of a broader coping response triggered by misfolded Htt whose efficacy may depend on the extent to which it clears toxic forms of mutant Htt. We will describe how IB formation might be regulated and which factors could determine different coping responses in different subsets of neurons. A differential regulation of IB formation as a function of the cellular context could, eventually, explain part of the neuronal vulnerability observed in HD. PMID:22200539

  12. Sectoral shifts and aggregate unemployment

    SciTech Connect

    Loungani, P.

    1986-01-01

    Some recent research has taken the view that sectoral or industry-specific shocks significantly affect aggregate unemployment by increasing the amount of inter-industry labor reallocation required. The empirical evidence for this view rests on the finding that during the 1950s - and again during the 1970s - there was a positive correlation between aggregate unemployment and the dispersion of employment growth rates. This thesis demonstrates that this correlation arises largely because oil price shocks affect both unemployment and the dispersion of employment growth. Once the dispersion due to oil shocks is accounted for, the residual dispersion in employment has very low explanatory power for unemployment. Since the dispersion index does not measure pure sectoral shifts, an alternate measure of dispersion is developed that serves as a better proxy for the amount of inter-industry labor reallocation required each period. Estimates using this measure suggest that, during the 1950s, temporary increases in the relative price of oil were responsible for generating the observed correlation. On the other hand, sectoral shifts were important during the 1970s; in particular, the 1973 oil price increase has had significant reallocative effects on the economy. This contention is subjected to further tests by looking at the time-series behavior of employment in durable-goods industries and also by following the inter-industry movements of workers over time through the use of panel data.

  13. Attracted diffusion-limited aggregation.

    PubMed

    Rahbari, S H Ebrahimnazhad; Saberi, A A

    2012-07-01

    In this paper we present results of extensive Monte Carlo simulations of diffusion-limited aggregation (DLA) with a seed placed on an attractive plane as a simple model in connection with the electrical double layers. We compute the fractal dimension of the aggregated patterns as a function of the attraction strength α. For the patterns grown in both two and three dimensions, the fractal dimension shows a significant dependence on the attraction strength for small values of α and approaches that of the ordinary two-dimensional (2D) DLA in the limit of large α. For the nonattracting case with α = 1, our results in three dimensions reproduce the patterns of 3D ordinary DLA, while in two dimensions our model leads to the formation of a compact cluster with dimension 2. For intermediate α, the 3D clusters have a quasi-2D structure with a fractal dimension very close to that of the ordinary 2D DLA. This allows one to control the morphology of a growing cluster by tuning a single external parameter α. PMID:23005417

  14. Attracted diffusion-limited aggregation

    NASA Astrophysics Data System (ADS)

    Rahbari, S. H. Ebrahimnazhad; Saberi, A. A.

    2012-07-01

    In this paper we present results of extensive Monte Carlo simulations of diffusion-limited aggregation (DLA) with a seed placed on an attractive plane as a simple model in connection with the electrical double layers. We compute the fractal dimension of the aggregated patterns as a function of the attraction strength α. For the patterns grown in both two and three dimensions, the fractal dimension shows a significant dependence on the attraction strength for small values of α and approaches that of the ordinary two-dimensional (2D) DLA in the limit of large α. For the nonattracting case with α=1, our results in three dimensions reproduce the patterns of 3D ordinary DLA, while in two dimensions our model leads to the formation of a compact cluster with dimension 2. For intermediate α, the 3D clusters have a quasi-2D structure with a fractal dimension very close to that of the ordinary 2D DLA. This allows one to control the morphology of a growing cluster by tuning a single external parameter α.

  15. Asphaltene Aggregation and Fouling Behavior

    NASA Astrophysics Data System (ADS)

    Derakhshesh, Marzie

    This thesis explored the properties of asphaltene nano-aggregates in crude oil and toluene based solutions and fouling at process furnace temperatures, and the links between these two phenomena. The link between stability of asphaltenes at ambient conditions and fouling at the conditions of a delayed coker furnace, at over 450 °C, was examined by blending crude oil with an aliphatic diluent in different ratios. The stability of the blends were measured using a S-value analyzer, then fouling rates were measured on electrically heated stainless steel 316 wires in an autoclave reactor. The less stable the blend, the greater the rate and extent of fouling. The most severe fouling occurred with the unstable asphaltenes. SEM imaging of the foulant illustrates very different textures, with the structure becoming more porous with lower stability. Under cross-polarized light, the coke shows the presence of mesophase in the foulant layer. These data suggest a correlation between the fouling rate at high temperature furnace conditions and the stability index of the crude oil. Three organic polysulfides were introduced to the crude oil to examine their effect on fouling. The polysulfides are able to reduce coking and carbon monoxide generation in steam crackers. The fouling results demonstrated that polysulfide with more sulfur content increased the amount of corrosion-fouling of the wire. Various additives, solvents, ultrasound, and heat were employed to attempt to completely disaggregate the asphaltene nano-aggregates in solution at room temperature. The primary analytical technique used to monitor the nano-aggregation state of the asphaltenes in solution was the UV-visible spectroscopy. The results indicate that stronger solvents, such as pyridine and quinoline, combined with ionic liquids yield a slight reduction in the apparent absorbance at longer wavelengths, indicative of a decrease in the nano-aggregate size although the magnitude of the decrease is not significant

  16. Natural aggregates of the conterminous United States

    USGS Publications Warehouse

    Langer, William H.

    1988-01-01

    Crushed stone and sand and gravel are the two main sources of natural aggregates. These materials are commonly used construction materials and frequently can be interchanged with one another. They are widely used throughout the United States, with every State except two producing crushed stone. Together they amount to about half the mining volume in the United States. Approximately 96 percent of sand and gravel and 77 percent of the crushed stone produced in the United States are used in the construction industry. Natural aggregates are widely distributed throughout the United States in a variety of geologic environments. Sand and gravel deposits commonly are the results of the weathering of bedrock and subsequent transportation and deposition of the material by water or ice (glaciers). As such, they commonly occur as river or stream deposits or in glaciated areas as glaciofluvial and other deposits. Crushed stone aggregates are derived from a wide variety of parent bedrock materials. Limestone and other carbonates account for approximately three quarters of the rocks used for crushed stone, with granite and other igneous rocks making up the bulk of the remainder. Limestone deposits are widespread throughout the Central and Eastern United States and are scattered in the West. Granites are widely distributed in the Eastern and Western United States, with few exposures in the Midwest. Igneous rocks (excluding granites) are largely concentrated in the Western United States and in a few isolated localities in the East. Even though natural aggregates are widely distributed throughout the United States, they are not universally available for consumptive use. Some areas are devoid of sand and gravel, and potential sources of crushed stone may be covered with sufficient unconsolidated material to make surface mining impractical. In some areas many aggregates do not meet the physical property requirements for certain uses, or they may contain mineral constituents that react

  17. Comparison of gene expression profiles induced by coarse, fine, and ultrafile particulate matter

    EPA Science Inventory

    Coarse, fine, and ultrafine particulate matter (PM) fractions possess different physical properties and chemical compositions and may produce different adverse health effects. Studies were undertaken to determine whether or not gene expression patterns may be used to discriminate...

  18. Coarse-grained description of polymer blends as chains of interacting soft particles

    NASA Astrophysics Data System (ADS)

    Walton, Kevin; Guenza, Marina

    We present an analytic pair potential in a coarse grain description of a polymer blend where each chain is represented as a chain of soft-colloidal particles. This coarse grain model is based on integral theory that can represent the chains at variable levels.The particles have soft repulsion at separation less than the size of each coarse grain unit and a long repulsive tail with small attractive portion. While the short range pieces of the potential dominates the liquid structure, the long range tail dominate the thermodynamics of the system. So an accurate potential in both the short and long range distances is need to keep give correct structure and thermodynamical properties in the coarse grain description.

  19. Coarse alignment of thin-shell, segmented mirrors for Wolter-I telescopes

    NASA Astrophysics Data System (ADS)

    Donovan, Benjamin D.; Hertz, Edward; Marquez, Vanessa; McMuldroch, Stuart; Reid, Paul B.; Allured, Ryan

    2015-09-01

    The alignment of thin-shell, segmented mirrors for Wolter-I telescopes frequently involves the use of a Hartmann test. In order to get optical throughput in the Hartmann test, the mirrors must first be coarsely aligned to one another and to the metrology system. In the past, the coarse alignment of these mirrors at the Smithsonian Astrophysical Observatory has largely relied upon component machine tolerances and contact measurements with a coordinate measurement machine (CMM). This process takes time and does not produce reliable nor repeatable results. Thus, methods were developed to allow for the quick and reliable coarse alignment of thin- shell, segmented mirrors at their final locations in the mirror assembly. We present the coarse alignment system developed at the Smithsonian Astrophysical Observatory and its use in the alignment of thin-shell, segmented mirrors for the adjustable X-ray optics program.

  20. Recycling ground granulated blast furnace slag as cold bonded artificial aggregate partially used in self-compacting concrete.

    PubMed

    Gesoğlu, Mehmet; Güneyisi, Erhan; Mahmood, Swara Fuad; Öz, Hatice Öznur; Mermerdaş, Kasım

    2012-10-15

    Ground granulated blast furnace slag (GGBFS), a by-product from iron industry, was recycled as artificial coarse aggregate through cold bonding pelletization process. The artificial slag aggregates (ASA) replaced partially the natural coarse aggregates in production of self-compacting concrete (SCC). Moreover, as being one of the most widely used mineral admixtures in concrete industry, fly ash (FA) was incorporated as a part of total binder content to impart desired fluidity to SCCs. A total of six concrete mixtures having various ASA replacement levels (0%, 20%, 40%, 60%, and 100%) were designed with a water-to-binder (w/b) ratio of 0.32. Fresh properties of self-compacting concretes (SCC) were observed through slump flow time, flow diameter, V-funnel flow time, and L-box filling height ratio. Compressive strength of hardened SCCs was also determined at 28 days of curing. It was observed that increasing the replacement level of ASA resulted in decrease in the amount of superplasticizer to achieve a constant slump flow diameter. Moreover, passing ability and viscosity of SCC's enhanced with increasing the amount of ASA in the concrete. The maximum compressive strength was achieved for the SCC having 60% ASA replacement. PMID:22951223

  1. Aggregation server for grid-integrated vehicles

    SciTech Connect

    Kempton, Willett

    2015-05-26

    Methods, systems, and apparatus for aggregating electric power flow between an electric grid and electric vehicles are disclosed. An apparatus for aggregating power flow may include a memory and a processor coupled to the memory to receive electric vehicle equipment (EVE) attributes from a plurality of EVEs, aggregate EVE attributes, predict total available capacity based on the EVE attributes, and dispatch at least a portion of the total available capacity to the grid. Power flow may be aggregated by receiving EVE operational parameters from each EVE, aggregating the received EVE operational parameters, predicting total available capacity based on the aggregated EVE operational parameters, and dispatching at least a portion of the total available capacity to the grid.

  2. Multiscale simulation of red blood cell aggregation

    NASA Astrophysics Data System (ADS)

    Bagchi, P.; Popel, A. S.

    2004-11-01

    In humans and other mammals, aggregation of red blood cells (RBC) is a major determinant to blood viscosity in microcirculation under physiological and pathological conditions. Elevated levels of aggregation are often related to cardiovascular diseases, bacterial infection, diabetes, and obesity. Aggregation is a multiscale phenomenon that is governed by the molecular bond formation between adjacent cells, morphological and rheological properties of the cells, and the motion of the extra-cellular fluid in which the cells circulate. We have developed a simulation technique using front tracking methods for multiple fluids that includes the multiscale characteristics of aggregation. We will report the first-ever direct computer simulation of aggregation of deformable cells in shear flows. We will present results on the effect of shear rate, strength of the cross-bridging bonds, and the cell rheological properties on the rolling motion, deformation and subsequent breakage of an aggregate.

  3. Waves and aggregation patterns in myxobacteria

    NASA Astrophysics Data System (ADS)

    Igoshin, Oleg A.; Welch, Roy; Kaiser, Dale; Oster, George

    2004-03-01

    Under starvation conditions, a population of myxobacteria aggregates to build a fruiting body whose shape is species-specific and within which the cells sporulate. Early in this process, cells often pass through a "ripple phase" characterized by traveling linear, concentric, and spiral waves. These waves are different from the waves observed during slime mold aggregation that depend on diffusible morphogens, because myxobacteria communicate by direct contact. The difference is most dramatic when waves collide: rather than annihilating one another, myxobacterial waves appear to pass through one another unchanged. Under certain conditions, the spacing and location of the nascent fruiting bodies is determined by the wavelength and pattern of the waves. Later in fruiting body development, waves are replaced by streams of cells that circulate around small initial aggregates enlarging and rounding them. Still later, pairs of motile aggregates coalesce to form larger aggregates that develop into fruiting bodies. Here we present a mathematical model that quantitatively explains these wave and aggregation phenomena.

  4. A dimension map for molecular aggregates.

    PubMed

    Jian, Cuiying; Tang, Tian; Bhattacharjee, Subir

    2015-05-01

    A pair of gyradius ratios, defined from the principal radii of gyration, are used to generate a dimension map that describes the geometry of molecular aggregates in water and in organic solvents. Molecular dynamics simulations were performed on the aggregation of representative biomolecules and polyaromatic compounds to demonstrate application of the dimension map. It was shown that molecular aggregate data on the dimension map were bounded by two boundary curves, and that the map could be separated into three regions representing three groups of structures: one-dimensional rod-like structures; two-dimensional planar structures or short-cylinder-like structures; and three-dimensional sphere-like structures. Examining the location of the aggregates on the dimension map and how the location changes with solvent type and solute material parameter provides a simple yet effective way to infer the aggregation manner and to study solubility and mechanism of aggregation. PMID:25768393

  5. Impact of coarse-grained measurement with finite range on continuous-variable quantum key distribution

    NASA Astrophysics Data System (ADS)

    Wang, Tianyi; Yu, Song; Gu, Wanyi

    2016-03-01

    In continuous-variable quantum key distribution, detectors are necessarily coarse grained and of finite range. We analyze the impact of both features and demonstrate that while coarse graining adds a fixed error to the estimated excess noise, finite range degrades the estimation accuracy of both transmission and excess noise. Moreover, the inaccurate estimation due to finite range may results in secret key rate underestimation, even misjudgment of security. To compensate these consequences, tuning the modulation variance is a possible way.

  6. Properties of concrete with tire derived aggregate and crumb rubber as a lighthweight substitute for mineral aggregates in the concrete mix

    NASA Astrophysics Data System (ADS)

    Siringi, Gideon Momanyi

    Scrap tires continue to be a nuisance to the environment and this research proposes one way of recycling them as a lightweight aggregate which can substitute for mineral aggregates in concrete. Aggregates derived from scrap tires are often referred to as Tire Derived Aggregate (TDA). First, the focus is how much mineral aggregate can be replaced by these waste tires and how the properties of concrete are affected with the introduction of rubber. This is being mindful of the fact that for a new material to be acceptable as an engineering material, its properties and behavior has to be well understood, the materials must perform properly and be acceptable to the regulating agencies. The role played by the quantity of TDA and Crumb Rubber replacing coarse aggregate and fine aggregate respectively as well as different treatment and additives in concrete on its properties are examined. Conventional concrete (without TDA) and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, Splitting Tensile Strength based on ASTM C496, Modulus of Rupture (flexural strength) based on ASTM C78 and Bond strength of concrete developed with reinforcing steel based on ASTM C234.Through stress-strain plots, the rubberized concrete is compared in terms of change in ductility, toughness and Elastic Modulus. Results indicate that while replacement of mineral aggregates with TDA results in reduction in compressive strength, this may be mitigated by addition of silica fume or using a smaller size of TDA to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product with lower density while utilizing recycled TDA. From the results, it is observed that 7-10% of weight of mineral aggregates can be replaced by an equal volume of TDA to produce concrete with compressive strength of up to 4000 psi (27.5 MPa). Rubberized concrete would have higher ductility and toughness with

  7. Nanoarchitectonics of Molecular Aggregates: Science and Technology

    SciTech Connect

    Ramanathan, Nathan Muruganathan; Hong, Kunlun; Ji, Dr. Qingmin; Hill, Dr. Jonathan P; Ariga, Katsuhiko; Yusuke, Yonamine

    2014-01-01

    The field of making, studying and using molecular aggregates, in which the individual molecules (monomers) are arranged in a regular fashion, has come a long way. Taking control over the aggregation of small molecules and polymers in bulk, on surfaces and at interfaces pose a considerable challenge for their utilization in modern high tech applications. In this review we provide a detailed insight into recent trends in molecular aggregates from the perspectives of nanoarchitectonics.

  8. Diffusion Limited Aggregation: Algorithm optimization revisited

    NASA Astrophysics Data System (ADS)

    Braga, F. L.; Ribeiro, M. S.

    2011-08-01

    The Diffusion Limited Aggregation (DLA) model developed by Witten and Sander in 1978 is useful in modeling a large class of growth phenomena with local dependence. Besides its simplicity this aggregation model has a complex behavior that can be observed at the patterns generated. We propose on this work a brief review of some important proprieties of this model and present an algorithm to simulate a DLA aggregates that simpler and efficient compared to others found in the literature.

  9. Systematic and Simulation-Free Coarse-Graining of Polymer Melts using Soft Potentials

    NASA Astrophysics Data System (ADS)

    Yang, Delian; Wang, Qiang

    2014-03-01

    Full atomistic simulations of multi-chain systems are not feasible at present due to their formidable computational requirements. Molecular simulations with coarse-grained models have to be used instead, where each segment represents, for example, the center-of-mass of a group of atoms or real monomers. While atoms interact with hard excluded-volume interactions (e.g., the Lennard-Jones potential) and cannot overlap, the coarse-grained segments can certainly overlap and should therefore interact with soft potentials that allow complete particle overlapping. Coarse-grained models, however, reduce the chain conformational entropy, which plays an essential role in the behavior of polymeric systems. In this work, we use integral-equation theories, instead of molecular simulations, to perform both the structure-based and relative-entropy-based coarse-graining of homopolymer melts, and systematically examine how the coarse-grained soft potential varies with N (the number of segments on each chain) and how well the coarse-grained models reproduce both the structural and thermodynamic properties of the original system. This provides us with a quantitative basis for choosing small N-values that can still capture the chain conformational entropy, a characteristics of polymers.

  10. YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models.

    PubMed

    Tan, Robert K Z; Petrov, Anton S; Harvey, Stephen C

    2006-05-01

    Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently and some models need customized versions of the standard molecular mechanics methods. The most flexible way to meet these diverse needs is to provide access to internal data structures and a programming language to manipulate these structures. We have created YUP, a general-purpose program for coarse-grained and multi-scaled models. YUP extends the Python programming language by adding new data types. We have then used the extended language to implement three classes of coarse-grained models. The coarse-grained RNA model type is an unusual non-linear polymer and the assembly was easily handled with a simple program. The molecular dynamics algorithm had to be extended for a coarse-grained DNA model so that it could detect a failure that is invisible to a standard implementation. A third model type took advantage of access to the force field to simulate the packing of DNA in viral capsid. We find that objects are easy to modify, extend and redeploy. Thus, new classes of coarse-grained models can be implemented easily. PMID:22844233

  11. Systematic coarse-graining of the wormlike chain model for dynamic simulations

    NASA Astrophysics Data System (ADS)

    Koslover, Elena; Spakowitz, Andrew

    2014-03-01

    One of the key goals of macromolecular modeling is to elucidate how macroscale physical properties arise from the microscale behavior of the polymer constituents. For many biological and industrial applications, a direct simulation approach is impractical due to to the wide range of length and time scales that must be spanned by the model, necessitating physically sound and practically relevant procedures for coarse-graining polymer systems. We present a highly general systematic coarse-graining procedure that maps any detailed polymer model onto effective elastic-chain models at intermediate and large length scales, and we specifically focus on the wormlike chain model of semiflexible polymers. Our approach defines a continuous flow of coarse-grained models starting from the wormlike chain model, proceeding through an intermediate-scale stretchable, shearable wormlike chain, and finally resolving to a Gaussian chain at the longest lengths. Using Brownian dynamic simulations of our coarse grained polymer, we show that this approach to coarse graining the wormlike chain model captures analytical predictions for stress relaxation in a semiflexible polymer. Since we can arbitrarily coarse grain the polymer in these dynamic simulations, our approach greatly accelerates simulations.

  12. Immunogenicity of therapeutic proteins: Influence of aggregation

    PubMed Central

    Derrick, Jeremy P.; Dearman, Rebecca J.; Kimber, Ian

    2014-01-01

    The elicitation of anti-drug antibodies (ADA) against biotherapeutics can have detrimental effects on drug safety, efficacy, and pharmacokinetics. The immunogenicity of biotherapeutics is, therefore, an important issue. There is evidence that protein aggregation can result in enhanced immunogenicity; however, the precise immunological and biochemical mechanisms responsible are poorly defined. In the context of biotherapeutic drug development and safety assessment, understanding the mechanisms underlying aggregate immunogenicity is of considerable interest. This review provides an overview of the phenomenon of protein aggregation, the production of unwanted aggregates during bioprocessing, and how the immune response to aggregated protein differs from that provoked by non-aggregated protein. Of particular interest is the nature of the interaction of aggregates with the immune system and how subsequent ADA responses are induced. Pathways considered here include ‘classical’ activation of the immune system involving antigen presenting cells and, alternatively, the breakdown of B-cell tolerance. Additionally, methods available to screen for aggregation and immunogenicity will be described. With an increased understanding of aggregation-enhanced immune responses, it may be possible to develop improved manufacturing and screening processes to avoid, or at least reduce, the problems associated with ADA. PMID:23919460

  13. Microbial aggregates in anaerobic wastewater treatment.

    PubMed

    Kosaric, N; Blaszczyk, R

    1990-01-01

    The phenomenon aggregation of anaerobic bacteria gives an opportunity to speed up the digestion rate during methanogenesis. The aggregates are mainly composed of methanogenic bacteria which convert acetate and H2/CO2 into methane. Other bacteria are also included in the aggregates but their concentration is rather small. The aggregates may also be formed during acetogenesis or even hydrolysis but such aggregates are not stable and disrupt quickly when not fed. A two stage process seems to be suitable when high concentrated solid waste must be treated. Special conditions are necessary to promote aggregate formation from methanogenic bacteria but aggregates once formed are stable without feeding even for a few years. The structure, texture and activity of bacterial aggregates depend on several parameters: (1)--temperature and pH, (2)--wastewater composition and (3)--hydrodynamic conditions within the reactor. The common influence of all these parameters is still rather unknown but some recommendations may be given. Temperature and pH should be maintained in the range which is optimal for methanogenic bacteria e.g. a temperature between 32 and 50 degrees C and a value pH between 6.5 and 7.5. Wastewaters should contain soluble wastes and the specific loading rate should be around one kgCOD(kgVSS)-1 d-1. The concentration of the elements influences aggregate composition and probably structure and texture. At high calcium concentration a change in the colour of the granules has been observed. Research is necessary to investigate the influence of other elements and organic toxicants on maintenance of the aggregates. Hydrodynamic conditions seem to influence the stability of the granules over long time periods. At low liquid stream rates, aggregates may starve and lysis within the aggregates is possible which results in hollowing of aggregates and their floating. At high liquid stream rates the aggregates may be disrupted and washed out of the reactor as a flocculent

  14. Bouncing behavior of microscopic dust aggregates

    NASA Astrophysics Data System (ADS)

    Seizinger, A.; Kley, W.

    2013-03-01

    Context. Bouncing collisions of dust aggregates within the protoplanetary disk may have a significant impact on the growth process of planetesimals. Yet, the conditions that result in bouncing are not very well understood. Existing simulations studying the bouncing behavior used aggregates with an artificial, very regular internal structure. Aims: Here, we study the bouncing behavior of sub-mm dust aggregates that are constructed applying different sample preparation methods. We analyze how the internal structure of the aggregate alters the collisional outcome and we determine the influence of aggregate size, porosity, collision velocity, and impact parameter. Methods: We use molecular dynamics simulations where the individual aggregates are treated as spheres that are made up of several hundred thousand individual monomers. The simulations are run on graphic cards (GPUs). Results: Statistical bulk properties and thus bouncing behavior of sub-mm dust aggregates depend heavily on the preparation method. In particular, there is no unique relation between the average volume filling factor and the coordination number of the aggregate. Realistic aggregates bounce only if their volume filling factor exceeds 0.5 and collision velocities are below 0.1 ms-1. Conclusions: For dust particles in the protoplanetary nebula we suggest that the bouncing barrier may not be such a strong handicap in the growth phase of dust agglomerates, at least in the size range of ≈100 μm.

  15. A competitive aggregation model for flash nanoprecipitation.

    PubMed

    Cheng, Janine Chungyin; Vigil, R D; Fox, R O

    2010-11-15

    Flash NanoPrecipitation (FNP) is a novel approach for producing functional nanoparticles stabilized by amphiphilic block copolymers. FNP involves the rapid mixing of a hydrophobic active (organic) and an amphiphilic di-block copolymer with a non-solvent (water) and subsequent co-precipitation of nanoparticles composed of both the organic and copolymer. During this process, the particle size distribution (PSD) is frozen and stabilized by the hydrophilic portion of the amphiphilic di-block copolymer residing on the particle surface. That is, the particle growth is kinetically arrested and thus a narrow PSD can be attained. To model the co-precipitation process, a bivariate population balance equation (PBE) has been formulated to account for the competitive aggregation of the organic and copolymer versus pure organic-organic or copolymer-copolymer aggregation. Aggregation rate kernels have been derived to account for the major aggregation events: free coupling, unimer insertion, and aggregate fusion. The resulting PBE is solved both by direct integration and by using the conditional quadrature method of moments (CQMOM). By solving the competitive aggregation model under well-mixed conditions, it is demonstrated that the PSD is controlled primarily by the copolymer-copolymer aggregation process and that the energy barrier to aggregate fusion plays a key role in determining the PSD. It is also shown that the characteristic aggregation times are smaller than the turbulent mixing time so that the FNP process is always mixing limited. PMID:20800847

  16. Deterministic aggregation kinetics of superparamagnetic colloidal particles

    NASA Astrophysics Data System (ADS)

    Reynolds, Colin P.; Klop, Kira E.; Lavergne, François A.; Morrow, Sarah M.; Aarts, Dirk G. A. L.; Dullens, Roel P. A.

    2015-12-01

    We study the irreversible aggregation kinetics of superparamagnetic colloidal particles in two dimensions in the presence of an in-plane magnetic field at low packing fractions. Optical microscopy and image analysis techniques are used to follow the aggregation process and in particular study the packing fraction and field dependence of the mean cluster size. We compare these to the theoretically predicted scalings for diffusion limited and deterministic aggregation. It is shown that the aggregation kinetics for our experimental system is consistent with a deterministic mechanism, which thus shows that the contribution of diffusion is negligible.

  17. Neuronal aggregates: formation, clearance and spreading

    PubMed Central

    Lim, Junghyun; Yue, Zhenyu

    2015-01-01

    Summary Proteostasis is maintained by multiple cellular pathways, including protein synthesis, quality control and degradation. An imbalance of neuronal proteostasis, associated with protein misfolding and aggregation, leads to proteinopathies or neurodegeneration. While genetic variations and protein modifications contribute to aggregate formation, components of the proteostasis network dictate the fate of protein aggregates. Here we provide an overview of proteostasis pathways and their interplay (particularly autophagy) with the metabolism of disease-related proteins. We review recent studies on neuronal activity-mediated regulation of proteostasis and transcellular propagation of protein aggregates in the nervous system. Targeting proteostasis pathways therapeutically remains an attractive but challenging task. PMID:25710535

  18. Spatial and Temporal Variability of Outdoor Coarse Particulate Matter Mass Concentrations Measured with a New Coarse Particulate Sampler during the Detroit Exposure and Aerosol Research Study

    EPA Science Inventory

    The Detroit Exposure and Aerosol Research Study (DEARS) provided data to compare outdoor residential coarse particulate matter (PM10-2.5) concentrations in six different areas of Detroit with data from a central monitoring site. Daily and seasonal influences on the spa...

  19. Collisional Aggregation Due to Turbulence

    NASA Astrophysics Data System (ADS)

    Pumir, Alain; Wilkinson, Michael

    2016-03-01

    Collisions between particles suspended in a fluid play an important role in many physical processes. As an example, collisions of microscopic water droplets in clouds are a necessary step in the production of macroscopic raindrops. Collisions of dust grains are also conjectured to be important for planet formation in the gas surrounding young stars and to play a role in the dynamics of sand storms. In these processes, collisions are favored by fast turbulent motions. Here we review recent advances in the understanding of collisional aggregation due to turbulence. We discuss the role of fractal clustering of particles and caustic singularities of their velocities. We also discuss limitations of the Smoluchowski equation for modeling such processes. These advances lead to a semiquantitative understanding on the influence of turbulence on collision rates and point to deficiencies in the current understanding of rainfall and planet formation.

  20. Swarms: Optimum aggregations of spacecraft

    NASA Technical Reports Server (NTRS)

    Mayer, H. L.

    1980-01-01

    Swarms are aggregations of spacecraft or elements of a space system which are cooperative in function, but physically isolated or only loosely connected. For some missions the swarm configuration may be optimum compared to a group of completely independent spacecraft or a complex rigidly integrated spacecraft or space platform. General features of swarms are induced by considering an ensemble of 26 swarms, examples ranging from Earth centered swarms for commercial application to swarms for exploring minor planets. A concept for a low altitude swarm as a substitute for a space platform is proposed and a preliminary design studied. The salient design feature is the web of tethers holding the 30 km swarm in a rigid two dimensional array in the orbital plane. A mathematical discussion and tutorial in tether technology and in some aspects of the distribution of services (mass, energy, and information to swarm elements) are included.

  1. Aggregate Remote Memory Copy Interface

    Energy Science and Technology Software Center (ESTSC)

    2006-02-23

    The purpose of the Aggregate Remote Memory Copy (ARMCI) library is to provide a general- purpose, efficient, and Widely portable remote memory access (RMA) operations (one-sided communication) optimized for Contiguous and noncontiguous (strided, scatter/gather, I/O vector) data transfers. In addition, ARMCI includes a set of atomic and mutual exclusion operations. The development ARMCI is driven by the need to support the global-addres space communication model in context of distributed regular or irregular distributed data structures,more » communication libraries, and compilers. ARMCI is a standalone system that could be used to support user-level libraries and applications that use MPI or PVM.« less

  2. Morphological classification of nanoceramic aggregates

    NASA Astrophysics Data System (ADS)

    Crosta, Giovanni F.; Kang, Bongwoo; Ospina, Carolina; Sung, Changmo

    2005-01-01

    Aluminum silicate nanoaggregates grown at near-room temperature on an organic template under a variety of experimental conditions have been imaged by transmission electron microscopy. Images have been automatically classified by an algorithm based on "spectrum enhancement", multivariate statistics and supervised optimization. Spectrum enhancement consists of subtracting, in the log scale, a known function of wavenumber from the angle averaged power spectral density of the image. Enhanced spectra of each image, after polynomial interpolation, have been regarded as morphological descriptors and as such submitted to principal components analysis nested with a multiobjective parameter optimization algorithm. The latter has maximized pairwise discrimination between classes of materials. The role of the organic template and of a reaction parameter on aggregate morphology has been assessed at two magnification scales. Classification results have also been related to crystal structure data derived from selected area electron diffraction patterns.

  3. Colloidal aggregation in polymer blends.

    PubMed

    Benhamou, M; Ridouane, H; Hachem, E-K; Derouiche, A; Rahmoune, M

    2005-06-22

    We consider here a low-density assembly of colloidal particles immersed in a critical polymer mixture of two chemically incompatible polymers. We assume that, close to the critical point of the free mixture, the colloids prefer to be surrounded by one polymer (critical adsorption). As result, one is assisted to a reversible colloidal aggregation in the nonpreferred phase, due the existence of a long-range attractive Casimir force between particles. This aggregation is a phase transition driving the colloidal system from dilute to dense phases, as the usual gas-liquid transition. We are interested in a quantitative investigation of the phase diagram of the immersed colloids. We suppose that the positions of particles are disordered, and the disorder is quenched and follows a Gaussian distribution. To apprehend the problem, use is made of the standard phi(4) theory, where the field phi represents the composition fluctuation (order parameter), combined with the standard cumulant method. First, we derive the expression of the effective free energy of colloids and show that this is of Flory-Huggins type. Second, we find that the interaction parameter u between colloids is simply a linear combination of the isotherm compressibility and specific heat of the free mixture. Third, with the help of the derived effective free energy, we determine the complete shape of the phase diagram (binodal and spinodal) in the (Psi,u) plane, with Psi as the volume fraction of immersed colloids. The continuous "gas-liquid" transition occurs at some critical point K of coordinates (Psi(c) = 0.5,u(c) = 2). Finally, we emphasize that the present work is a natural extension of that, relative to simple liquid mixtures incorporating colloids. PMID:16035822

  4. Detergent-mediated protein aggregation

    PubMed Central

    Neale, Chris; Ghanei, Hamed; Holyoake, John; Bishop, Russell E.; Privé, Gilbert G.; Pomès, Régis

    2016-01-01

    Because detergents are commonly used to solvate membrane proteins for structural evaluation, much attention has been devoted to assessing the conformational bias imparted by detergent micelles in comparison to the native environment of the lipid bilayer. Here, we conduct six 500-ns simulations of a system with >600,000 atoms to investigate the spontaneous self assembly of dodecylphosphocholine detergent around multiple molecules of the integral membrane protein PagP. This detergent formed equatorial micelles in which acyl chains surround the protein’s hydrophobic belt, confirming existing models of the detergent solvation of membrane proteins. In addition, unexpectedly, the extracellular and periplasmic apical surfaces of PagP interacted with the headgroups of detergents in other micelles 85 and 60% of the time, respectively, forming complexes that were stable for hundreds of nanoseconds. In some cases, an apical surface of one molecule of PagP interacted with an equatorial micelle surrounding another molecule of PagP. In other cases, the apical surfaces of two molecules of PagP simultaneously bound a neat detergent micelle. In these ways, detergents mediated the non-specific aggregation of folded PagP. These simulation results are consistent with dynamic light scattering experiments, which show that, at detergent concentrations ≥600 mM, PagP induces the formation of large scattering species that are likely to contain many copies of the PagP protein. Together, these simulation and experimental results point to a potentially generic mechanism of detergent-mediated protein aggregation. PMID:23466535

  5. Impact of Particle Aggregation on Nanoparticle Reactivity

    NASA Astrophysics Data System (ADS)

    Jassby, David

    2011-12-01

    The prevalence of nanoparticles in the environment is expected to grow in the coming years due to their increasing pervasiveness in consumer and industrial applications. Once released into the environment, nanoparticles encounter conditions of pH, salinity, UV light, and other solution conditions that may alter their surface characteristics and lead to aggregation. The unique properties that make nanoparticles desirable are a direct consequence of their size and increased surface area. Therefore, it is critical to recognize how aggregation alters the reactive properties of nanomaterials, if we wish to understand how these properties are going to behave once released into the environment. The size and structure of nanoparticle aggregates depend on surrounding conditions, including hydrodynamic ones. Depending on these conditions, aggregates can be large or small, tightly packed or loosely bound. Characterizing and measuring these changes to aggregate morphology is important to understanding the impact of aggregation on nanoparticle reactive properties. Examples of decreased reactivity due to aggregation include the case where tightly packed aggregates have fewer available surface sites compared to loosely packed ones; also, photocatalytic particles embedded in the center of large aggregates will experience less light when compared to particles embedded in small aggregates. However, aggregation also results in an increase in solid-solid interfaces between nanoparticles. This can result in increased energy transfer between neighboring particles, surface passivation, and altered surface tension. These phenomena can lead to an increase in reactivity. The goal of this thesis is to examine the impacts of aggregation on the reactivity of a select group of nanomaterials. Additionally, we examined how aggregation impacts the removal efficiency of fullerene nanoparticles using membrane filtration. The materials we selected to study include ZnS---a metal chalcogenide

  6. Principal role of the stepwise aggregation mechanism in ionic surfactant solutions near the critical micelle concentration. Molecular dynamics study.

    PubMed

    Burov, Stanislav V; Vanin, Alexandr A; Brodskaya, Elena N

    2009-08-01

    The validity of the assumption on the predominant contribution of the stepwise processes to the ionic micelle formation/destruction in the vicinity of critical micelle concentration was investigated by molecular dynamics simulation. A coarse-grained model was used to describe the surfactant/water mixture. The cluster size distribution was estimated directly from molecular dynamics simulations or obtained from a reduced set of kinetic equations. The good agreement between two approaches shows that the neglect of the terms responsible for cluster fusion/fission is fully justified and that such processes are less important than stepwise aggregation. PMID:19591445

  7. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... other activities and actions. (See 40 CFR 1508.25(a)). (2) Consider reasonable alternative courses of... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification §...

  8. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... other activities and actions. (See 40 CFR 1508.25(a)). (2) Consider reasonable alternative courses of... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification §...

  9. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... other activities and actions. (See 40 CFR 1508.25(a)). (2) Consider reasonable alternative courses of... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification §...

  10. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... other activities and actions. (See 40 CFR 1508.25(a)). (2) Consider reasonable alternative courses of... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Project aggregation. 58.32 Section... Environmental Review Process: Documentation, Range of Activities, Project Aggregation and Classification §...

  11. 7 CFR 1.6 - Aggregating requests.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 1 2010-01-01 2010-01-01 false Aggregating requests. 1.6 Section 1.6 Agriculture Office of the Secretary of Agriculture ADMINISTRATIVE REGULATIONS Official Records § 1.6 Aggregating requests. When an agency reasonably believes that a requester, or a group of requesters acting in...

  12. 7 CFR 1.6 - Aggregating requests.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 1 2013-01-01 2013-01-01 false Aggregating requests. 1.6 Section 1.6 Agriculture Office of the Secretary of Agriculture ADMINISTRATIVE REGULATIONS Official Records § 1.6 Aggregating requests. When an agency reasonably believes that a requester, or a group of requesters acting in...

  13. Streaming instability of aggregating slime mold amoebae

    NASA Astrophysics Data System (ADS)

    Levine, Herbert; Reynolds, William

    1991-05-01

    We propose a new model of aggregation in the cellular slime mold D. Discoideum. Our approach couples the excitable signaling system to amoeba chemotaxis; the resultant system of equations is tractable to analytical and numerical approaches. Using our model, we derive the existence of a streaming instability for the concentric target aggregation pattern.

  14. Choosing Aggregation Rules for Composite Indicators

    ERIC Educational Resources Information Center

    Munda, Giuseppe

    2012-01-01

    From a formal point of view, a composite indicator is an aggregate of all dimensions, objectives, individual indicators and variables used for its construction. This implies that what defines a composite indicator is the set of properties underlying its mathematical aggregation convention. In this article, I try to revise the theoretical debate on…

  15. Biomass round bales infield aggregation logistic scenarios

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biomass bales often need to be aggregated (collected into groups and transported) to a field-edge stack for temporary storage for feedlots or processing facilities. Aggregating the bales with the least total distance involved is a goal of producers and bale handlers. Several logistics scenarios for ...

  16. 24 CFR 50.21 - Aggregation.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Aggregation. 50.21 Section 50.21 Housing and Urban Development Office of the Secretary, Department of Housing and Urban Development... Aggregation. Activities which are geographically related and are logical parts of a composite of...

  17. 42 CFR 411.106 - Aggregation rules.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 2 2010-10-01 2010-10-01 false Aggregation rules. 411.106 Section 411.106 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES MEDICARE PROGRAM... Under Group Health Plans: General Provisions § 411.106 Aggregation rules. The following rules apply...

  18. Teaching Aggregate Demand and Supply Models

    ERIC Educational Resources Information Center

    Wells, Graeme

    2010-01-01

    The author analyzes the inflation-targeting model that underlies recent textbook expositions of the aggregate demand-aggregate supply approach used in introductory courses in macroeconomics. He shows how numerical simulations of a model with inflation inertia can be used as a tool to help students understand adjustments in response to demand and…

  19. Biology of the Coarse Aerosol Mode: Insights Into Urban Aerosol Ecology

    NASA Astrophysics Data System (ADS)

    Dueker, E.; O'Mullan, G. D.; Montero, A.

    2015-12-01

    Microbial aerosols have been understudied, despite implications for climate studies, public health, and biogeochemical cycling. Because viable bacterial aerosols are often associated with coarse aerosol particles, our limited understanding of the coarse aerosol mode further impedes our ability to develop models of viable bacterial aerosol production, transport, and fate in the outdoor environment, particularly in crowded urban centers. To address this knowledge gap, we studied aerosol particle biology and size distributions in a broad range of urban and rural settings. Our previously published findings suggest a link between microbial viability and local production of coarse aerosols from waterways, waste treatment facilities, and terrestrial systems in urban and rural environments. Both in coastal Maine and in New York Harbor, coarse aerosols and viable bacterial aerosols increased with increasing wind speeds above 4 m s-1, a dynamic that was observed over time scales ranging from minutes to hours. At a New York City superfund-designated waterway regularly contaminated with raw sewage, aeration remediation efforts resulted in significant increases of coarse aerosols and bacterial aerosols above that waterway. Our current research indicates that bacterial communities in aerosols at this superfund site have a greater similarity to bacterial communities in the contaminated waterway with wind speeds above 4 m s-1. Size-fractionated sampling of viable microbial aerosols along the urban waterfront has also revealed significant shifts in bacterial aerosols, and specifically bacteria associated with coarse aerosols, when wind direction changes from onshore to offshore. This research highlights the key connections between bacterial aerosol viability and the coarse aerosol fraction, which is important in assessments of production, transport, and fate of bacterial contamination in the urban environment.

  20. Aggregate size distribution of the soil loss

    NASA Astrophysics Data System (ADS)

    Szabó, Judit Alexandra; Jakab, Gergely; Szabó, Boglárka; Józsa, Sándor; Szalai, Zoltán; Centeri, Csaba

    2016-04-01

    In agricultural areas the soil erosion and soil loss estimation is vital information in long-term planning. During the initial period of the erosion a part of the soil particles and aggregates get transportable and nutrients and organic matter could be transported due to the effect of water or wind. This preliminary phase was studied with laboratory-scale rainfall simulator. Developed surface crust and aggregate size composition of the runoff was examined in six different slope-roughness-moisture content combination of a Cambisol and a Regosol. The ratio of micro- and macro aggregates in the runoff indicate the stability of the aggregates and determine the transport capacity of the runoff. Both soil samples were taken from field where the water erosion is a potential hazard. During the experiment the whole amount of runoff and sediment was collected through sieve series to a bucket to separate the micro- and macro aggregates. In case of both samples the micro aggregates dominate in the runoff and the runoff rates are similar. Although the runoff of the Regosol - with dominant >1000μm macro aggregate content - contained almost nothing but <50μm sized micro aggregates. Meanwhile the runoff of the Cambisol - with more balanced micro and macro aggregate content - contained dominantly 50-250μm sized micro aggregates and in some case remarkable ratio 250-1000μm sized macro aggregates. This difference occurred because the samples are resistant against drop erosion differently. In case of both sample the selectivity of the erosion and substance matrix redistribution manifested in mineral crusts in the surface where the quartz deposited in place while the lighter organic matter transported with the sediment. The detachment of the aggregates and the redistribution of the particles highly effect on the aggregate composition of the runoff which is connected with the quality of the soil loss. So while the estimation of soil loss quantity is more or less is easy, measuring

  1. Crushed aggregates for roads and their properties for frost protection

    NASA Astrophysics Data System (ADS)

    Kuznetsova, Elena; Willy Danielsen, Svein

    2015-04-01

    of the road system. According to new specification; the size of large stones for this layer should be maximum 0.5 m (longest edge) or ½ layer thickness. And minimum 30% of stones should be less than 90 mm. Fines content (<0.063 mm) should be maximum 15% of the material less than 22.4 mm. Analysing these new requirements, several questions are arising. First of all how this materials size will affect heat exchange in the layer, secondly - if the allowable fines content will make the materials frost susceptible. For calculations of frost protection layer thickness the knowledge of thermal conductivity of the aggregate layers is required. Handbook for geotechnical investigations of the soils provides this data for natural gravel which is limited by 0.7 - 1.3 W/mK. But when it comes to the crushed rocks, it can be significantly increased due to the higher conductivity of minerals (especially if they contain high amount of quartz), as well as due to higher effective conductivity. In rock-fill materials, i.e. materials with large particles and low degree of saturation, convection and radiation are the predominant heat transfer mechanisms. Convection and radiation can increase the effective conductivity by factor 2-10. Lebeau and Konrad (2007) showed that convection heat transfer could lead to the formation of undesirable permafrost conditions in toe drains of embankment dams located in Northern Quebec, i.e. in areas where there are no naturally occurring permafrost soils. In a frost design method the required parameter values of crushed rock aggregates are thermal conductivity, density and water content. The heat transfer during the freezing of natural soils is assumed proportional to thermal conductivity of the material. In a coarse-grained material with abundant pore space, convective heat transfer and radiation may be a considerable factor, sometimes even more significant than conduction. Specifications used by pavement engineers in most countries are solely based on

  2. Therapeutic Protein Aggregation: Mechanisms, Design, and Control

    PubMed Central

    Roberts, Christopher J.

    2014-01-01

    While it is well known that proteins are only marginally stable in their folded states, it is often less well appreciated that most proteins are inherently aggregation-prone in their unfolded or partially unfolded states, and the resulting aggregates can be extremely stable and long-lived. For therapeutic proteins, aggregates are a significant risk factor for deleterious immune responses in patients, and can form via a variety of mechanisms. Controlling aggregation using a mechanistic approach may allow improved design of therapeutic protein stability, as a complement to existing design strategies that target desired protein structures and function. Recent results highlight the importance of balancing protein environment with the inherent aggregation propensities of polypeptide chains. PMID:24908382

  3. Formation of Tethers from Spreading Cellular Aggregates.

    PubMed

    Beaune, Grégory; Winnik, Françoise M; Brochard-Wyart, Françoise

    2015-12-01

    Membrane tubes are commonly extruded from cells and vesicles when a point-like force is applied on the membrane. We report here the unexpected formation of membrane tubes from lymph node cancer prostate (LNCaP) cell aggregates in the absence of external applied forces. The spreading of LNCaP aggregates deposited on adhesive glass substrates coated with fibronectin is very limited because cell-cell adhesion is stronger than cell-substrate adhesion. Some cells on the aggregate periphery are very motile and try to escape from the aggregate, leading to the formation of membrane tubes. Tethered networks and exchange of cargos between cells were observed as well. Growth of the tubes is followed by either tube retraction or tube rupture. Hence, even very cohesive cells are successful in escaping aggregates, which may lead to epithelial mesenchymal transition and tumor metastasis. We interpret the dynamics of formation and retraction of tubes in the framework of membrane mechanics. PMID:26509898

  4. Aggregation of sodium alkylbenzenesulfonates in aqueous solution

    SciTech Connect

    Magid, L.J.; Shaver, R.J.; Gulari, E.; Bedwell, B.; Alkhafaji, S.

    1981-01-01

    The surfactant 6 phenyl C/sub 12/SNa forms small spherical micelles in aqueous solution, having an aggregation number of 20 to 30 and a fractional charge of 0.45. These micelles are hydrated to the extent of approximately 18 moles H/sub 2/O per moles of surfactant. A second larger aggregate is also present in 6 phenyl C/sub 12/SNa solutions; its importance increases with solution age. Addition of NaCl causes both aggregates to apparently increase modestly in size. The surfactant 8 phenyl C/sub 16/SNa also contains both aggregates in its solutions; the larger one is relatively more important here. The larger aggregate does not correspond to dispersed bits of a liquid crystalline mesophase.

  5. Protein aggregates stimulate macropinocytosis facilitating their propagation.

    PubMed

    Yerbury, Justin J

    2016-03-01

    Temporal and spatial patterns of pathological changes such as loss of neurons and presence of pathological protein aggregates are characteristic of neurodegenerative diseases such as Amyotrophic Lateral Sclerosis, Frontotemporal Dementia, Alzheimer's disease and Parkinson's disease. These patterns are consistent with the propagation of protein misfolding and aggregation reminiscent of the prion diseases. There is a surge of evidence that suggests that large protein aggregates of a range of proteins are able to enter cells via macropinocytosis. Our recent work suggests that this process is activated by the binding of aggregates to the neuron cell surface. The current review considers the potential role of cell surface receptors in the triggering of macropinocytosis by protein aggregates and the possibility of utilizing macropinocytosis pathways as a therapeutic target. PMID:26963158

  6. Imbibition kinetics of spherical colloidal aggregates.

    PubMed

    Debacker, A; Makarchuk, S; Lootens, D; Hébraud, P

    2014-07-11

    The imbibition kinetics of a millimeter-sized aggregate of 300 nm diameter colloidal particles by a wetting pure solvent is studied. Three successive regimes are observed. First, the imbibition proceeds by compressing the air inside the aggregate. Next, the solvent stops when the pressure of the compressed air is equal to the excess of capillary pressure at the meniscus of the wetting solvent in the porous aggregate. The interface is pinned and the aggregate slowly degases up to the point where the pressure of the entrapped air stops decreasing and is controlled by the capillary pressure. Finally, the imbibition starts again at a constant excess of pressure, smaller than the capillary pressure but larger than the one of the atmosphere. This last stage leads to the complete infiltration of the aggregate. PMID:25062241

  7. Competitive aggregation dynamics using phase wave signals.

    PubMed

    Sakaguchi, Hidetsugu; Maeyama, Satomi

    2014-10-21

    Coupled equations of the phase equation and the equation of cell concentration n are proposed for competitive aggregation dynamics of slime mold in two dimensions. Phase waves are used as tactic signals of aggregation in this model. Several aggregation clusters are formed initially, and target patterns appear around the localized aggregation clusters. Owing to the competition among target patterns, the number of the localized aggregation clusters decreases, and finally one dominant localized pattern survives. If the phase equation is replaced with the complex Ginzburg-Landau equation, several spiral patterns appear, and n is localized near the center of the spiral patterns. After the competition among spiral patterns, one dominant spiral survives. PMID:24956327

  8. [The equation for platelet aggregation rate].

    PubMed

    Vrzheshch, P V; Verkhusha, V V; Varfolomeev, S D

    1990-01-01

    A platelet aggregation model in shear flow taking into account the kinetics of intercellular fibrinogen bond formation limited by aggregated platelets rotation time was considered. For this consideration the average duration of platelets interaction in flow with shear rate value G is shown to be pi/4G. One fibrinogen bond is sufficient to form a solid aggregate between two platelets. The equation for single platelets disappearance rate concerned with intercellular fibrinogen bond formation, stochastic character of bond distribution in collided platelets and hydrodynamically controlled interaction time was obtained. The Hill's approximation for the obtained aggregation rate dependences was suggested and appropriate constants were determined. The qualitative criterion of platelets aggregating systems behavior was introduced. PMID:2245229

  9. Excited-state dynamics of astaxanthin aggregates

    NASA Astrophysics Data System (ADS)

    Fuciman, Marcel; Durchan, Milan; Šlouf, Václav; Keşan, Gürkan; Polívka, Tomáš

    2013-05-01

    Astaxanthin forms three types of aggregates in hydrated dimethyl sulfoxide (DMSO). In DMSO/water ratio of 1:1, a red-shifted J-aggregate with maximum at 570 nm is generated, while a ratio of 1:9 produces blue-shifted H-aggregates with peaks at 386 nm (H1) and 460 nm (H2). Monomeric astaxanthin in DMSO has an S1 lifetime of 5.3 ps, but a long-lived (33 ps) S∗ signal was also identified. Aggregation changes the S1 lifetimes to 17 ps (H1), 30 ps (H2), and 14 ps (J). Triplet state of astaxanthin, most likely generated via singlet homofission, was observed in H1 and H2 aggregates.

  10. Reuse potential of low-calcium bottom ash as aggregate through pelletization.

    PubMed

    Geetha, S; Ramamurthy, K

    2010-01-01

    Coal combustion residues which include fly ash, bottom ash and boiler slag is one of the major pollutants as these residues require large land area for their disposal. Among these residues, utilization of bottom ash in the construction industry is very low. This paper explains the use of bottom ash through pelletization. Raw bottom ash could not be pelletized as such due to its coarseness. Though pulverized bottom ash could be pelletized, the pelletization efficiency was low, and the aggregates were too weak to withstand the handling stresses. To improve the pelletization efficiency, different clay and cementitious binders were used with bottom ash. The influence of different factors and their interaction effects were studied on the duration of pelletization process and the pelletization efficiency through fractional factorial design. Addition of binders facilitated conversion of low-calcium bottom ash into aggregates. To achieve maximum pelletization efficiency, the binder content and moisture requirements vary with type of binder. Addition of Ca(OH)(2) improved the (i) pelletization efficiency, (ii) reduced the duration of pelletization process from an average of 14-7 min, and (iii) reduced the binder dosage for a given pelletization efficiency. For aggregate with clay binders and cementitious binder, Ca(OH)(2) and binder dosage have significant effect in reducing the duration of pelletization process. PMID:20400282

  11. Classification and Characterization of Therapeutic Antibody Aggregates

    PubMed Central

    Joubert, Marisa K.; Luo, Quanzhou; Nashed-Samuel, Yasser; Wypych, Jette; Narhi, Linda O.

    2011-01-01

    A host of diverse stress techniques was applied to a monoclonal antibody (IgG2) to yield protein particles with varying attributes and morphologies. Aggregated solutions were evaluated for percent aggregation, particle counts, size distribution, morphology, changes in secondary and tertiary structure, surface hydrophobicity, metal content, and reversibility. Chemical modifications were also identified in a separate report (Luo, Q., Joubert, M. K., Stevenson, R., Narhi, L. O., and Wypych, J. (2011) J. Biol. Chem. 286, 25134–25144). Aggregates were categorized into seven discrete classes, based on the traits described. Several additional molecules (from the IgG1 and IgG2 subtypes as well as intravenous IgG) were stressed and found to be defined with the same classification system. The mechanism of protein aggregation and the type of aggregate formed depends on the nature of the stress applied. Different IgG molecules appear to aggregate by a similar mechanism under the same applied stress. Aggregates created by harsh mechanical stress showed the largest number of subvisible particles, and the class generated by thermal stress displayed the largest number of visible particles. Most classes showed a disruption of the higher order structure, with the degree of disorder depending on the stress process. Particles in all classes (except thermal stress) were at least partially reversible upon dilution in pH 5 buffer. High copper content was detected in isolated metal-catalyzed aggregates, a stress previously shown to produce immunogenic aggregates. In conclusion, protein aggregates can be a very heterogeneous population, whose qualities are the result of the type of stress that was experienced. PMID:21454532

  12. Predictors of coarse particulate matter and associated endotoxin concentrations in residential environments

    NASA Astrophysics Data System (ADS)

    Bari, Md. Aynul; MacNeill, Morgan; Kindzierski, Warren B.; Wallace, Lance; Héroux, Marie-Ève; Wheeler, Amanda J.

    2014-08-01

    Exposure to coarse particulate matter (PM), i.e., particles with an aerodynamic diameter between 2.5 and 10 μm (PM10-2.5), is of increasing interest due to the potential for health effects including asthma, allergy and respiratory symptoms. Limited information is available on indoor and outdoor coarse PM and associated endotoxin exposures. Seven consecutive 24-h samples of indoor and outdoor coarse PM were collected during winter and summer 2010 using Harvard Coarse Impactors in a total of 74 Edmonton homes where no reported smoking took place. Coarse PM filters were subsequently analyzed for endotoxin content. Data were also collected on indoor and outdoor temperature, relative humidity, air exchange rate, housing characteristics and occupants' activities. During winter, outdoor concentrations of coarse PM (median = 6.7 μg/m3, interquartile range, IQR = 3.4-12 μg/m3) were found to be higher than indoor concentrations (median 3.4 μg/m3, IQR = 1.6-5.7 μg/m3); while summer levels of indoor and outdoor concentrations were similar (median 4.5 μg/m3, IQR = 2.3-6.8 μg/m3, and median 4.7 μg/m3, IQR = 2.1-7.9 μg/m3, respectively). Similar predictors were identified for indoor coarse PM in both seasons and included corresponding outdoor coarse PM concentrations, whether vacuuming, sweeping or dusting was performed during the sampling period, and number of occupants in the home. Winter indoor coarse PM predictors also included the number of dogs and indoor endotoxin concentrations. Summer median endotoxin concentrations (indoor: 0.41 EU/m3, outdoor: 0.64 EU/m3) were 4-fold higher than winter concentrations (indoor: 0.12 EU/m3, outdoor: 0.16 EU/m3). Other than outdoor endotoxin concentrations, indoor endotoxin concentration predictors for both seasons were different. Winter endotoxin predictors also included presence of furry pets and whether the vacuum had a high efficiency particulate air (HEPA) filter. Summer endotoxin predictors were problems with mice in the

  13. The fractal aggregation of asphaltenes.

    PubMed

    Hoepfner, Michael P; Fávero, Cláudio Vilas Bôas; Haji-Akbari, Nasim; Fogler, H Scott

    2013-07-16

    This paper discusses time-resolved small-angle neutron scattering results that were used to investigate asphaltene structure and stability with and without a precipitant added in both crude oil and model oil. A novel approach was used to isolate the scattering from asphaltenes that are insoluble and in the process of aggregating from those that are soluble. It was found that both soluble and insoluble asphaltenes form fractal clusters in crude oil and the fractal dimension of the insoluble asphaltene clusters is higher than that of the soluble clusters. Adding heptane also increases the size of soluble asphaltene clusters without modifying the fractal dimension. Understanding the process of insoluble asphaltenes forming fractals with higher fractal dimensions will potentially reveal the microscopic asphaltene destabilization mechanism (i.e., how a precipitant modifies asphaltene-asphaltene interactions). It was concluded that because of the polydisperse nature of asphaltenes, no well-defined asphaltene phase stability envelope exists and small amounts of asphaltenes precipitated even at dilute precipitant concentrations. Asphaltenes that are stable in a crude oil-precipitant mixture are dispersed on the nanometer length scale. An asphaltene precipitation mechanism is proposed that is consistent with the experimental findings. Additionally, it was found that the heptane-insoluble asphaltene fraction is the dominant source of small-angle scattering in crude oil and the previously unobtainable asphaltene solubility at low heptane concentrations was measured. PMID:23808932

  14. Force aggregation using genetic algortihms

    NASA Astrophysics Data System (ADS)

    Shea, Peter J.; Peterson, John; Alexander, Kathleen; Azevedo, Alcino

    2004-01-01

    A surveillance system needs to accurately locate and identify not only single targets, but also groups of targets engaged in a common activity. Most existing tracking systems are capable of tracking individual targets quite accurately; however, they fail to use information related to group behavior in order to improve these estimates. Furthermore, in wide area surveillance situations a military operator is required to sort through hundreds to thousands of individual targets in order to develop an understanding of the situation. Having the ability to collapse the behavior of individual targets into a common, coordinated motion can greatly enhance the productively and situational awareness of the operator. Our long-term approach to solving this problem is to develop an understanding of how to define a group and then to understand the inter-relationships between the various characteristics that describe a group. Then using this information, we will be able to partition the set of target into groups that can be aggregated over the entire military force hierarchy. This goal of this paper is to describe an approach that is based upon genetic algorithms for solving the military force hierarchy problem. This paper will describe the underlying genetic algorithm, scoring function, and some initial results.

  15. Force aggregation using genetic algortihms

    NASA Astrophysics Data System (ADS)

    Shea, Peter J.; Peterson, John; Alexander, Kathleen; Azevedo, Alcino

    2003-12-01

    A surveillance system needs to accurately locate and identify not only single targets, but also groups of targets engaged in a common activity. Most existing tracking systems are capable of tracking individual targets quite accurately; however, they fail to use information related to group behavior in order to improve these estimates. Furthermore, in wide area surveillance situations a military operator is required to sort through hundreds to thousands of individual targets in order to develop an understanding of the situation. Having the ability to collapse the behavior of individual targets into a common, coordinated motion can greatly enhance the productively and situational awareness of the operator. Our long-term approach to solving this problem is to develop an understanding of how to define a group and then to understand the inter-relationships between the various characteristics that describe a group. Then using this information, we will be able to partition the set of target into groups that can be aggregated over the entire military force hierarchy. This goal of this paper is to describe an approach that is based upon genetic algorithms for solving the military force hierarchy problem. This paper will describe the underlying genetic algorithm, scoring function, and some initial results.

  16. Anisotropic diffusion-limited aggregation.

    PubMed

    Popescu, M N; Hentschel, H G E; Family, F

    2004-06-01

    Using stochastic conformal mappings, we study the effects of anisotropic perturbations on diffusion-limited aggregation (DLA) in two dimensions. The harmonic measure of the growth probability for DLA can be conformally mapped onto a constant measure on a unit circle. Here we map m preferred directions for growth to a distribution on the unit circle, which is a periodic function with m peaks in [-pi,pi) such that the angular width sigma of the peak defines the "strength" of anisotropy kappa= sigma(-1) along any of the m chosen directions. The two parameters (m,kappa) map out a parameter space of perturbations that allows a continuous transition from DLA (for small enough kappa ) to m needlelike fingers as kappa--> infinity. We show that at fixed m the effective fractal dimension of the clusters D(m,kappa) obtained from mass-radius scaling decreases with increasing kappa from D(DLA) approximately 1.71 to a value bounded from below by D(min) = 3 / 2. Scaling arguments suggest a specific form for the dependence of the fractal dimension D(m,kappa) on kappa for large kappa which compares favorably with numerical results. PMID:15244564

  17. Aggregate Models of Climate Change

    NASA Astrophysics Data System (ADS)

    Hooss, G.; Voss, R.; Hasselmann, K.; Maier-Reimer, E.; Joos, F.

    Integrated assessment of climate change generally requires the evaluation of many transient scenario simulations of century-timescale changes in atmospheric compo- sition and climate, desirably with the accuracy of state-of-the-art three-dimensional (3D) coupled atmosphere-ocean general circulation models (GCMs). Such multi- scenario GCM computations are possible through appropriate representation of the models in aggregate forms. For this purpose, we developed Nonlinear Impulse- response projections of 3D models of the global (oceanic and terrestrial) Carbon cycle and the atmosphere-ocean Climate System (NICCS). For higher CO2 forcing, appli- cability is extended beyond the linear response domain through explicit treatment of dominant nonlinear effects. The climate change module was furthermore augmented with spatial patterns of change in some of the most impact-relevant fields. Applied to three long-term CO2 emission scenarios, the model demonstrates (a) the minor rela- tive role of the terrestrial carbon sink through CO2 fertilization, and (b) the necessity to reduce fossil carbon emissions to a very small fraction of today's rates within the next few decades if a major climate change is to be avoided.

  18. Changes in soil aggregate, carbon, and nitrogen storages following the conversion of cropland to alfalfa forage land in the marginal oasis of northwest China.

    PubMed

    Su, Yong Zhong; Liu, Wen Jie; Yang, Rong; Chang, Xue Xiang

    2009-06-01

    Maintenance of soil organic carbon (SOC) is important for sustainable use of soil resources due to the multiple effects of SOC on soil nutrient status and soil structural stability. The objective of this study was to identify the changes in soil aggregate distribution and stability, SOC, and nitrogen (N) concentrations after cropland was converted to perennial alfalfa (Medicago sativa L. Algonguin) grassland for 6 years in the marginal oasis of the middle of Hexi Corridor region, northwest China. Significant changes in the size distribution of dry-sieving aggregates and water-stable aggregates, SOC, and N concentrations occurred after the conversion from crop to alfalfa. SOC and N stocks increased by 20.2% and 18.5%, respectively, and the estimated C and N sequestration rates were 0.4 Mg C ha(-1) year(-1) and 0.04 Mg N ha(-1) year(-1) following the conversion. The large aggregate (>5 mm) was the most abundant dry aggregate size fraction in both crop and alfalfa soils, and significant difference in the distribution of dry aggregates between the two land use types occurred only in the >5 mm aggregate fraction. The percentage of water-stable macroaggregates (>2, 2-0.25 mm) and aggregate stability (mean weight diameter of water-stable aggregates, WMWD) were significantly higher in alfalfa soils than in crop soils. There was a significant linear relationship between total SOC concentration and aggregate parameters (mean weight diameter) for alfalfa soils, indicating that aggregate stability was closely associated with increased SOC concentration following the conversion of crops to alfalfa. The SOC and N concentrations and the C/N ratio were greatest in the >2 mm water-stable aggregates and the smallest in the 0.25-0.05 mm aggregates in crop and alfalfa soils. For the same aggregate, SOC and N concentrations in aggregate fractions increased with increasing total SOC and N concentrations. The result showed that the conversion of annual crops to alfalfa in the marginal

  19. Boltzmann rovibrational collisional coarse-grained model for internal energy excitation and dissociation in hypersonic flows.

    PubMed

    Munafò, A; Panesi, M; Magin, T E

    2014-02-01

    A Boltzmann rovibrational collisional coarse-grained model is proposed to reduce a detailed kinetic mechanism database developed at NASA Ames Research Center for internal energy transfer and dissociation in N(2)-N interactions. The coarse-grained model is constructed by lumping the rovibrational energy levels of the N(2) molecule into energy bins. The population of the levels within each bin is assumed to follow a Boltzmann distribution at the local translational temperature. Excitation and dissociation rate coefficients for the energy bins are obtained by averaging the elementary rate coefficients. The energy bins are treated as separate species, thus allowing for non-Boltzmann distributions of their populations. The proposed coarse-grained model is applied to the study of nonequilibrium flows behind normal shock waves and within converging-diverging nozzles. In both cases, the flow is assumed inviscid and steady. Computational results are compared with those obtained by direct solution of the master equation for the rovibrational collisional model and a more conventional multitemperature model. It is found that the proposed coarse-grained model is able to accurately resolve the nonequilibrium dynamics of internal energy excitation and dissociation-recombination processes with only 20 energy bins. Furthermore, the proposed coarse-grained model provides a superior description of the nonequilibrium phenomena occurring in shock heated and nozzle flows when compared with the conventional multitemperature models. PMID:25353565

  20. A general method for spatially coarse-graining Metropolis Monte Carlo simulations onto a lattice

    NASA Astrophysics Data System (ADS)

    Liu, Xiao; Seider, Warren D.; Sinno, Talid

    2013-03-01

    A recently introduced method for coarse-graining standard continuous Metropolis Monte Carlo simulations of atomic or molecular fluids onto a rigid lattice of variable scale [X. Liu, W. D. Seider, and T. Sinno, Phys. Rev. E 86, 026708 (2012)], 10.1103/PhysRevE.86.026708 is further analyzed and extended. The coarse-grained Metropolis Monte Carlo technique is demonstrated to be highly consistent with the underlying full-resolution problem using a series of detailed comparisons, including vapor-liquid equilibrium phase envelopes and spatial density distributions for the Lennard-Jones argon and simple point charge water models. In addition, the principal computational bottleneck associated with computing a coarse-grained interaction function for evolving particle positions on the discretized domain is addressed by the introduction of new closure approximations. In particular, it is shown that the coarse-grained potential, which is generally a function of temperature and coarse-graining level, can be computed at multiple temperatures and scales using a single set of free energy calculations. The computational performance of the method relative to standard Monte Carlo simulation is also discussed.

  1. Symmetry-adapted digital modeling III. Coarse-grained icosahedral viruses.

    PubMed

    Janner, A

    2016-05-01

    Considered is the coarse-grained modeling of icosahedral viruses in terms of a three-dimensional lattice (the digital modeling lattice) selected among the projected points in space of a six-dimensional icosahedral lattice. Backbone atomic positions (Cα's for the residues of the capsid and phosphorus atoms P for the genome nucleotides) are then indexed by their nearest lattice point. This leads to a fine-grained lattice point characterization of the full viral chains in the backbone approximation (denoted as digital modeling). Coarse-grained models then follow by a proper selection of the indexed backbone positions, where for each chain one can choose the desired coarseness. This approach is applied to three viruses, the Satellite tobacco mosaic virus, the bacteriophage MS2 and the Pariacoto virus, on the basis of structural data from the Brookhaven Protein Data Bank. In each case the various stages of the procedure are illustrated for a given coarse-grained model and the corresponding indexed positions are listed. Alternative coarse-grained models have been derived and compared. Comments on related results and approaches, found among the very large set of publications in this field, conclude this article. PMID:27126109

  2. Coarse-grained variables for particle-based models: diffusion maps and animal swarming simulations

    NASA Astrophysics Data System (ADS)

    Liu, Ping; Safford, Hannah R.; Couzin, Iain D.; Kevrekidis, Ioannis G.

    2014-12-01

    As microscopic (e.g. atomistic, stochastic, agent-based, particle-based) simulations become increasingly prevalent in the modeling of complex systems, so does the need to systematically coarse-grain the information they provide. Before even starting to formulate relevant coarse-grained equations, we need to determine the right macroscopic observables—the right variables in terms of which emergent behavior will be described. This paper illustrates the use of data mining (and, in particular, diffusion maps, a nonlinear manifold learning technique) in coarse-graining the dynamics of a particle-based model of animal swarming. Our computational data-driven coarse-graining approach extracts two coarse (collective) variables from the detailed particle-based simulations, and helps formulate a low-dimensional stochastic differential equation in terms of these two collective variables; this allows the efficient quantification of the interplay of "informed" and "naive" individuals in the collective swarm dynamics. We also present a brief exploration of swarm breakup and use data-mining in an attempt to identify useful predictors for it. In our discussion of the scope and limitations of the approach we focus on the key step of selecting an informative metric, allowing us to usefully compare different particle swarm configurations.

  3. Boltzmann rovibrational collisional coarse-grained model for internal energy excitation and dissociation in hypersonic flows

    NASA Astrophysics Data System (ADS)

    Munafò, A.; Panesi, M.; Magin, T. E.

    2014-02-01

    A Boltzmann rovibrational collisional coarse-grained model is proposed to reduce a detailed kinetic mechanism database developed at NASA Ames Research Center for internal energy transfer and dissociation in N2-N interactions. The coarse-grained model is constructed by lumping the rovibrational energy levels of the N2 molecule into energy bins. The population of the levels within each bin is assumed to follow a Boltzmann distribution at the local translational temperature. Excitation and dissociation rate coefficients for the energy bins are obtained by averaging the elementary rate coefficients. The energy bins are treated as separate species, thus allowing for non-Boltzmann distributions of their populations. The proposed coarse-grained model is applied to the study of nonequilibrium flows behind normal shock waves and within converging-diverging nozzles. In both cases, the flow is assumed inviscid and steady. Computational results are compared with those obtained by direct solution of the master equation for the rovibrational collisional model and a more conventional multitemperature model. It is found that the proposed coarse-grained model is able to accurately resolve the nonequilibrium dynamics of internal energy excitation and dissociation-recombination processes with only 20 energy bins. Furthermore, the proposed coarse-grained model provides a superior description of the nonequilibrium phenomena occurring in shock heated and nozzle flows when compared with the conventional multitemperature models.

  4. Effective rates from thermodynamically consistent coarse-graining of models for molecular motors with probe particles

    NASA Astrophysics Data System (ADS)

    Zimmermann, Eva; Seifert, Udo

    2015-02-01

    Many single-molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom representing the motor. We present a coarse-graining method that maps a model comprising two coupled degrees of freedom which represent motor and probe particle to such an effective one-particle model by eliminating the dynamics of the probe particle in a thermodynamically and dynamically consistent way. The coarse-grained rates obey a local detailed balance condition and reproduce the net currents. Moreover, the average entropy production as well as the thermodynamic efficiency is invariant under this coarse-graining procedure. Our analysis reveals that only by assuming unrealistically fast probe particles, the coarse-grained transition rates coincide with the transition rates of the traditionally used one-particle motor models. Additionally, we find that for multicyclic motors the stall force can depend on the probe size. We apply this coarse-graining method to specific case studies of the F1-ATPase and the kinesin motor.

  5. Anisotropic Coarse-Grained Model for Proteins Based On Gay–Berne and Electric Multipole Potentials

    PubMed Central

    2015-01-01

    Gay–Berne anisotropic potential has been widely used to evaluate the nonbonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay–Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library), as well as from atomistic force field simulations (using AMOEBA, AMBER, and CHARMM force fields), while saving the computational cost by a factor of about 10–200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of nonbonded interactions (particularly electrostatic component) between hetero/homodimers (such as peptide–peptide, peptide–water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems. PMID:24659927

  6. Prediction of Coarse Particle Nitrate From Fine Particle Measurements in a Coastal Environment

    NASA Astrophysics Data System (ADS)

    Campbell, S. W.; Evans, M. C.; Poor, N. D.

    2003-12-01

    Nutrient induced algal growth is one cause of decreased seagrass in the Tampa Bay Estuary. This influx of nutrients arises from the presence of fixed nitrogen in various flows and discharges to the estuary and from atmospheric deposition. One of the goals of BRACE (Bay Regional Atmospheric Chemistry Experiment) is to obtain improved estimates of the atmospheric nitrogen deposition to Tampa Bay. Previous estimates of atmospheric dry deposition of nitrogen to Tampa Bay have been based on Annular Denuder System (ADS) measurements of gaseous nitric acid and ammonia and fine particle (PM2.5) nitrate and ammonium, which extend back to 1996. However, recent coarse particle measurements indicate that, while ammonium primarily exists in fine particles, nitrate is preferentially found in the coarse fraction. The goal of this study is to examine whether the historical data for fine particle nitrate can be used to predict the amount of nitrate in the coarse fraction so as to obtain a more accurate estimate of dry particle deposition of nitrate to the Tampa Bay Estuary. Specifically, it is shown that averaged nitrate distributions obtained from recent micro-orifice impactor data can be used to predict the coarse to fine ratios observed for dichotomous samplers and the fine particle concentrations obtained from the Annular Denuder System. This provides some confidence that the impactor results may be used in conjunction with earlier fine particle data to obtain an estimate of coarse particle nitrate concentrations, and therefore an improved estimate of nitrate flux to the estuary.

  7. Bryophyte species associations with coarse woody debris and stand ages in Oregon

    USGS Publications Warehouse

    Rambo, T.; Muir, Patricia S.

    1998-01-01

    We quantified the relationships of 93 forest floor bryophyte species, including epiphytes from incorporated litterfall, to substrate and stand age in Pseudotsuga menziesii-Tsuga heterophylla stands at two sites in western Oregon. We used the method of Dufr??ne and Legendre that combines a species' relative abundance and relative frequency, to calculate that species' importance in relation to environmental variables. The resulting 'indicator value' describes a species' reliability for indicating the given environmental parameter. Thirty-nine species were indicative of either humus, a decay class of coarse woody debris, or stand age. Bryophyte community composition changed along the continuum of coarse woody debris decomposition from recently fallen trees with intact bark to forest floor humus. Richness of forest floor bryophytes will be enhanced when a full range of coarse woody debris decay classes is present. A suite of bryophytes indicated old-growth forest. These were mainly either epiphytes associated with older conifers or liverworts associated with coarse woody debris. Hardwood-associated epiphytes mainly indicated young stands. Mature conifers, hardwoods, and coarse woody debris are biological legacies that can be protected when thinning managed stands to foster habitat complexity and biodiversity, consistent with an ecosystem approach to forest management.

  8. NIRCam Long Wavelength Channel grisms as the Dispersed Fringe Sensor for JWST segment mirror coarse phasing

    NASA Astrophysics Data System (ADS)

    Shi, Fang; King, Brian M.; Sigrist, Norbert; Basinger, Scott A.

    2008-07-01

    The baseline wavefront sensing and control for James Webb Space Telescope (JWST) includes the Dispersed Hartmann Sensors (DHS) for segment mirror coarse phasing. The two DHS devices, residing on the pupil wheel of the JWST's Near Infrared Camera (NIRCam) Short Wavelength Channel (SWC), can sense the JWST segment mirror pistons by measuring the heights of 20 inter-segment edges from the dispersed fringes. JWST also incorporates two identical grisms in the NIRCam's Long Wavelength Channel (LWC). The two grisms, designed as the Dispersed Fringe Sensor (DFS), are used as the backup sensor for JWST segment mirror coarse phasing. The versatility of DFS enables a very flexible JWST segment coarse phasing process and the DFS is designed to have larger piston capture range than that of DHS, making the coarse phasing more robust. The DFS can also be a useful tool during JWST ground integration and test (I&T). In this paper we describe the DFS design details and use the JWST optical model to demonstrate the DFS coarse phasing process during flight and ground I&T.

  9. Coarse dark patterning functionally constrains adaptive shifts from aposematism to crypsis in strawberry poison frogs.

    PubMed

    Qvarnström, Anna; Rudh, Andreas; Edström, Torkel; Ödeen, Anders; Løvlie, Hanne; Tullberg, Birgitta S

    2014-10-01

    Ecological specialization often requires tight coevolution of several traits, which may constrain future evolutionary pathways and make species more prone to extinction. Aposematism and crypsis represent two specialized adaptations to avoid predation. We tested whether the combined effects of color and pattern on prey conspicuousness functionally constrain or facilitate shifts between these two adaptations. We combined data from 17 natural populations of strawberry poison frogs, Oophaga pumilio with an experimental approach using digitalized images of frogs and chickens as predators. We show that bright coloration often co-occurs with coarse patterning among the natural populations. Dull green frogs with coarse patterning are rare in nature but in the experiment they were as easily detected as bright red frogs suggesting that this trait combination represents a transient evolutionary state toward aposematism. Hence, a gain of either bright color or coarse patterning leads to conspicuousness, but a transition back to crypsis would be functionally constrained in populations with both bright color and coarse patterning by requiring simultaneous changes in two traits. Thus, populations (or species) signaling aposematism by conspicuous color should be less likely to face an evolutionary dead end and more likely to radiate than populations with both conspicuous color and coarse patterning. PMID:24990085

  10. Can intra-aggregate pore structures affect the aggregate's effectiveness in protecting carbon?

    SciTech Connect

    Ananyeva, K; Wang, W; Smucker, A J.M.; Rivers, M L; Kravchenko, A N

    2012-11-15

    Aggregates are known to provide physical protection to soil organic matter shielding it from rapid decomposition. Spatial arrangement and size distribution of intra-aggregate pores play an important role in this process. This study examined relationships between intra-aggregate pores measured using X-ray computed micro-tomography images and concentrations of total C in 4–6 mm macro-aggregates from two contrasting land use and management practices, namely, conventionally tilled and managed row crop agricultural system (CT) and native succession vegetation converted from tilled agricultural land in 1989 (NS). Previous analyses of these aggregates indicated that small (<15 μm) and large (>100 μm) pores prevail in NS aggregates while medium (30–90 μm) pores are more abundant in CT aggregates (Kravchenko et al., 2011; Wang et al., 2012). We hypothesized that these differences in pore size distributions affect the ability of macro-aggregates to protect C. The results of this study supported this hypothesis. Consistent with greater heterogeneity of pore distributions within NS aggregates we observed higher total C and greater intra-aggregate C variability in NS as compared with CT aggregates. Total C concentrations and intra-aggregate C standard deviations were negatively correlated with fractions of medium sized pores, indicating that presence of such pores was associated with lower but more homogeneously distributed total C. While total C was positively correlated with presence of small and large pores. The results suggest that because of their pore structure NS macro-aggregates provide more effective physical protection to C than CT aggregates.

  11. Collision simulation of sintered dust aggregates

    NASA Astrophysics Data System (ADS)

    Sirono, Sin-iti; Ueno, Haruta

    Collisional evolution of dust aggregates is the initial process of the planet formation. Sticking velocity, below which collisional sticking of an aggregate happens, is a crucial quantity in the collisional evolution. In the standard model of protoplanetary nebula, the maximum collisional velocity is around 50m/s. Therefore, if a planetesimal is formed through direct collisional sticking, the sticking velocity should be higher than 50m/s. Even if a planetesimal is formed by other mechanism such as anticyclonic vortices, substantial growth of an aggregate is required because the motion of an aggregate should be decoupled from that of gas. Collisional simulation of icy dust aggregates (Wada et al. 2009, ApJ 702, 1490) showed that the sticking velocity was larger than 50m/s and planetesimal formation by collisional sticking was possible. However, sintering of ice proceeds in a wide area of a protoplanetary nebula (Sirono 2011, ApJ 765, 50). Sintering enlarges a neck, connection between adjacent dust grains, and changes the mechanical properties of a dust aggregate. Here we performed collisional simulations between sintered dust aggregates taking account of sintering. We found that the sticking velocity was decreased substantially down to 20m/s. This result suggests that a planetesimal is not formed by direct collisional sticking and that the planetesimal formation proceeded in particular regions in a protoplanetary nebula.

  12. Local aggregation characteristics of microscale blood flows

    NASA Astrophysics Data System (ADS)

    Kaliviotis, Efstathios; Sherwood, Joseph M.; Dusting, Jonathan; Balabani, Stavroula

    2015-11-01

    Erythrocyte aggregation (EA) is an important aspect of microvascular flows affecting blood flow and viscosity. Microscale blood flows have been studied extensively in recent years using computational and microfluidic based approaches. However, the relationship between the local structural characteristics of blood and the velocity field has not been quantified. We report simultaneous measurements of the local velocity, aggregation and haematocrit distributions of human erythrocytes flowing in a microchannel. EA was induced using Dextran and flows were imaged using brightfield microscopy. Local aggregation characteristics were investigated using statistical and edge-detection image processing techniques while velocity profiles were obtained using PIV algorithms. Aggregation intensity was found to strongly correlate with local variations in velocity in both the central and wall regions of the channel. The edge detection method showed that near the side wall large aggregates are associated with high local velocities and low local shear rates. In the central region large aggregates occurred in regions of low velocity and high erythrocyte concentration. The results demonstrate the combined effect of haematocrit and velocity distributions on local aggregation characteristics.

  13. A unified data representation theory for network visualization, ordering and coarse-graining

    NASA Astrophysics Data System (ADS)

    Kovács, István A.; Mizsei, Réka; Csermely, Péter

    2015-09-01

    Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of extensive data sets, by revealing the large-scale structure of complex networks in a comprehensible form.

  14. Compact cell-centered discretization stencils at fine-coarse block structured grid interfaces

    NASA Astrophysics Data System (ADS)

    Pletzer, Alexander; Jamroz, Ben; Crockett, Robert; Sides, Scott

    2014-03-01

    Different strategies for coupling fine-coarse grid patches are explored in the context of the adaptive mesh refinement (AMR) method. We show that applying linear interpolation to fill in the fine grid ghost values can produce a finite volume stencil of comparable accuracy to quadratic interpolation provided the cell volumes are adjusted. The volume of fine cells expands whereas the volume of neighboring coarse cells contracts. The amount by which the cells contract/expand depends on whether the interface is a face, an edge, or a corner. It is shown that quadratic or better interpolation is required when the conductivity is spatially varying, anisotropic, the refinement ratio is other than two, or when the fine-coarse interface is concave.

  15. A novel coarse-to-fine method for registration of multispectral images

    NASA Astrophysics Data System (ADS)

    Jin, Hongbin; Fan, Chunxiao; Li, Yong; Xu, Liangpeng

    2016-07-01

    Due to non-linear intensity changes between multispectral images, the existed descriptors often yield low matching performance. In order to build reliable keypoint mappings on multispectral images, a novel coarse-to-fine method is designed using projective transformation and the information of edge overlap. The method consists of a coarse process and a fine-tuning process. In the coarse process, initial keypoint mappings are built with the descriptors associated with keypoints and the relative distance constraints are employed on them to remove outliers. In the fine-tuning process, the edge overlap information is utilized as similarity metric and an iterative framework is applied to search correct keypoint mappings. The performance of the proposed is investigated with keypoints extracted by speeded-up robust features. The experiment results show that the proposed method can build more reliable keypoint mappings on multispectral images than existed methods.

  16. Systematic coarse graining flowing polymer melts: thermodynamically guided simulations and resulting constitutive model.

    PubMed

    Iig, Patrick

    2011-01-01

    Complex fluids, such as polymers, colloids, liquid-crystals etc., show intriguing viscoelastic properties, due to the complicated interplay between flow-induced structure formation and dynamical behavior. Starting from microscopic models of complex fluids, a systematic coarse-graining method is presented that allows us to derive closed-form and thermodynamically consistent constitutive equations for such fluids. Essential ingredients of the proposed approach are thermodynamically guided simulations within a consistent coarse-graining scheme. In addition to this new type of multiscale simulations, we reconstruct the building blocks that constitute the thermodynamically consistent coarse-grained model. We illustrate the method for low-molecular polymer melts, which are subject to different imposed flow fields like planar shear and different elongational flows. The constitutive equation for general flow conditions we obtain shows rheological behavior including shear thinning, normal stress differences, and elongational viscosities in good agreement with reference results. PMID:21678766

  17. A Hybrid Coarse-graining Approach for Lipid Bilayers at Large Length and Time Scales

    PubMed Central

    Ayton, Gary S.; Voth, Gregory A.

    2009-01-01

    A hybrid analytic-systematic (HAS) coarse-grained (CG) lipid model is developed and employed in a large-scale simulation of a liposome. The methodology is termed hybrid analyticsystematic as one component of the interaction between CG sites is variationally determined from the multiscale coarse-graining (MS-CG) methodology, while the remaining component utilizes an analytic potential. The systematic component models the in-plane center of mass interaction of the lipids as determined from an atomistic-level MD simulation of a bilayer. The analytic component is based on the well known Gay-Berne ellipsoid of revolution liquid crystal model, and is designed to model the highly anisotropic interactions at a highly coarse-grained level. The HAS CG approach is the first step in an “aggressive” CG methodology designed to model multi-component biological membranes at very large length and timescales. PMID:19281167

  18. Hybrid coarse-graining approach for lipid bilayers at large length and time scales.

    PubMed

    Ayton, Gary S; Voth, Gregory A

    2009-04-01

    A hybrid analytic-systematic (HAS) coarse-grained (CG) lipid model is developed and employed in a large-scale simulation of a liposome. The methodology is termed hybrid analytic-systematic because one component of the interaction between CG sites is variationally determined from the multiscale coarse-graining (MS-CG) methodology, whereas the remaining component utilizes an analytic potential. The systematic component models the in-plane center-of-mass interaction of the lipids as determined from an atomistic-level MD simulation of a bilayer. The analytic component is based on the well-known Gay-Berne ellipsoid-of-revolution liquid-crystal model and is designed to model the highly anisotropic interactions at a highly coarse-grained level. The HAS CG approach is the first step in an "aggressive" CG methodology designed to model multicomponent biological membranes at very large length and time scales. PMID:19281167

  19. Improved calibration of IMU biases in analytic coarse alignment for AHRS

    NASA Astrophysics Data System (ADS)

    Lu, Jiazhen; Lei, Chaohua; Li, Baoguo; Wen, Ting

    2016-07-01

    An improved method for the inertial measurement unit (IMU) calibration of coarse alignment for the low-accuracy attitude heading reference system (AHRS) is proposed in this paper. The sensitivities of the Euler angles with respect to the inertial sensor biases are studied based on the analytic coarse alignment principle, and the errors of earth rotation rate and local gravity in the body frame caused by initial attitude error are analyzed. Then, an improved analytic coarse alignment algorithm with accelerometer and gyro bias calibration in an arbitrary three-position is proposed. Simulation and experiment results show that the novel method can calibrate accelerometer and gyro biases, reduce Euler angle attitude error, and improve navigation precision in practical applications. Moreover, this method can be applied to other low-accuracy inertial navigation systems.

  20. Multiscale dynamics of semiflexible polymers from a universal coarse-graining procedure.

    PubMed

    Koslover, Elena F; Spakowitz, Andrew J

    2014-07-01

    Simulating the dynamics of a semiflexible polymer across time and length scales that bridge the rigid and flexible regimes requires a physically sound method for generating coarse-grained representations of the polymer. Here, we study the dynamic behavior of the discrete stretchable, shearable wormlike chain model, which can be used to coarse-grain a continuous semi-elastic chain at an arbitrary discretization. We show that the dynamics of this universal model match those of the wormlike chain at length scales above the discretization length. The evolution of the stress correlation, as probed through Brownian dynamics simulations, is found to reproduce the predicted behavior in both the rigid and flexible regimes, spanning over six orders of magnitude in time scales. The coarse-graining approach employed here thus enables dynamic simulation of semiflexible polymers at lengths and times that were previously inaccessible with conventional methods. PMID:25122407

  1. Multiscale dynamics of semiflexible polymers from a universal coarse-graining procedure

    NASA Astrophysics Data System (ADS)

    Koslover, Elena F.; Spakowitz, Andrew J.

    2014-07-01

    Simulating the dynamics of a semiflexible polymer across time and length scales that bridge the rigid and flexible regimes requires a physically sound method for generating coarse-grained representations of the polymer. Here, we study the dynamic behavior of the discrete stretchable, shearable wormlike chain model, which can be used to coarse-grain a continuous semi-elastic chain at an arbitrary discretization. We show that the dynamics of this universal model match those of the wormlike chain at length scales above the discretization length. The evolution of the stress correlation, as probed through Brownian dynamics simulations, is found to reproduce the predicted behavior in both the rigid and flexible regimes, spanning over six orders of magnitude in time scales. The coarse-graining approach employed here thus enables dynamic simulation of semiflexible polymers at lengths and times that were previously inaccessible with conventional methods.

  2. A unified data representation theory for network visualization, ordering and coarse-graining

    PubMed Central

    Kovács, István A.; Mizsei, Réka; Csermely, Péter

    2015-01-01

    Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of extensive data sets, by revealing the large-scale structure of complex networks in a comprehensible form. PMID:26348923

  3. Bottom-up coarse-graining of a simple graphene model: the blob picture.

    PubMed

    Kauzlarić, David; Meier, Julia T; Español, Pep; Succi, Sauro; Greiner, Andreas; Korvink, Jan G

    2011-02-14

    The coarse-graining of a simple all-atom 2D microscopic model of graphene, in terms of "blobs" described by center of mass variables, is presented. The equations of motion of the coarse-grained variables take the form of dissipative particle dynamics (DPD). The coarse-grained conservative forces and the friction of the DPD model are obtained via a bottom-up procedure from molecular dynamics (MD) simulations. The separation of timescales for blobs of 24 and 96 carbon atoms is sufficiently pronounced for the Markovian assumption, inherent to the DPD model, to provide satisfactory results. In particular, the MD velocity autocorrelation function of the blobs is well reproduced by the DPD model, provided that the effect of friction and noise is taken into account. However, DPD cross-correlations between neighbor blobs show appreciable discrepancies with respect to the MD results. Possible extensions to mend these discrepancies are briefly outlined. PMID:21322660

  4. Exciton dynamics in perturbed vibronic molecular aggregates

    PubMed Central

    Brüning, C.; Wehner, J.; Hausner, J.; Wenzel, M.; Engel, V.

    2015-01-01

    A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states. PMID:26798840

  5. On aggregation in spatial econometric modelling

    NASA Astrophysics Data System (ADS)

    Paelinck, Jean H. P.

    The spatial aggregation problem - also termed the modifiable areal unit problem - has attracted regular attention in spatial statistics and econometrics. In this study econometric aggregation analysis is used to investigate the formal composition of meso-areal parameters given micro-areal underlying relations with spatial dependence. Impact on stochastic terms (possible meso-areal spatial autocorrelation) is also studied. Finally consequences for meso-areal estimation are derived, the general finding having been that spatial aggregation leads to meso-region specific parameter values, with the estimation problems this implies.

  6. Aggregation of ice crystals in cirrus

    NASA Technical Reports Server (NTRS)

    Kajikawa, Masahiro; Heymsfield, Andrew J.

    1989-01-01

    Results are given from analysis of the aggregation of thick plate, columnar, and bullet rosette ice crystals in cirrus. Data were obtained from PMS 2D-C images, oil coated slides, and aircraft meteorological measurements. Crystal size ranged from 100 to 900 microns in temperatures from -30 to -45 C. The results indicate that the ratio of the sizes of aggregating crystals and the difference of their terminal velocities are important in aggregation. The collection efficiency was calculated for the thick plate crystals from the same data.

  7. Directional sensing and streaming in Dictyostelium aggregation

    NASA Astrophysics Data System (ADS)

    Almeida, Sofia; Dilão, Rui

    2016-05-01

    We merge the Kessler-Levine simple discrete model for Dictyostelium cyclic adenosine monophosphate (cAMP) production and diffusion with the Dilão-Hauser directional sensing aggregation mechanism. The resulting compound model describes all the known transient patterns that emerge during Dictyostelium aggregation, which include the spontaneous formation of cAMP self-sustained target and spiral waves and streaming. We show that the streaming patterns depend on the speed of the amoebae, on the relaxation time for the production of cAMP, on the cAMP degradation rate, and on directional sensing. Moreover, we show that different signaling centers emerge during Dictyostelium aggregation.

  8. Antiplatelet aggregation principles from Ephemerantha lonchophylla.

    PubMed

    Chen, C C; Huang, Y L; Teng, C M

    2000-05-01

    Bioactivity-directed separation led to the identification of four compounds, viz. denbinobin (1), 3,7-dihydroxy-2,4-dimethoxyphenanthrene (2), 3-methylgigantol (3), and erianthridin (4) from the ethanolic extract of Ephemerantha lonchophylla. Antiplatelet tests were carried out using 4 different aggregation inducers, viz. arachidonic acid (AA), thrombin, collagen and platelet activating factor (PAF). The results indicated that only compounds 2, 3, and 4 exhibited generally significant anti-aggregation activities with that against AA-induced aggregation being most effective. Estimated IC50, values in this regard for 2, 3, and 4 were 24 microM, 30 microM and 9 microM, respectively. PMID:10865460

  9. A look at construction aggregates production

    USGS Publications Warehouse

    Willett, Jason Christopher

    2009-01-01

    Construction aggregates are defined as the combination of crushed stone and construction sand and gravel. Aggregates are one of the most accessible natural resources on Earth and one of the fundamental building blocks of our society. They have been used from the earliest times of our civilization for a variety of applications that have increased in number and complexity with time and technological progress. Despite the relatively low but increasing unit value of its basic products, the construction aggregates industry is a major contributor to and an indicator of the economic well-being of the nation.

  10. Exciton dynamics in perturbed vibronic molecular aggregates.

    PubMed

    Brüning, C; Wehner, J; Hausner, J; Wenzel, M; Engel, V

    2016-07-01

    A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states. PMID:26798840

  11. Observations of fine and coarse particle nitrate at several rural locations in the United States

    NASA Astrophysics Data System (ADS)

    Lee, Taehyoung; Yu, Xiao-Ying; Ayres, Benjamin; Kreidenweis, Sonia M.; Malm, William C.; Collett, Jeffrey L.

    Nitrate comprises an important part of aerosol mass at many non-urban locations during some times of the year. Little is known, however, about the chemical form and size distribution of particulate nitrate in these environments. While submicron ammonium nitrate is often assumed to be the dominant species, this assumption is rarely tested. Properties of aerosol nitrate were characterized at several IMPROVE monitoring sites during a series of field studies. Study sites included Bondville, Illinois (February 2003), San Gorgonio Wilderness Area, California (April and July 2003), Grand Canyon National Park, Arizona (May 2003), Brigantine National Wildlife Refuge, New Jersey (November 2003), and Great Smoky Mountains National Park, Tennessee (July/August 2004). Nitrate was found predominantly in submicron ammonium nitrate particles during the Bondville and San Gorgonio (April) campaigns. Coarse mode nitrate particles, resulting from reactions of nitric acid or its precursors with sea salt or soil dust, were more important at Grand Canyon and Great Smoky Mountains. Both fine and coarse mode nitrate were important during the studies at Brigantine and San Gorgonio (July). These results, which complement earlier findings about the importance of coarse particle nitrate at Yosemite and Big Bend National Parks, suggest a need to more closely examine common assumptions regarding the importance of ammonium nitrate at non-urban sites, to include pathways for coarse mode nitrate formation in regional models, and to consider impacts of coarse particle nitrate on visibility. Because coarse particle nitrate modes often extend well below 2.5 μm aerodynamic diameter, measurements of PM 2.5 nitrate in these environments should not automatically be assumed to contain only ammonium nitrate.

  12. Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study

    NASA Astrophysics Data System (ADS)

    Yang, Delian; Wang, Qiang

    2015-02-01

    We propose a systematic and simulation-free strategy for coarse graining of homopolymer melts, where each chain of Nm monomers is uniformly divided into N segments, with the spatial position of each segment corresponding to the center-of-mass of its monomers. We use integral-equation theories suitable for the study of equilibrium properties of polymers, instead of many-chain molecular simulations, to obtain the structural and thermodynamic properties of both original and coarse-grained (CG) systems, and quantitatively examine how the effective pair potentials between CG segments and the thermodynamic properties of CG systems vary with N. Our systematic and simulation-free strategy is much faster than those using many-chain simulations, thus effectively solving the transferability problem in coarse graining, and provides the quantitative basis for choosing the appropriate N-values. It also avoids the problems caused by finite-size effects and statistical uncertainties in many-chain simulations. Taking the simple hard-core Gaussian thread model [K. S. Schweizer and J. G. Curro, Chem. Phys. 149, 105 (1990)] as the original system, we demonstrate our strategy applied to structure-based coarse graining, which is quite general and versatile, and compare in detail the various integral-equation theories and closures for coarse graining. Our numerical results show that the effective CG potentials for various N and closures can be collapsed approximately onto the same curve, and that structure-based coarse graining cannot give thermodynamic consistency between original and CG systems at any N < Nm.

  13. A transferable coarse-grained model for hydrogen-bonding liquids.

    PubMed

    Golubkov, Pavel A; Wu, Johnny C; Ren, Pengyu

    2008-04-21

    We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effective-potential based approaches. The previous center-of-mass framework (P. A. Golubkov and P. Ren, J. Chem. Phys., 2006, 125, 64103) is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic-level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations. PMID:18688358

  14. Observations of Fine and Coarse Particle Nitrate at Several Rural Locations in the United States

    SciTech Connect

    Lee, Taehyoung; Yu, Xiao-Ying; Ayres, Benjamin; Kreidenweis, Sonia M.; Malm, William C.; Collett, Jeffrey L.

    2008-04-01

    Nitrate comprises an important part of aerosol mass at many non-urban locations during some times of the year. Little is known, however, about the chemical form and size distribution of particulate nitrate in these environments. While submicron ammonium nitrate is often assumed to be the dominant species, this assumption is rarely tested. Properties of aerosol nitrate were characterized at several IMPROVE monitoring sites during a series of field studies. Study sites included Bondville, Illinois (February 2003), San Gorgonio Wilderness Area, California (April and July 2003), Grand Canyon National Park, Arizona (May 2003), Brigantine National Wildlife Refuge, New Jersey (November 2003), and Great Smoky Mountains National Park, Tennessee (July/August 2004). Nitrate was found predominantly in submicron ammonium nitrate particles during the Bondville and San Gorgonio (April) campaigns. Coarse mode nitrate particles, resulting from reactions of nitric acid or its precursors with sea salt or soil dust, were more important at Grand Canyon and Great Smoky Mountains. Both fine and coarse mode nitrate were important during the studies at Brigantine and San Gorgonio (July). These results, which complement earlier findings about the importance of coarse particle nitrate at Yosemite and Big Bend National Parks, suggest a need to more closely examine common assumptions regarding the importance of ammonium nitrate at non-urban sites, to include pathways for coarse mode nitrate formation in regional models, and to consider impacts of coarse particle nitrate on visibility. Because coarse particle nitrate modes often extend well below 2.5 µm aerodynamic diameter, measurements of PM2.5 nitrate in these environments should not automatically be assumed to contain only ammonium nitrate.

  15. Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study

    SciTech Connect

    Yang, Delian; Wang, Qiang

    2015-02-07

    We propose a systematic and simulation-free strategy for coarse graining of homopolymer melts, where each chain of N{sub m} monomers is uniformly divided into N segments, with the spatial position of each segment corresponding to the center-of-mass of its monomers. We use integral-equation theories suitable for the study of equilibrium properties of polymers, instead of many-chain molecular simulations, to obtain the structural and thermodynamic properties of both original and coarse-grained (CG) systems, and quantitatively examine how the effective pair potentials between CG segments and the thermodynamic properties of CG systems vary with N. Our systematic and simulation-free strategy is much faster than those using many-chain simulations, thus effectively solving the transferability problem in coarse graining, and provides the quantitative basis for choosing the appropriate N-values. It also avoids the problems caused by finite-size effects and statistical uncertainties in many-chain simulations. Taking the simple hard-core Gaussian thread model [K. S. Schweizer and J. G. Curro, Chem. Phys. 149, 105 (1990)] as the original system, we demonstrate our strategy applied to structure-based coarse graining, which is quite general and versatile, and compare in detail the various integral-equation theories and closures for coarse graining. Our numerical results show that the effective CG potentials for various N and closures can be collapsed approximately onto the same curve, and that structure-based coarse graining cannot give thermodynamic consistency between original and CG systems at any N < N{sub m}.

  16. Cell-Specific Oxidative Stress and Cytotoxicity after Wildfire Coarse Particulate Matter Instillation into Mouse Lung

    PubMed Central

    Williams, Keisha M.; Franzi, Lisa M.; Last, Jerold A.

    2012-01-01

    Our previous work has shown that coarse particulate matter (PM10-2.5) from wildfire smoke is more toxic to lung macrophages on an equal dose (by mass) basis than coarse PM isolated from normal ambient air, as evidenced by decreased numbers of macrophages in lung lavage fluid 6 and 24 hours after PM instillation into mouse lungs in vivo and by cytotoxicity to a macrophage cell line observed directly in vitro. We hypothesized that pulmonary macrophages from mice instilled with wildfire coarse PM would undergo more cytotoxicity than macrophages from controls, and that there would be an increase in oxidative stress in their lungs. Cytotoxicity was quantified as decreased viable macrophages and increased percentages of dead macrophages in the bronchoalveolar lavage fluid (BALF) of mice instilled with wildfire coarse PM. At one hour after PM instillation, we observed both decreased numbers of viable macrophages and increased dead macrophage percentages as compared to controls. An increase in free isoprostanes, an indicator of oxidative stress, from control values of 28.1±3.2 pg/mL to 83.9±12.2 pg/mL was observed a half-hour after PM instillation. By one hour after PM instillation, isoprostane values had returned to 30.4±7.6pg/mL, not significantly different from control concentrations. Lung sections from mice instilled with wildfire coarse PM showed rapid Clara cell responses, with decreased intracellular staining for the Clara cell secretory protein CCSP 1 hour after wildfire PM instillation. In conclusion, very rapid cytotoxicity occurs in pulmonary macrophages and oxidative stress responses are seen 0.5-1 hour after wildfire coarse PM instillation. These results define early cellular and biochemical events occurring in vivo and support the hypothesis that oxidative stress-mediated macrophage toxicity plays a key role in the initial response of the mouse lung to wildfire PM exposure. PMID:23142465

  17. Cell-specific oxidative stress and cytotoxicity after wildfire coarse particulate matter instillation into mouse lung.

    PubMed

    Williams, Keisha M; Franzi, Lisa M; Last, Jerold A

    2013-01-01

    Our previous work has shown that coarse particulate matter (PM(10-2.5)) from wildfire smoke is more toxic to lung macrophages on an equal dose (by mass) basis than coarse PM isolated from normal ambient air, as evidenced by decreased numbers of macrophages in lung lavage fluid 6 and 24hours after PM instillation into mouse lungs in vivo and by cytotoxicity to a macrophage cell line observed directly in vitro. We hypothesized that pulmonary macrophages from mice instilled with wildfire coarse PM would undergo more cytotoxicity than macrophages from controls, and that there would be an increase in oxidative stress in their lungs. Cytotoxicity was quantified as decreased viable macrophages and increased percentages of dead macrophages in the bronchoalveolar lavage fluid (BALF) of mice instilled with wildfire coarse PM. At 1hour after PM instillation, we observed both decreased numbers of viable macrophages and increased dead macrophage percentages as compared to controls. An increase in free isoprostanes, an indicator of oxidative stress, from control values of 28.1±3.2pg/mL to 83.9±12.2pg/mL was observed a half-hour after PM instillation. By 1hour after PM instillation, isoprostane values had returned to 30.4±7.6pg/mL, not significantly different from control concentrations. Lung sections from mice instilled with wildfire coarse PM showed rapid Clara cell responses, with decreased intracellular staining for the Clara cell secretory protein CCSP 1hour after wildfire PM instillation. In conclusion, very rapid cytotoxicity occurs in pulmonary macrophages and oxidative stress responses are seen 0.5-1hour after wildfire coarse PM instillation. These results define early cellular and biochemical events occurring in vivo and support the hypothesis that oxidative stress-mediated macrophage toxicity plays a key role in the initial response of the mouse lung to wildfire PM exposure. PMID:23142465

  18. Metal concentrations in aggregate interiors, exteriors, whole aggregates, and bulk of Costa Rican soils

    SciTech Connect

    Wilcke, W.; Kretzschmar, S.; Bundt, M.; Zech, W.

    1999-10-01

    In many temperate soils the preferential weathering and leaching of aggregate surfaces and the nonaggregated material between aggregates depletes geogenic metals. It also shifts metals from strongly to more weakly bound metal forms. Deposited metals are sorbed preferentially on aggregate surfaces and between aggregates. The authors examined whether preferential desilication under tropical climate causes an enrichment in the aggregate exteriors in oxidic forms of metals. They also studied where deposited metals are bound in these soils. Aggregates (2--20 mm) were selected manually from the A horizons of eight Oxisols, six Andisols, two Mollisols, and two Inceptisols in Costa Rica. All samples were fractionated into interior and exterior portions and treated with a seven-step sequence to extract Al, Cd, Cu, Fe, Mn, Pb, and Zn. Total concentrations of all metals except Zn were higher in the aggregate exteriors than in the interiors. The average Cd and Pb concentrations in easily extractable fractions were significantly higher in the aggregate exteriors. There were no significant differences in metal partitioning between interiors and exteriors except for Pb, which had higher proportions in extractable forms with NH{sub 2}OH {center{underscore}dot} HCl {gt} NH{sub 4} - acetate, pH 6.0 {gt} EDTA in the exteriors. There were few significant differences in metal concentrations and partitioning between bulk soil and whole aggregates. The results may be explained by (i) preferential desilication of the aggregate exteriors and (ii) preferential sorption of deposited heavy metals mainly in easily extractable forms.

  19. Relationship between the initial rate of protein aggregation and the lag period for amorphous aggregation.

    PubMed

    Borzova, Vera A; Markossian, Kira A; Kurganov, Boris I

    2014-07-01

    Lag period is an inherent characteristic of the kinetic curves registered for protein aggregation. The appearance of a lag period is connected with the nucleation stage and the stages of the formation of folding or unfolding intermediates prone to aggregation (for example, the stage of protein unfolding under stress conditions). Discovering the kinetic regularities essential for elucidation of the protein aggregation mechanism comprises deducing the relationship between the lag period and aggregation rate. Fändrich proposed the following equation connecting the duration of the lag phase (tlag) and the aggregate growth rate (kg) in the amyloid fibrillation: kg=const/tlag. To establish the relationship between the initial rate of protein aggregation (v) and the lag period (t0) in the case of amorphous aggregation, the kinetics of dithithreitol-induced aggregation of holo-α-lactalbumin from bovine milk was studied (0.1M Na-phosphate buffer, pH 6.8; 37°C). The order of aggregation with respect to protein (n) was calculated from the dependence of the initial rate of protein aggregation on the α-lactalbumin concentration (n=5.3). The following equation connecting v and t0 has been proposed: v(1/n)=const/(t0-t0,lim), where t0,lim is the limiting value of t0 at high concentrations of the protein. PMID:24794200

  20. Aggregate structure, morphology and the effect of aggregation mechanisms on viscosity at elevated protein concentrations.

    PubMed

    Barnett, Gregory V; Qi, Wei; Amin, Samiul; Neil Lewis, E; Roberts, Christopher J

    2015-12-01

    Non-native aggregation is a common issue in a number of degenerative diseases and during manufacturing of protein-based therapeutics. There is a growing interest to monitor protein stability at intermediate to high protein concentrations, which are required for therapeutic dosing of subcutaneous injections. An understanding of the impact of protein structural changes and interactions on the protein aggregation mechanisms and resulting aggregate size and morphology may lead to improved strategies to reduce aggregation and solution viscosity. This report investigates non-native aggregation of a model protein, α-chymotrypsinogen, under accelerated conditions at elevated protein concentrations. Far-UV circular dichroism and Raman scattering show structural changes during aggregation. Size exclusion chromatography and laser light scattering are used to monitor the progression of aggregate growth and monomer loss. Monomer loss is concomitant with increased β-sheet structures as monomers are added to aggregates, which illustrate a transition from a native monomeric state to an aggregate state. Aggregates grow predominantly through monomer-addition, resulting in a semi-flexible polymer morphology. Analysis of aggregation growth kinetics shows that pH strongly affects the characteristic timescales for nucleation (τn) and growth (τg), while the initial protein concentration has only minor effects on τn or τg. Low-shear viscosity measurements follow a common scaling relationship between average aggregate molecular weight (Mw(agg)) and concentration (σ), which is consistent with semi-dilute polymer-solution theory. The results establish a link between aggregate growth mechanisms, which couple Mw(agg) and σ, to increases in solution viscosity even at these intermediate protein concentrations (less than 3w/v %). PMID:26284891