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Sample records for coarse aggregates

  1. Recycled Coarse Aggregate Produced by Pulsed Discharge in Water

    NASA Astrophysics Data System (ADS)

    Namihira, Takao; Shigeishi, Mitsuhiro; Nakashima, Kazuyuki; Murakami, Akira; Kuroki, Kaori; Kiyan, Tsuyoshi; Tomoda, Yuichi; Sakugawa, Takashi; Katsuki, Sunao; Akiyama, Hidenori; Ohtsu, Masayasu

    In Japan, the recycling ratio of concrete scraps has been kept over 98 % after the Law for the Recycling of Construction Materials was enforced in 2000. In the present, most of concrete scraps were recycled as the Lower Subbase Course Material. On the other hand, it is predicted to be difficult to keep this higher recycling ratio in the near future because concrete scraps increase rapidly and would reach to over 3 times of present situation in 2010. In addition, the demand of concrete scraps as the Lower Subbase Course Material has been decreased. Therefore, new way to reuse concrete scraps must be developed. Concrete scraps normally consist of 70 % of coarse aggregate, 19 % of water and 11 % of cement. To obtain the higher recycling ratio, the higher recycling ratio of coarse aggregate is desired. In this paper, a new method for recycling coarse aggregate from concrete scraps has been developed and demonstrated. The system includes a Marx generator and a point to hemisphere mesh electrode immersed in water. In the demonstration, the test piece of concrete scrap was located between the electrodes and was treated by the pulsed discharge. After discharge treatment of test piece, the recycling coarse aggregates were evaluated under JIS and TS and had enough quality for utilization as the coarse aggregate.

  2. 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.

  3. Chemical-mineralogical characterisation of coarse recycled concrete aggregate.

    PubMed

    Limbachiya, M C; Marrocchino, E; Koulouris, A

    2007-01-01

    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 (SiO2, Al2O3 and CaO) of concrete, but thereafter there was a marginal decrease in SiO2 and increase in Al2O3 and CaO contents with increase in RCA content in the mix, reflecting the original constituent's composition.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Evaluation of steel slag coarse aggregate in hot mix asphalt concrete.

    PubMed

    Ahmedzade, Perviz; Sengoz, Burak

    2009-06-15

    This paper presents the influences of the utilization of steel slag as a coarse aggregate on the properties of hot mix asphalt. Four different asphalt mixtures containing two types of asphalt cement (AC-5; AC-10) and coarse aggregate (limestone; steel slag) were used to prepare Marshall specimens and to determine optimum bitumen content. Mechanical characteristics of all mixtures were evaluated by Marshall stability, indirect tensile stiffness modulus, creep stiffness, and indirect tensile strength tests. The electrical sensitivity of the specimens were also investigated in accordance with ASTM D257-91. It was observed that steel slag used as a coarse aggregate improved the mechanical properties of asphalt mixtures. Moreover, volume resistivity values demonstrated that the electrical conductivity of steel slag mixtures were better than that of limestone mixtures.

  10. 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.

  11. Bonding Behavior of Deformed Steel Rebars in Sustainable Concrete Containing both Fine and Coarse Recycled Aggregates

    PubMed Central

    Kim, Sun-Woo; Park, Wan-Shin; Jang, Young-Il; Jang, Seok-Joon; Yun, Hyun-Do

    2017-01-01

    In order to assess the bond behavior of deformed steel rebars in recycled-aggregate concrete (RAC) incorporating both fine and coarse recycled aggregate, pull-out tests were carried out in this study on 16-mm diameter deformed steel rebars embedded concentrically in RAC. The concrete was designed using equivalently mixed proportions of both recycled coarse aggregate and recycled fine aggregate. The tests employed five types of recycled aggregate replacement combinations and three types of rebar placement orientation (i.e., vertical bars and two-tiered and three-tiered horizontal bars). Based on the pull-out test results, the maximum bond strength tended to decrease and the slip at the maximum bond strength increased as the average water absorption of the aggregate increased, irrespective of the rebar orientation or placement location within the concrete member. The pull-out test results for the horizontal steel rebars embedded in RAC indicate that the casting position effect could be determined from the mid-depth of the concrete member, irrespective of the member’s height. The normalized bond versus slip relationship between the deformed rebar and the RAC could be predicted using an empirical model based on regression analysis of the experimental data. PMID:28906441

  12. Bonding Behavior of Deformed Steel Rebars in Sustainable Concrete Containing both Fine and Coarse Recycled Aggregates.

    PubMed

    Kim, Sun-Woo; Park, Wan-Shin; Jang, Young-Il; Jang, Seok-Joon; Yun, Hyun-Do

    2017-09-14

    In order to assess the bond behavior of deformed steel rebars in recycled-aggregate concrete (RAC) incorporating both fine and coarse recycled aggregate, pull-out tests were carried out in this study on 16-mm diameter deformed steel rebars embedded concentrically in RAC. The concrete was designed using equivalently mixed proportions of both recycled coarse aggregate and recycled fine aggregate. The tests employed five types of recycled aggregate replacement combinations and three types of rebar placement orientation (i.e., vertical bars and two-tiered and three-tiered horizontal bars). Based on the pull-out test results, the maximum bond strength tended to decrease and the slip at the maximum bond strength increased as the average water absorption of the aggregate increased, irrespective of the rebar orientation or placement location within the concrete member. The pull-out test results for the horizontal steel rebars embedded in RAC indicate that the casting position effect could be determined from the mid-depth of the concrete member, irrespective of the member's height. The normalized bond versus slip relationship between the deformed rebar and the RAC could be predicted using an empirical model based on regression analysis of the experimental data.

  13. 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

  14. 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.

  15. Effect of coarse aggregate type on mechanical properties of concretes with different strengths

    SciTech Connect

    Oezturan, T.; Cecen, C.

    1997-02-01

    Tests were carried out to study the effect of the type of coarse aggregate on the compressive, flexural and splitting tensile strength on concrete produced at different strength levels. Concretes with 28 day target compressive strengths of 30, 60 and 90 MPa were produced using basalt, limestone and gravel coarse aggregates. The gravel aggregate concrete with 90 MPa target strength was also replicated by using a cement of higher strength, keeping the other parameters same. Twenty eight day test results have indicated that, in high strength concrete, basalt produced the highest, whereas gravel gave the lowest compressive strengths. Normal strength concretes made with basalt and gravel gave similar compressive strengths while the concrete containing limestone attained somewhat higher strength. Higher tensile strengths were obtained with crushed basalt and limestone compared to the gravel aggregate when used in high strength concrete. In the replicate mixture, approximately 30 percent increase in flexural and splitting tensile strengths were obtained as a result of using a stronger cement, while the compressive strength was not affected at all.

  16. Membrane Remodeling by Surface-Bound Protein Aggregates: Insights from Coarse-Grained Molecular Dynamics Simulation

    PubMed Central

    2015-01-01

    The mechanism of curvature generation in membranes has been studied for decades due to its important role in many cellular functions. However, it is not clear if, or how, aggregates of lipid-anchored proteins might affect the geometry and elastic property of membranes. As an initial step toward addressing this issue, we performed structural, geometrical, and stress field analyses of coarse-grained molecular dynamics trajectories of a domain-forming bilayer in which an aggregate of lipidated proteins was asymmetrically bound. The results suggest a general mechanism whereby asymmetric incorporation of lipid-modified protein aggregates curve multidomain membranes primarily by expanding the surface area of the monolayer in which the lipid anchor is inserted. PMID:24803997

  17. Microstructure and mechanical properties of halite/coarse muscovite synthetic aggregates deformed in torsion

    NASA Astrophysics Data System (ADS)

    Marques, F. O.; Burlini, L.; Burg, J.-P.

    2011-04-01

    We investigated the behavior of a synthetic two-phase aggregate composed of 80% halite + 20% coarse muscovite under torsion deformation, at 100, 200 and 300 °C, a confining pressure of 250 MPa, and a constant strain rate of 3E-4 s -1. At all temperatures, the two-phase aggregate deformed homogeneously at the sample scale. The strength of the aggregate and muscovite deformation depended on temperature, strain rate and initial orientation of muscovite greatest dimension relative to the shear plane. With muscovite initially parallel to the shear plane, halite flowed plastically and long muscovite grains were not strong enough to behave as a rigid inclusion rotating in a ductile matrix. Instead, high aspect ratio grains deformed by folding, which was visibly accomplished by slip along mica {001} cleavage and by great flattening of halite in the core of the folds. When initially normal to the shear plane, high aspect ratio muscovite grains passively rotated towards the shear plane. In both cases, small and low aspect ratio muscovite grains behaved mostly as mica-fish, with mica grains tilted opposite to shear sense. Similarly to natural mylonites, σ-porphyroclast systems and rolling structures were also common in the microstructure. A strong foliation made of halite ribbons and aligned muscovite flakes rapidly developed but did not make the composite aggregate weaker when compared with single-phase halite. Comparison with synthetic aggregates of single-phase halite shows that the two-phase aggregate was much stronger than single-phase halite in all cases. Comparison with a synthetic aggregate with calcite porphyroclasts shows that the strength of the aggregate with muscovite at 100 °C was lower below a strain of ca. 2.6 and higher beyond this value, and that the aggregate with calcite was stronger at 200 °C. Strain rate stepping tests (1E-5 s -1-2E-3 s -1) indicate that the two-phase aggregate behaved as power-law viscous, with stress exponents of ca. 12 and 10 at

  18. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. 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.

  20. 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.

  1. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26723608

  3. 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.

  4. An experimental study on the hazard assessment and mechanical properties of porous concrete utilizing coal bottom ash coarse aggregate in Korea.

    PubMed

    Park, Seung Bum; Jang, Young Il; Lee, Jun; Lee, Byung Jae

    2009-07-15

    This study evaluates quality properties and toxicity of coal bottom ash coarse aggregate and analyzes mechanical properties of porous concrete depending on mixing rates of coal bottom ash. As a result, soundness and resistance to abrasion of coal bottom ash coarse aggregate were satisfied according to the standard of coarse aggregate for concrete. To satisfy the standard pertaining to chloride content, the coarse aggregates have to be washed more than twice. In regards to the result of leaching test for coal bottom ash coarse aggregate and porous concrete produced with these coarse aggregates, it was satisfied with the environment criteria. As the mixing rate of coal bottom ash increased, influence of void ratio and permeability coefficient was very little, but compressive and flexural strength decreased. When coal bottom ash was mixed over 40%, strength decreased sharply (compressive strength: by 11.7-27.1%, flexural strength: by maximum 26.4%). Also, as the mixing rate of coal bottom ash increased, it was confirmed that test specimens were destroyed by aggregate fracture more than binder fracture and interface fracture. To utilize coal bottom ash in large quantities, it is thought that an improvement method in regards to strength has to be discussed such as incorporation of reinforcing materials and improvement of aggregate hardness.

  5. Fundamental Study on the Development of Structural Lightweight Concrete by Using Normal Coarse Aggregate and Foaming Agent.

    PubMed

    Lee, Han-Seung; Ismail, Mohamed A; Woo, Young-Je; Min, Tae-Beom; Choi, Hyun-Kook

    2014-06-13

    Structural lightweight concrete (SLWC) has superior properties that allow the optimization of super tall structure systems for the process of design. Because of the limited supply of lightweight aggregates in Korea, the development of structural lightweight concrete without lightweight aggregates is needed. The physical and mechanical properties of specimens that were cast using normal coarse aggregates and different mixing ratios of foaming agent to evaluate the possibility of creating structural lightweight concrete were investigated. The results show that the density of SLWC decreases as the dosage of foaming agent increases up to a dosage of 0.6%, as observed by SEM. It was also observed that the foaming agent induced well separated pores, and that the size of the pores ranged from 50 to 100 μm. Based on the porosity of concrete specimens with foaming agent, compressive strength values of structural lightweight foam concrete (SLWFC) were obtained. It was also found that the estimated values from proposed equations for compressive strength and modulus of elasticity of SLWFC, and values obtained by actual measurements were in good agreement. Thus, this study confirms that new structural lightweight concrete using normal coarse aggregates and foaming agent can be developed successfully.

  6. Fundamental Study on the Development of Structural Lightweight Concrete by Using Normal Coarse Aggregate and Foaming Agent

    PubMed Central

    Lee, Han-Seung; Ismail, Mohamed A.; Woo, Young-Je; Min, Tae-Beom; Choi, Hyun-Kook

    2014-01-01

    Structural lightweight concrete (SLWC) has superior properties that allow the optimization of super tall structure systems for the process of design. Because of the limited supply of lightweight aggregates in Korea, the development of structural lightweight concrete without lightweight aggregates is needed. The physical and mechanical properties of specimens that were cast using normal coarse aggregates and different mixing ratios of foaming agent to evaluate the possibility of creating structural lightweight concrete were investigated. The results show that the density of SLWC decreases as the dosage of foaming agent increases up to a dosage of 0.6%, as observed by SEM. It was also observed that the foaming agent induced well separated pores, and that the size of the pores ranged from 50 to 100 μm. Based on the porosity of concrete specimens with foaming agent, compressive strength values of structural lightweight foam concrete (SLWFC) were obtained. It was also found that the estimated values from proposed equations for compressive strength and modulus of elasticity of SLWFC, and values obtained by actual measurements were in good agreement. Thus, this study confirms that new structural lightweight concrete using normal coarse aggregates and foaming agent can be developed successfully. PMID:28788691

  7. 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.

  8. 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})

  9. 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.

  10. 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.

  11. Peptide Aggregation and Pore Formation in a Lipid Bilayer: A Combined Coarse-Grained and All Atom Molecular Dynamics Study

    PubMed Central

    Thøgersen, Lea; Schiøtt, Birgit; Vosegaard, Thomas; Nielsen, Niels Chr.; Tajkhorshid, Emad

    2008-01-01

    We present a simulation study where different resolutions, namely coarse-grained (CG) and all-atom (AA) molecular dynamics simulations, are used sequentially to combine the long timescale reachable by CG simulations with the high resolution of AA simulations, to describe the complete processes of peptide aggregation and pore formation by alamethicin peptides in a hydrated lipid bilayer. In the 1-μs CG simulations the peptides spontaneously aggregate in the lipid bilayer and exhibit occasional transitions between the membrane-spanning and the surface-bound configurations. One of the CG systems at t = 1 μs is reverted to an AA representation and subjected to AA simulation for 50 ns, during which water molecules penetrate the lipid bilayer through interactions with the peptide aggregates, and the membrane starts leaking water. During the AA simulation significant deviations from the α-helical structure of the peptides are observed, however, the size and arrangement of the clusters are not affected within the studied time frame. Solid-state NMR experiments designed to match closely the setup used in the molecular dynamics simulations provide strong support for our finding that alamethicin peptides adopt a diverse set of configurations in a lipid bilayer, which is in sharp contrast to the prevailing view of alamethicin oligomers formed by perfectly aligned helical alamethicin peptides in a lipid bilayer. PMID:18676652

  12. Comparison of non-parametric methods for ungrouping coarsely aggregated data.

    PubMed

    Rizzi, Silvia; Thinggaard, Mikael; Engholm, Gerda; Christensen, Niels; Johannesen, Tom Børge; Vaupel, James W; Lindahl-Jacobsen, Rune

    2016-05-23

    Histograms are a common tool to estimate densities non-parametrically. They are extensively encountered in health sciences to summarize data in a compact format. Examples are age-specific distributions of death or onset of diseases grouped in 5-years age classes with an open-ended age group at the highest ages. When histogram intervals are too coarse, information is lost and comparison between histograms with different boundaries is arduous. In these cases it is useful to estimate detailed distributions from grouped data. From an extensive literature search we identify five methods for ungrouping count data. We compare the performance of two spline interpolation methods, two kernel density estimators and a penalized composite link model first via a simulation study and then with empirical data obtained from the NORDCAN Database. All methods analyzed can be used to estimate differently shaped distributions; can handle unequal interval length; and allow stretches of 0 counts. The methods show similar performance when the grouping scheme is relatively narrow, i.e. 5-years age classes. With coarser age intervals, i.e. in the presence of open-ended age groups, the penalized composite link model performs the best. We give an overview and test different methods to estimate detailed distributions from grouped count data. Health researchers can benefit from these versatile methods, which are ready for use in the statistical software R. We recommend using the penalized composite link model when data are grouped in wide age classes.

  13. 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

  14. 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.

  15. 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

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

    PubMed

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

    2014-11-19

    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 component, 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 ?. 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 < 0.0701 u (b) transition regime, 0.0701 u ≤ Δ ≤ 0.0916 u and (c) thick coating regime, Δ > 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 < Δ < 7.0 nm transition regime, 7.0 < Δ < 9.2 nm and thick coating, Δ > 9.2 nm (5) The minimum minority TAG concentration required to undergo nano-phase separation is, approximately, 0.29% (thin coatings) and 0.94% (thick coatings). Minority

  17. Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model.

    PubMed

    Spill, Yannick G; Pasquali, Samuela; Derreumaux, Philippe

    2011-05-10

    The simulation of amyloid fibril formation is impossible if one takes into account all chemical details of the amino acids and their detailed interactions with the solvent. We investigate the folding and aggregation of two model peptides using the optimized potential for efficient structure prediction (OPEP) coarse-grained model and replica exchange molecular dynamics (REMD) simulations coupled with either the Langevin or the Berendsen thermostat. For both the monomer of blocked penta-alanine and the trimer of the 25-35 fragment of the Alzheimer's amyloid β protein, we find little variations in the equilibrium structures and heat capacity curves using the two thermostats. Despite this high similarity, we detect significant differences in the populations of the dominant conformations at low temperatures, whereas the configurational distributions remain the same in proximity of the melting temperature. Aβ25-35 trimers at 300 K have an averaged β-sheet content of 12% and are primarily characterized by fully disordered peptides or a small curved two-stranded β-sheet stabilized by a disordered peptide. In addition, OPEP molecular dynamics simulations of Aβ25-35 hexamers at 300 K with a small curved six-stranded antiparallel β-sheet do not show any extension of the β-sheet content. These data support the idea that the mechanism of Aβ25-35 amyloid formation does not result from a high fraction of extended β-sheet-rich trimers and hexamers.

  18. Does mycorrhizal inoculation improve plant survival, aggregate stability, and fine root development on a coarse-grained soil in an alpine eco-engineering field experiment?

    NASA Astrophysics Data System (ADS)

    Bast, A.; Wilcke, W.; Graf, F.; Lüscher, P.; Gärtner, H.

    2016-08-01

    Steep vegetation-free talus slopes in high mountain environments are prone to superficial slope failures and surface erosion. Eco-engineering measures can reduce slope instabilities and thus contribute to risk mitigation. In a field experiment, we established mycorrhizal and nonmycorrhizal research plots and determined their biophysical contribution to small-scale soil fixation. Mycorrhizal inoculation impact on plant survival, aggregate stability, and fine root development was analyzed. Here we present plant survival (ntotal = 1248) and soil core (ntotal = 108) analyses of three consecutive years in the Swiss Alps. Soil cores were assayed for their aggregate stability coefficient (ASC), root length density (RLD), and mean root diameter (MRD). Inoculation improved plant survival significantly, but it delayed aggregate stabilization relative to the noninoculated site. Higher aggregate stability occurred only after three growing seasons. Then also RLD tended to be higher and MRD increased significantly at the mycorrhizal treated site. There was a positive correlation between RLD, ASC, and roots <0.5 mm, which had the strongest impact on soil aggregation. Our results revealed a temporal offset between inoculation effects tested in laboratory and field experiments. Consequently, we recommend to establish an intermediate to long-term field experimental monitoring before transferring laboratory results to the field.

  19. 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.

  20. Predictive coarse-graining

    NASA Astrophysics Data System (ADS)

    Schöberl, Markus; Zabaras, Nicholas; Koutsourelakis, Phaedon-Stelios

    2017-03-01

    We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method [1] and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the coarse-graining process. Furthermore, it can be readily extended to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo - Expectation-Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model.

  1. Coarse-grained protein molecular dynamics simulations.

    PubMed

    Derreumaux, Philippe; Mousseau, Normand

    2007-01-14

    A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Abeta16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four Abeta16-22 peptides can form a three-stranded beta sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.

  2. Coarse-grained protein molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Derreumaux, Philippe; Mousseau, Normand

    2007-01-01

    A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.

  3. 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

  4. Coarse coal hydraulic transport

    SciTech Connect

    Petry, E.F.

    1982-10-01

    Discusses the development of coarse coal pipeline technology requiring a minimum of product size reduction. Initial concentration on continuous face haulage and later on mainline haulage areas led eventually to the system in operation at Loveridge mine in West Virginia. Key features of the hydraulic transport system (as shown in diagram) include the pump house, vertical hoisting, overland slurry lines, a preparation/ dewatering plant, a continuous miner, a coal crusher/injection vehicle, a flexible hose hauler, a rigid slurry line, a longwall injection station, and a slurry storage/reclaim system. Explains that the system was built primarily to serve a longwall face, but it also handles coal from 2 continuous miners on longwall development work.

  5. Study of Bond Characteristics of Reinforced Waste Glass Aggregate Concrete

    NASA Astrophysics Data System (ADS)

    Rajagopalan, P.; Balaji, V.; Unnikrishnan, N.; Jainul Haq, T.; Bhuvaneshwari, P.

    2017-07-01

    The conformity of properties of waste glass aggregate with conventional aggregate was found out. Nine cubes (150mm x 150mm x 150mm) were cast out of which three were used for control concrete, three were fully replaced with waste glass as coarse aggregate, three were partially replaced(50%) with waste glass as fine aggregate. Six cylinders (150mm x 300mm) were cast out of which two for control concrete, two cylinders with coarse aggregate fully replaced with waste glass aggregate(WGA) and remaining two cylinders with partially replaced (50%) fine aggregate with waste glass aggregate. Cured specimens were subjected to compression and split-tensile test to ascertain the characteristic compressive strength and split tensile strength. Since the surface of the coarse aggregate plays a significant role in bonding of the rebar in reinforced concrete, pull-out test on both control and Waste Glass Aggregate (WGA) cube specimens (150mm x 150mm with 20mm diameter steel rods) were conducted. Scanning Electron Microscopy (SEM) analysis has been done for better understanding of bonding properties in waste glass fine aggregate(WGFA) and waste glass coarse aggregate(WGCA) concrete. Comparison of the results with that of control specimens showed that waste glass could be effectively used as aggregates in reinforced concrete construction.

  6. Beneficiation of natural aggregates by polymer impregnation

    SciTech Connect

    Webster, R.P.; Fontana, J.J.

    1980-09-01

    The use of polymer impregnation as a means of upgrading natural aggregates has been investigated. The effect of polymer impregnation on the physical and mechanical properties was evaluated in a series of tests performed using four aggregates of varying quality. The strength of concrete cast with polymer impregnated coarse aggregate was also tested. Two monomer systems were used in the investigation; a methyl methacrylate-based system and a styrene-based system. In general, significant improvements in the physical and mechanical properties of each of the four aggregates resulted from polymer impregnation. The strength of concrete cast with impregnated aggregates varied, being increased in some cases and decreased in others.

  7. Deriving Coarse-Grained Charges from All-Atom Systems: An Analytic Solution.

    PubMed

    McCullagh, Peter; Lake, Peter T; McCullagh, Martin

    2016-09-13

    An analytic method to assign optimal coarse-grained charges based on electrostatic potential matching is presented. This solution is the infinite size and density limit of grid-integration charge-fitting and is computationally more efficient by several orders of magnitude. The solution is also minimized with respect to coarse-grained positions which proves to be an extremely important step in reproducing the all-atom electrostatic potential. The joint optimal-charge optimal-position coarse-graining procedure is applied to a number of aggregating proteins using single-site per amino acid resolution. These models provide a good estimate of both the vacuum and Debye-Hückel screened all-atom electrostatic potentials in the vicinity and in the far-field of the protein. Additionally, these coarse-grained models are shown to approximate the all-atom dimerization electrostatic potential energy of 10 aggregating proteins with good accuracy.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. Estimating the carbon in coarse woody debris with perpendicular distance sampling. Chapter 6

    Treesearch

    Harry T. Valentine; Jeffrey H. Gove; Mark J. Ducey; Timothy G. Gregoire; Michael S. Williams

    2008-01-01

    Perpendicular distance sampling (PDS) is a design for sampling the population of pieces of coarse woody debris (logs) in a forested tract. In application, logs are selected at sample points with probability proportional to volume. Consequently, aggregate log volume per unit land area can be estimated from tallies of logs at sample points. In this chapter we provide...

  14. Spectral coarse grained controllability of complex networks

    NASA Astrophysics Data System (ADS)

    Wang, Pei; Xu, Shuang

    2017-07-01

    With the accumulation of interaction data from various systems, a fundamental question in network science is how to reduce the sizes while keeping certain properties of complex networks. Combined the spectral coarse graining theory and the structural controllability of complex networks, we explore the structural controllability of undirected complex networks during coarse graining processes. We evidence that the spectral coarse grained controllability (SCGC) properties for the Erdös-Rényi (ER) random networks, the scale-free (SF) random networks and the small-world (SW) random networks are distinct from each other. The SW networks are very robust, while the SF networks are sensitive during the coarse graining processes. As an emergent properties for the dense ER networks, during the coarse graining processes, there exists a threshold value of the coarse grained sizes, which separates the controllability of the reduced networks into robust and sensitive to coarse graining. Investigations on some real-world complex networks indicate that the SCGC properties are varied among different categories and different kinds of networks, some highly organized social or biological networks are more difficult to be controlled, while many man-made power networks and infrastructure networks can keep the controllability properties during the coarse graining processes. Furthermore, we speculate that the SCGC properties of complex networks may depend on their degree distributions. The associated investigations have potential implications in the control of large-scale complex networks, as well as in the understanding of the organization of complex networks.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Peculiar Traits of Coarse AP (Briefing Charts)

    DTIC Science & Technology

    2014-12-01

    at differing rates due to pressure and temperature influences in both isolated crystals and solid propellant combustions. Consolidated coarse AP...phase AP is a primary actor during combustions. At very high pressures AP self combustion exhibits differential recession rates depending on whether...different reaction rates are also observed between low and high pressure confinements. In solid propellants coarse AP promotes dark zone combustion, low

  1. 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.

  2. 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.

  3. Optimizing the durability of the coarse fraction of porous asphalt RAP for effective recycling

    NASA Astrophysics Data System (ADS)

    Holleran, Irina; Wilson, Douglas J.; Black, Philippa; Holleran, Glynn; Walubita, Lubinda F.

    2017-09-01

    Porous asphalt (PA) durability depends not only on the binder used to manufacture the mix, but also on the aggregates chosen, particularly the coarse fraction component. Aggregates for PA should be of the highest quality and highly durable to withstand the effects of weather and traffic. To recycle PA into a new PA mix, without compromising the long-term performance, the durability of the recovered aggregates from PA-derived reclaimed asphalt pavement (RAP) should be assessed alongside the aged binder properties. In this study, the Micro-Deval (MD) Abrasion test, combined with water absorption, was found to be a good predictor of asphalt mix performance for PA. Minerology of the aggregates is an important factor when setting limits for MD loss. New Zealand (NZ) aggregates are significantly younger in geological terms, and chemically and physically less stable compared to the aggregates used in many other countries. This is especially true for greywacke, the most used aggregate in NZ for road construction. If the MD limits reported in some literature are applied to NZ PA-derived RAP aggregates, poor performing material can be erroneously incorporated in asphalt mixes. Findings from this study contributes in understanding how PA-derived RAP can be recycled into new value PA mixes.

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    PubMed

    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.

  6. Interplay Between Hydrophobic Effect and Dipole Interactions in Peptide Aggregation

    NASA Astrophysics Data System (ADS)

    Ganesan, Sai; Matysiak, Silvina

    In the past decade, the development of various coarse-grained models for proteins have provided key insights into the driving forces in folding and aggregation.We recently developed a low resolution Water Explicit Polarizable PROtein coarse-grained Model 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 interface using elastin-like octapeptides (GV)4 as a model system.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 increase in aggregate size in water and interface.Based on this cooperative effect, we provide a potential explanation for the observed nucleus size in peptide aggregation pathways.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.

  7. 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.

  8. 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.

  9. Coarse-grained short-range correlations

    NASA Astrophysics Data System (ADS)

    Simo, I. Ruiz; Pérez, R. Navarro; Amaro, J. E.; Ruiz Arriola, E.

    2017-05-01

    We develop a scheme to take into account the effects of short-range nucleon-nucleon correlations in the nucleon-pair wave function by solving the Bethe-Goldstone equation for a coarse-grained delta shell potential in S -wave configuration. The S -wave delta shell potential has been adjusted to reproduce the 1S0 phase shifts of the AV18 potential for this partial wave up to 2 GeV in the laboratory kinetic energy. We show that a coarse-grained potential can describe the high momentum tail of the back-to-back correlated pairs and the G matrix in momentum space. We discuss the easiness and robustness of the calculation in coordinate space and the future improvements and utilities of this model. This work suggests the possibility of using perturbation theory for describing the short-range correlations and, related to this, to substitute the G matrix by an appropriate coarse-grained potential.

  10. Chondrule Pyroxene Embedded in Cores of Amoeboid Olivine Aggregates from Allende: Evidence of Overlapping Formation Times of AOAs and Chondrules

    NASA Astrophysics Data System (ADS)

    Fagan, T. J.; Komatsu, M.; Nishijima, E.; Fukushima, H.; Yasuda, T.

    2016-08-01

    Coarse low-Ca pyroxene has been identified in two amoeboid olivine aggregates in the CV3 Allende. The pyroxene crystals appear to be relict chondrule phenocrysts. If so, the texture indicates overlapping formation times of AOAs and chondrules.

  11. 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.

  12. Study on Mechanical Properties of Concrete Using Plastic Waste as an Aggregate

    NASA Astrophysics Data System (ADS)

    Jaivignesh, B.; Sofi, A.

    2017-07-01

    Disposal of large quantity of plastic causes land, water and air pollution etc.., so a study is conducted to recycle the plastic in concrete. This work investigates about the replacement of natural aggregate with non-biodegradable plastic aggregate made up of mixed plastic waste in concrete. Several tests are conducted such as compressive strength of cube, split tensile strength of cylinder, flexural strength test of prism to identify the properties and behavior of concrete using plastic aggregate. Replacement of fine aggregate weight by 10%, 15%, 20% with Plastic fine (PF) aggregate and for each replacement of fine aggregate 15%, 20%, 25% of coarse aggregate replacement also conducted with Plastic Coarse(PC) aggregate. In literatures reported that the addition of plastic aggregate in concrete causes the reduction of strength in concrete due to poor bonding between concrete and plastic aggregate, so addition of 0.3% of steel fiber by weight of cement in concrete is done to improve the concrete strength. Totally 60 cubes, 60 cylinders and 40 prisms are casted to identify the compressive strength, split tensile strength and flexural strength respectively. Casted specimens are tested at 7 and 28 days. The identified results from concrete using plastic aggregate are compared with conventional concrete. Result shows that reduction in mechanical properties of plastic aggregate added concrete. This reduction in strength is mainly due to poor bond strength between cement and plastic aggregate.

  13. 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.

  14. Sampling coarse woody debris along spoked transects

    Treesearch

    Paul C. Van Deusen; Jeffery H. Gove

    2011-01-01

    Line transects are commonly used for sampling coarse woody debris (CWD). The USDA Forest Service Forest Inventory and Analysis programme uses a variant of this method that involves sampling for CWD along transects that radiate from the centre of a circular plot-like spokes on a wheel. A new approach for analysis of data collected with spoked transects is developed....

  15. Early Deterioration of Coarse Woody Debris

    Treesearch

    F.H. Tainter; J.W. McMinn

    1999-01-01

    Coarse woody debris (CWD) is an important structural component of southern forest ecosystems. CWD loading may be affected by different decomposition rates on sites of varying quality. Bolts of red oak and loblolly pine were placed on plots at each of three (hydric, mesic. and xeric) sites at the Savannah River Site and sampled over a 16-week period. Major changes...

  16. Folding, Binding, Misfolding and Aggregation with AWSEM

    NASA Astrophysics Data System (ADS)

    Schafer, Nicholas P.

    This thesis discusses our recent results using the Associative-memory, Water-mediated, Structure and Energy Model (AWSEM), an optimized, coarse-grained molecular dynamics protein folding model, to fold, bind, and predict the misfolding behavior of proteins. AWSEM is capable of performing de novo structure prediction on small alpha-helical protein domains and predict the binding interfaces of homo- and hetero-dimers. More recent work demonstrates how the misfolding behavior of tandem constructs in AWSEM is consistent with crucial aspects of ensemble and single molecule experiments on the aggregation and misfolding of these constructs. The first chapter is a review of the energy landscape theory of protein folding as it applies to the problem of protein structure prediction, and more specifically how energy landscape theory and the principle of minimal frustration can be used to optimize parameters of coarse-grained protein folding simulation models. The subsequent four chapters are reports of novel research performed with one such model.

  17. 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.

  18. Sequence dependent aggregation of peptides and fibril formation

    NASA Astrophysics Data System (ADS)

    Hung, Nguyen Ba; Le, Duy-Manh; Hoang, Trinh X.

    2017-09-01

    Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.

  19. Sequence dependent aggregation of peptides and fibril formation.

    PubMed

    Hung, Nguyen Ba; Le, Duy-Manh; Hoang, Trinh X

    2017-09-14

    Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.

  20. 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

  1. Computational approaches to understanding protein aggregation in neurodegeneration.

    PubMed

    Redler, Rachel L; Shirvanyants, David; Dagliyan, Onur; Ding, Feng; Kim, Doo Nam; Kota, Pradeep; Proctor, Elizabeth A; Ramachandran, Srinivas; Tandon, Arpit; Dokholyan, Nikolay V

    2014-04-01

    The generation of toxic non-native protein conformers has emerged as a unifying thread among disorders such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Atomic-level detail regarding dynamical changes that facilitate protein aggregation, as well as the structural features of large-scale ordered aggregates and soluble non-native oligomers, would contribute significantly to current understanding of these complex phenomena and offer potential strategies for inhibiting formation of cytotoxic species. However, experimental limitations often preclude the acquisition of high-resolution structural and mechanistic information for aggregating systems. Computational methods, particularly those combine both all-atom and coarse-grained simulations to cover a wide range of time and length scales, have thus emerged as crucial tools for investigating protein aggregation. Here we review the current state of computational methodology for the study of protein self-assembly, with a focus on the application of these methods toward understanding of protein aggregates in human neurodegenerative disorders.

  2. 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.

  3. Synthetic aggregates from combustion ashes using an innovative rotary kiln.

    PubMed

    Wainwright, P J; Cresswell, D J

    2001-01-01

    This paper describes the use of a number of different combustion ashes to manufacture synthetic aggregates using an innovative rotary 'Trefoil' kiln. Three types of combustion ash were used, namely: incinerated sewage sludge ash (ISSA); municipal solid waste incinerator bottom ash (MSWIBA-- referred to here as BA); and pulverised fuel ash (Pfa). The fine waste ash fractions listed above were combined with a binder to create a plastic mix that was capable of being formed into 'green pellets'. These pellets were then fired in a Trefoil kiln to sinter the ashes into hard fused aggregates that were then tested for use as a replacement for the natural coarse aggregate in concrete. Results up to 28 days showed that these synthetic aggregates were capable of producing concretes with compressive strengths ranging from 33 to 51 MPa, equivalent to between 73 and 112% of that of the control concrete made with natural aggregates.

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

    NASA Astrophysics Data System (ADS)

    Ding, Yajun; Mittal, Jeetain

    2014-11-01

    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.

  5. Reusing recycled aggregates in structural concrete

    NASA Astrophysics Data System (ADS)

    Kou, Shicong

    The utilization of recycled aggregates in concrete can minimize environmental impact and reduce the consumption of natural resources in concrete applications. The aim of this thesis is to provide a scientific basis for the possible use of recycled aggregates in structure concrete by conducting a comprehensive programme of laboratory study to gain a better understanding of the mechanical, microstructure and durability properties of concrete produced with recycled aggregates. The study also explored possible techniques to of improve the properties of recycled aggregate concrete that is produced with high percentages (≧ 50%) of recycled aggregates. These techniques included: (a) using lower water-to-cement ratios in the concrete mix design; (b) using fly ash as a cement replacement or as an additional mineral admixture in the concrete mixes, and (c) precasting recycled aggregate concrete with steam curing regimes. The characteristics of the recycled aggregates produced both from laboratory and a commercially operated pilot construction and demolition (C&D) waste recycling plant were first studied. A mix proportioning procedure was then established to produce six series of concrete mixtures using different percentages of recycled coarse aggregates with and without the use of fly ash. The water-to-cement (binder) ratios of 0.55, 0.50, 0.45 and 0.40 were used. The fresh properties (including slump and bleeding) of recycled aggregate concrete (RAC) were then quantified. The effects of fly ash on the fresh and hardened properties of RAC were then studied and compared with those RAC prepared with no fly ash addition. Furthermore, the effects of steam curing on the hardened properties of RAC were investigated. For micro-structural properties, the interfacial transition zones of the aggregates and the mortar/cement paste were analyzed by SEM and EDX-mapping. Moreover, a detailed set of results on the fracture properties for RAC were obtained. Based on the experimental

  6. Coarse grain forces in star polymer melts.

    PubMed

    Liu, L; den Otter, W K; Briels, W J

    2014-10-21

    An analysis is presented of forces acting on the centers of mass of three-armed star polymers in the molten state. The arms consist of 35 Kremer-Grest beads, which is slightly larger than needed for one entanglement mass. For a given configuration of the centers of mass, instantaneous forces fluctuate wildly around averages which are two orders of magnitude smaller than their root mean square deviations. Average forces are well described by an implicit many-body potential, while pair models fail completely. The fluctuating forces are modelled by means of dynamical variables quantifying the degree of mixing of the various polymer pairs. All functions and parameters in a coarse grain model based on these concepts are obtained from the underlying small scale simulation. The coarse model reproduces both the diffusion coefficient and the shear relaxation modulus. Ways to improve the model suggest themselves on the basis of our findings.

  7. Coarse Grid CFD for underresolved simulation

    NASA Astrophysics Data System (ADS)

    Class, Andreas G.; Viellieber, Mathias O.; Himmel, Steffen R.

    2010-11-01

    CFD simulation of the complete reactor core of a nuclear power plant requires exceedingly huge computational resources so that this crude power approach has not been pursued yet. The traditional approach is 1D subchannel analysis employing calibrated transport models. Coarse grid CFD is an attractive alternative technique based on strongly under-resolved CFD and the inviscid Euler equations. Obviously, using inviscid equations and coarse grids does not resolve all the physics requiring additional volumetric source terms modelling viscosity and other sub-grid effects. The source terms are implemented via correlations derived from fully resolved representative simulations which can be tabulated or computed on the fly. The technique is demonstrated for a Carnot diffusor and a wire-wrap fuel assembly [1]. [4pt] [1] Himmel, S.R. phd thesis, Stuttgart University, Germany 2009, http://bibliothek.fzk.de/zb/berichte/FZKA7468.pdf

  8. 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.

  9. Coarse-graining polymers as soft colloids

    NASA Astrophysics Data System (ADS)

    Louis, A. A.; Bolhuis, P. G.; Finken, R.; Krakoviack, V.; Meijer, E. J.; Hansen, J. P.

    2002-04-01

    We show how to coarse-grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid- or end-points of the polymers. We also show how to extend these methods to polymers in poor solvents and mixtures of polymers. Treating polymers as soft colloids can greatly speed up the simulation of complex many-polymer systems, including polymer-colloid mixtures.

  10. Coarse graining flow of spin foam intertwiners

    NASA Astrophysics Data System (ADS)

    Dittrich, Bianca; Schnetter, Erik; Seth, Cameron J.; Steinhaus, Sebastian

    2016-12-01

    Simplicity constraints play a crucial role in the construction of spin foam models, yet their effective behavior on larger scales is scarcely explored. In this article we introduce intertwiner and spin net models for the quantum group SU (2 )k×SU (2 )k, which implement the simplicity constraints analogous to four-dimensional Euclidean spin foam models, namely the Barrett-Crane (BC) and the Engle-Pereira-Rovelli-Livine/Freidel-Krasnov (EPRL/FK) model. These models are numerically coarse grained via tensor network renormalization, allowing us to trace the flow of simplicity constraints to larger scales. In order to perform these simulations we have substantially adapted tensor network algorithms, which we discuss in detail as they can be of use in other contexts. The BC and the EPRL/FK model behave very differently under coarse graining: While the unique BC intertwiner model is a fixed point and therefore constitutes a two-dimensional topological phase, BC spin net models flow away from the initial simplicity constraints and converge to several different topological phases. Most of these phases correspond to decoupling spin foam vertices; however we find also a new phase in which this is not the case, and in which a nontrivial version of the simplicity constraints holds. The coarse graining flow of the BC spin net models indicates furthermore that the transitions between these phases are not of second order. The EPRL/FK model by contrast reveals a far more intricate and complex dynamics. We observe an immediate flow away from the original simplicity constraints; however, with the truncation employed here, the models generically do not converge to a fixed point. The results show that the imposition of simplicity constraints can indeed lead to interesting and also very complex dynamics. Thus we need to further develop coarse graining tools to efficiently study the large scale behavior of spin foam models, in particular for the EPRL/FK model.

  11. The Theory of Ultra Coarse-graining

    NASA Astrophysics Data System (ADS)

    Voth, Gregory

    2013-03-01

    Coarse-grained (CG) models provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms correlated over distance scales of many covalent bond lengths and long time scales. Variational methods based on information from simulations of finer-grained (e.g., all-atom) models, for example the multiscale coarse-graining (MS-CG) and relative entropy minimization methods, provide attractive tools for the systematic development of CG models. However, these methods have important drawbacks when used in the ``ultra coarse-grained'' (UCG) regime, e.g., at a resolution level coarser or much coarser than one amino acid residue per effective CG particle in proteins. This is due to the possible existece of multiple metastable states ``within'' the CG sites for a given UCG model configuration. In this talk I will describe systematic variational UCG methods specifically designed to CG entire protein domains and subdomains into single effective CG particles. This is accomplished by augmenting existing effective particle CG schemes to allow for discrete state transitions and configuration-dependent resolution. Additionally, certain conclusions of this work connect back to single-state force matching and open up new avenues for method development in that area. These results provide a formal statistical mechanical basis for UCG methods related to force matching and relative entropy CG methods and suggest practical algorithms for constructing optimal approximate UCG models from fine-grained simulation data.

  12. Multiscale coarse graining of diblock copolymer self-assembly: from monomers to ordered micelles.

    PubMed

    Pierleoni, Carlo; Addison, Chris; Hansen, Jean-Pierre; Krakoviack, Vincent

    2006-03-31

    Starting from a microscopic lattice model, we investigate clustering, micellization, and micelle ordering in semidilute solutions of AB diblock copolymers in a selective solvent. To bridge the gap in length scales, from monomers to ordered micellar structures, we implement a two-step coarse-graining strategy, whereby the AB copolymers are mapped onto ultrasoft dumbells with monomer-averaged effective interactions between the centers of mass of the blocks. Monte Carlo simulations of this coarse-grained model yield clear-cut evidence for self-assembly into micelles with a mean aggregation number n approximately 100 beyond a critical concentration. At a slightly higher concentration the micelles spontaneously undergo a disorder-order transition to a cubic phase. We determine the effective potential between these micelles from first principles.

  13. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. 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.

  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. The coarse-grained OPEP force field for non-amyloid and amyloid proteins.

    PubMed

    Chebaro, Yassmine; Pasquali, Samuela; Derreumaux, Philippe

    2012-08-02

    Coarse-grained protein models with various levels of granularity and degrees of freedom offer the possibility to explore many phenomena including folding, assembly, and recognition in terms of dynamics and thermodynamics that are inaccessible to all-atom representations in explicit aqueous solution. Here, we present a refined version of the coarse-grained optimized potential for efficient protein structure prediction (OPEP) based on a six-bead representation. The OPEP version 4.0 parameter set, which uses a new analytical formulation for the nonbonded interactions and adds specific side-chain-side-chain interactions for α-helix, is subjected to three tests. First, we show that molecular dynamics simulations at 300 K preserve the experimental rigid conformations of 17 proteins with 37-152 amino acids within a root-mean-square deviation (RMSD) of 3.1 Å after 30 ns. Extending the simulation time to 100 ns for five proteins does not change the RMSDs. Second, replica exchange molecular dynamics (REMD) simulations recover the NMR structures of three prototypical β-hairpin and α-helix peptides and the NMR three-stranded β-sheet topology of a 37-residue WW domain, starting from randomly chosen states. Third, REMD simulations on the ccβ peptide show a temperature transition from a three-stranded coiled coil to amyloid-like aggregates consistent with experiments, while simulations on low molecular weight aggregates of the prion protein helix 1 do not. Overall, these studies indicate the effectiveness of our OPEP4 coarse-grained model for protein folding and aggregation, and report two future directions for improvement.

  17. Coarse woody debris dynamics in two old-growth ecosystems

    SciTech Connect

    Harmon, M.E. ); Chen Hua )

    1991-10-01

    In this article, the dynamics of coarse woody debris are compound deciduous old-growth forest system Changbai Mountain Biosphere Reserve in China, and a coniferous old-growth forest system, H. J. Andrews Experimental Forest in Oregon. The objective is to compare in these two ecosystems the amount of coarse woody debris; the processes that affect coarse woody debris, such as tree mortality and decay rates; and the role of coarse woody debris in nutrient cycling. To assess importance in the global carbon budget, these two old-growth ecosystems are used to estimate the upper and lower limits of coarse woody debris mass for undisturbed temperate forests.

  18. 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.

  19. 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.

  20. On mean type aggregation.

    PubMed

    Yager, R R

    1996-01-01

    We introduce and define the concept of mean aggregation of a collection of n numbers. We point out that the lack of associativity of this operation compounds the problem of the extending mean of n numbers to n+1 numbers. The closely related concepts of self identity and the centering property are introduced as one imperative for extending mean aggregation operators. The problem of weighted mean aggregation is studied. A new concept of prioritized mean aggregation is then introduced. We next show that the technique of selecting an element based upon the performance of a random experiment can be considered as a mean aggregation operation.

  1. Effect of different sintering temperature on fly ash based geopolymer artificial aggregate

    NASA Astrophysics Data System (ADS)

    Abdullah, Alida; Abdullah, Mohd Mustafa Al Bakri; Hussin, Kamarudin; Tahir, Muhammad Faheem Mohd

    2017-04-01

    This research was conducted to study the mechanical and morphology of fly ash based geopolymer as artificial aggregate at different sintering temperature. The raw material that are used is fly ash, sodium hydroxide, sodium silicate, geopolymer artificial aggregate, Ordinary Portland Cement (OPC), coarse aggregate and fine aggregate. The research starts with the preparation of geopolymer artificial aggregate. Then, geopolymer artificial aggregate will be sintered at six difference temperature that is 400°C, 500°C, 600°C, 700°C, 800°C and 900°C to known at which temperature the geopolymer artificial aggregate will become a lightweight aggregate. In order to characterize the geopolymer artificial aggregate the X-ray Diffraction (XRD) and X-Ray Fluorescence (XRF) was done. The testing and analyses involve for the artificial aggregate is aggregate impact test, specific gravity test and Scanning Electron Microscopy (SEM). After that the process will proceed to produce concrete with two type of different aggregate that is course aggregate and geopolymer artificial aggregate. The testing for concrete is compressive strength test, water absorption test and density test. The result obtained will be compared and analyse.

  2. 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.

  3. Early deterioration of coarse woody debris.

    SciTech Connect

    Tainter, Frank, H.; McMinn, James, W.

    1999-02-16

    Tainter, F.H., and J.W. McMinn. 1999. Early deterioration of coarse woody debris. In: Proc. Tenth Bien. South. Silv. Res. Conf. Shreveport, LA, February 16-18, 1999. Pp. 232-237 Abstract - Coarse woody debris (CWD) is an important structural component of southern forest ecosystems. CWD loading may be affected by different decomposition rates on sites of varying quality. Bolts of red oak and loblolly pine were placed on plots at each of three (hydric, mesic. and xerlc) sites at the Savannah River Site and sampled over a I6-week period. Major changes were in moisture content and nonstructural carbohydrate content (total carbohydrates, reducing sugars, and starch) of sapwood. Early changes in nonstructural carbohydrate levels following placement of the bolts were likely due to reallocation of these materials by sapwood parenchyma cells. These carbohydrates later formed pools increasingly metabolized by bacteria and invading fungi. Most prevalent fungi in sapwood were Ceratocysfis spp. in pine and Hypoxy/on spp. in oak. Although pine sapwood became blue stained and oak sapwood exhibited yellow soft decay with black zone lines, estimators of decay (specific gravity, sodium hydroxide solubility, and holocellulose content) were unchanged during the 16-week study period. A small effect of site was detected for starch content of sapwood of both species. Fungal biomass in sapwood of both species, as measured by ergosterol content, was detectable at week zero, increased somewhat by week three and increased significantly by week 16.

  4. 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.

  5. 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.

  6. 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. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. Applicability of recycled aggregates in concrete piles for soft soil improvement.

    PubMed

    Medeiros-Junior, Ronaldo A; Balestra, Carlos Et; Lima, Maryangela G

    2017-01-01

    The expressive generation of construction and demolition waste is stimulating several studies for reusing this material. The improvement of soft soils by concrete compaction piles has been widely applied for 40 years in some Brazilian cities. This technique is used to improve the bearing capacity of soft soils, allowing executing shallow foundations instead of deep foundations. The compaction piles use a high volume of material. This article explored the possibility of using recycled aggregates from construction waste to replace the natural aggregates in order to improve the bearing capacity of the soft soil, regarding its compressive strength. Construction wastes from different stages of a construction were used in order to make samples of concrete with recycled aggregates. The strength of concretes with natural aggregates was compared with the strength of concretes with recycled (fine and coarse) aggregates. Results show that all samples met the minimum compressive strength specified for compaction piles used to improve the bearing capacity of soft soils. The concrete with recycled aggregate from the structural stage had even higher resistances than the concrete with natural aggregates. This behaviour was attributed to the large amount of cementitious materials in the composition of this type of concrete. It was also observed that concrete with recycled fine aggregate has a superior resistance to concrete with recycled coarse aggregate.

  8. Freezing promotes perception of coarse visual features.

    PubMed

    Lojowska, Maria; Gladwin, Thomas E; Hermans, Erno J; Roelofs, Karin

    2015-12-01

    Freezing is an evolutionarily preserved defensive behavior, characterized by immobility and heart rate deceleration, which is thought to promote visual perception. Rapid perceptual assessment of threat is crucial in life-threatening situations; for example, when policemen need to make split-second decisions about the use of deadly force. Here, we hypothesized that freezing is specifically associated with better perception of rapidly processed coarse, low-spatial frequency (LSF) features. We used a visual discrimination task in which participants determined the orientation of LSF and high-spatial frequency (HSF) gratings under threat of shock and safe conditions. As predicted, threat anticipation improved perception of LSF at the expense of HSF gratings. Crucially, stronger decrease in heart rate, a parasympathetic physiological index of freezing, was linked to better perception of LSF. These results provide empirical evidence for the comobilization of physiological and perceptual processes, which may play an important role in decision making under acute stress. (c) 2015 APA, all rights reserved).

  9. Coarse-graining approach to quantum cosmology

    NASA Astrophysics Data System (ADS)

    Calzetta, Esteban; Castagnino, Mario; Scoccimarro, Román

    1992-04-01

    We consider a Friedmann-Robertson-Walker model with both classical radiation and a massive (conformally coupled) quantum scalar field in the framework of quantum cosmology. We define a density matrix and introduce a notion of ``relevance'' which splits this density matrix into a ``relevant'' and an ``irrelevant'' part. A ``generalized coarse-graining method'' is used to obtain the evolution (in Robertson-Walker a ``time'') of the relevant density matrix, taking into account the back reaction of the irrelevant variables. We discuss the physical basis for the choice of a concept of relevance, and the features of cosmic evolution brought forward by the effective dynamics. In the limit of ``small universes,'' the relevant subdynamics is dissipative.

  10. Coarse-grained model of glycosaminoglycans.

    PubMed

    Samsonov, Sergey A; Bichmann, Leon; Pisabarro, M Teresa

    2015-01-26

    Glycosaminoglycans (GAGs) represent a class of anionic periodic linear polysaccharides, which mediate cell communication processes by interactions with their protein targets in the extracellular matrix. Due to their high flexibility, charged nature, periodicity, and polymeric nature, GAGs are challenging systems for computational approaches. To deal with the length challenge, coarse-grained (CG) modeling could be a promising approach. In this work, we develop AMBER-compatible CG parameters for GAGs using all-atomic (AA) molecular dynamics (MD) simulations in explicit solvent and the Boltzmann conversion approach. We compare both global and local properties of GAGs obtained in the simulations with AA and CG approaches, and we conclude that our CG model is appropriate for the MD approach of long GAG molecules at long time scales.

  11. Structure-based coarse-graining in liquid slabs.

    PubMed

    Jochum, Mara; Andrienko, Denis; Kremer, Kurt; Peter, Christine

    2012-08-14

    Structure-based coarse-graining relies on matching the pair correlation functions of a reference (atomistic) and a coarse-grained system. As such, it is designed for systems with uniform density distributions. Here, we demonstrate how it can be generalized for inhomogeneous systems by coarse-graining slabs of liquid water and methanol in vacuum, as well as a single benzene molecule at the water-vacuum interface. Our conclusion is that coarse-graining performed in inhomogeneous systems improves thermodynamic properties and the structure of interfaces without significant alterations to the local structure of the bulk liquid.

  12. Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

    DOE PAGES

    Mansbach, Rachael A.; Ferguson, Andrew L.

    2017-02-10

    Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately amore » branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.« less

  13. 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.

  14. 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

  15. Coarse-graining with information theory and the relative entropy

    NASA Astrophysics Data System (ADS)

    Shell, M. Scott

    2013-03-01

    There remain many both fundamental and practical/methodological questions regarding how coarse-grained models should be developed. Are there theoretically intuitive and numerically robust strategies for turning small-scale all-atom simulations into coarse models suitable for large-scale modeling? How can we identify what atomic details are unnecessary and can be discarded? Are there systematic ways to detect emergent physics? Here we discuss a fundamentally new approach to this problem. We propose that a natural way of viewing the coarse-graining problem is in terms of information theory. A quantity called the relative entropy measures the information lost upon coarse graining and hence the (inverse) fitness of a particular coarse-grained model. Minimization of the relative entropy thus provides a sort-of universal variational principle for coarse-graining, and a way to ``automatically'' discover and generate coarse models of many systems. We show that this new approach enables us to develop very simple but surprisingly accurate models of water, hydrophobic interactions, self-assembling peptides, and proteins that enable new physical insights as well as simulations of large-scale interactions. We discuss both theoretical and numerical aspects of this approach, in particular highlighting a new coarse-graining algorithm that efficiently optimizes coarse-grained models with even thousands of free parameters. We also discuss how the relative entropy approach suggests novel strategies for predicting the errors of coarse models, for identifying relevant degrees of freedom to retain, and for understanding the relationships among other coarse-graining methodologies.

  16. Pretreatment of turkey fat-containing wastewater in coarse sand and gravel/coarse sand bioreactors.

    PubMed

    Gaur, Rashmi Singh; Cai, Ling; Tuovinen, Olli H; Mancl, Karen M

    2010-02-01

    Fat, oil and grease in wastewater can be difficult to treat because of their slow decomposition. Traditional pretreatment facilities to remove fat, oil and grease from wastewater are increasingly costly. The hypothesis in this study was that pretreatment of animal fat-containing wastewater in sand and sand/gravel filters facilitates the conversion of slowly degradable organic matter measured as the difference between chemical oxygen demand (COD) and 5-day biochemical oxygen demand (BOD(5)) for subsequent biological treatment. The pretreatment was evaluated using simulated turkey-processing wastewater and coarse sand and sand/gravel filters at a constant hydraulic loading rate of 132L/m(2)/day. Two types of fixed media reactors were employed: (i) one set with a varying depth of coarse sand, and (ii) the second was similar but with an additional pea gravel cap. The results indicated that the relative removal of COD was slightly improved in the sand bioreactors with a pea gravel cap irrespective of the depth of coarse sand, but partial conversion to BOD(5) was not consistently demonstrated. Pea gravel may act as a sieve to entrap organic matter including fat globules from the wastewater. Multiple dosing at the same daily loading rate slightly improved the treatment efficiency of the sand bioreactors. The ratios of influent-COD/effluent-COD were always greater than 1.0 following a change in the dosing frequency after a rest period, suggesting that organic matter, specifically fat globules in this case, was retained by the column matrix.

  17. 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)

  18. 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)

  19. 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.

  20. 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. Copyright © 2010 Elsevier Ltd. All rights reserved.

  1. Marine Synechococcus Aggregation

    NASA Astrophysics Data System (ADS)

    Neuer, S.; Deng, W.; Cruz, B. N.; Monks, L.

    2016-02-01

    Cyanobacteria are considered to play an important role in the oceanic biological carbon pump, especially in oligotrophic regions. But as single cells are too small to sink, their carbon export has to be mediated by aggregate formation and possible consumption by zooplankton producing sinking fecal pellets. Here we report results on the aggregation of the ubiquitous marine pico-cyanobacterium Synechococcus as a model organism. We first investigated the mechanism behind such aggregation by studying the potential role of transparent exopolymeric particles (TEP) and the effects of nutrient (nitrogen or phosphorus) limitation on the TEP production and aggregate formation of these pico-cyanobacteria. We further studied the aggregation and subsequent settling in roller tanks and investigated the effects of the clays kaolinite and bentonite in a series of concentrations. Our results show that despite of the lowered growth rates, Synechococcus in nutrient limited cultures had larger cell-normalized TEP production, formed a greater volume of aggregates, and resulted in higher settling velocities compared to results from replete cultures. In addition, we found that despite their small size and lack of natural ballasting minerals, Synechococcus cells could still form aggregates and sink at measureable velocities in seawater. Clay minerals increased the number and reduced the size of aggregates, and their ballasting effects increased the sinking velocity and carbon export potential of aggregates. In comparison with the Synechococcus, we will also present results of the aggregation of the pico-cyanobacterium Prochlorococcus in roller tanks. These results contribute to our understanding in the physiology of marine Synechococcus as well as their role in the ecology and biogeochemistry in oligotrophic oceans.

  2. A vertical coarse approach scanning tunneling microscope

    NASA Astrophysics Data System (ADS)

    Drevniok, Benedict

    A Pan-style scanning tunneling microscope (STM), with a vertical coarse approach mechanism, was designed, built and tested. The microscope will be operated in ultra-high vacuum and also at cryogenic temperatures (8 K) inside a continuous flow cryostat. Fundamental differences in operating principle exist between the new microscope and the beetle-type inertial sliders [1] that have been the mainstay of the group for the last eight years. While Pan-style microscopes do already exist [2], they remain challenging to build, and an active area of research [3]. This system represents a bold departure from well-trodden paths, and will greatly expand the range of experiments that our group can perform. The operating principles of inertial piezoelectric motors are detailed. Design guidelines for a piezoelectric motor are given, and used in the design of the vertical coarse approach motor. A simple, inexpensive implementation for creating waveforms with an extremely fast fall time is discussed. Motor performance is tested, and a minimum step size of 20nm is found for frequencies ranging from 0 Hz to 3 kHz. The motor operates with high dynamic range: individual 20nm steps can be taken, as well as being able to move at a velocity of 0.4mm s-1. Little is known about the vibrational properties of Pan-style microscopes. Vibrational testing of the microscope revealed the expected scanner bending mode at 1.6 kHz (above the scanner bending mode of our beetles at 1.2 kHz), and a complicated response signal above this frequency. Custom extension springs for an eddy-current damping system are built and tested. A low resonant frequency of 1.8 Hz is found, which is ideal for the application. Initial testing of the STM in ambient conditions is performed on two different surfaces. A moire supermesh [4] with periodicity 3nm is observed on a highly-oriented pyrolytic graphite (HOPG) surface, and agrees well with previously published results. Using a flame-annealed Gold on mica surface, a low

  3. FINE AND COARSE PARTICLES: CONCENTRATION RELATIONSHIPS RELEVANT TO EPIDEMIOLOGICAL STUDIES

    EPA Science Inventory

    Fine particles and coarse particles are defined in terms of the modal structure of particle size distributions typically observed in the atmosphere. Differences among the various modes are discussed. The fractions of fine and coarse particles collected in specific size ranges, ...

  4. FINE AND COARSE PARTICLES: CONCENTRATION RELATIONSHIPS RELEVANT TO EPIDEMIOLOGICAL STUDIES

    EPA Science Inventory

    Fine particles and coarse particles are defined in terms of the modal structure of particle size distributions typically observed in the atmosphere. Differences among the various modes are discussed. The fractions of fine and coarse particles collected in specific size ranges, ...

  5. The production of synthetic aggregate from a quarry waste using an innovative style rotary kiln.

    PubMed

    Wainwright, R J; Cresswell, D J F; van der Sloot, H A

    2002-06-01

    The large volumes of wastes generated by industrialised society has led to efforts to find practical uses for these wastes, whilst also offsetting the consumption of natural resources. This paper describes the use of an innovative rotary kiln to produce synthetic aggregates from a variety of waste streams. The main waste used was a quarry fines which was blended with either paper sludge, clay, or a dredged harbour sediment. The different combinations were extruded and fired in the kiln to produce a material suitable for natural aggregate replacement. Two of the synthetic aggregates produced were tested by incorporation in to concrete as coarse aggregate replacement. The concrete 28-day compressive strengths achieved were above 40 N mm(-2) and compared favourably with control concretes made with natural aggregates and a commercially available lightweight aggregate (Lytag). Leaching tests have also been carried out to assess the potential environmental impact of utilisation. Although not finalised, these tests have also given favourable results.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Propagation of Tau aggregates.

    PubMed

    Goedert, Michel; Spillantini, Maria Grazia

    2017-05-30

    Since 2009, evidence has accumulated to suggest that Tau aggregates form first in a small number of brain cells, from where they propagate to other regions, resulting in neurodegeneration and disease. Propagation of Tau aggregates is often called prion-like, which refers to the capacity of an assembled protein to induce the same abnormal conformation in a protein of the same kind, initiating a self-amplifying cascade. In addition, prion-like encompasses the release of protein aggregates from brain cells and their uptake by neighbouring cells. In mice, the intracerebral injection of Tau inclusions induced the ordered assembly of monomeric Tau, followed by its spreading to distant brain regions. Short fibrils constituted the major species of seed-competent Tau. The existence of several human Tauopathies with distinct fibril morphologies has led to the suggestion that different molecular conformers (or strains) of aggregated Tau exist.

  12. Marine aggregate dynamics

    NASA Astrophysics Data System (ADS)

    The direction and scope of the Office of Naval Research's Marine Aggregate Dynamics Accelerated Research Initiative will be the topic of an open-house style meeting February 14, 7:30-10:00 P.M. in Ballroom D of the Hyatt Regency New Orleans at the Louisiana Superdome. This meeting is scheduled during the AGU/American Society of Limnology and Oceanography Ocean Sciences Meeting February 12-16 in New Orleans.The critical focus of the ARI is the measurement and modeling of the dynamics of the biological, physical, chemical and molecular processes that drive aggregation and produce aggregates. This new ARI will provide funding in Fiscal Years 1991-1995 to identify and quantify mechanisms that determine the distribution, abundance and size spectrum of aggregated particulate matter in the ocean.

  13. Aggregation and Averaging.

    ERIC Educational Resources Information Center

    Siegel, Irving H.

    The arithmetic processes of aggregation and averaging are basic to quantitative investigations of employment, unemployment, and related concepts. In explaining these concepts, this report stresses need for accuracy and consistency in measurements, and describes tools for analyzing alternative measures. (BH)

  14. 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.

  15. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals

    PubMed Central

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

    2016-01-01

    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

  16. 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.

  17. Aggregation of retail stores

    NASA Astrophysics Data System (ADS)

    Jensen, Pablo; Boisson, Jean; Larralde, Hernán

    2005-06-01

    We propose a simple model to understand the economic factors that induce aggregation of some businesses over small geographical regions. The model incorporates price competition with neighboring stores, transportation costs and the satisfaction probability of finding the desired product. We show that aggregation is more likely for stores selling expensive products and/or stores carrying only a fraction of the business variety. We illustrate our model with empirical data collected in the city of Lyon.

  18. Residential indoor and outdoor coarse particles and associated endotoxin exposures

    NASA Astrophysics Data System (ADS)

    Wheeler, Amanda J.; Dobbin, Nina A.; Lyrette, Ninon; Wallace, Lance; Foto, Mark; Mallick, Ranjeeta; Kearney, Jill; Van Ryswyk, Keith; Gilbert, Nicolas L.; Harrison, Ian; Rispler, Kathleen; Héroux, Marie-Eve

    2011-12-01

    There is a growing body of evidence demonstrating that coarse particles (PM 10-2.5) have detrimental impacts upon health, especially for respiratory effects. There are limited data available for indoor residential exposures. Some data exist regarding the composition of this PM size fraction with emphasis on crustal elements and biological components. This study includes data from 146 homes sampled in Regina, Saskatchewan (SK) where 5-day integrated concurrent monitoring of indoor and outdoor coarse particles was conducted during the winter and summer of 2007. The coarse particle filters were subsequently analysed for endotoxin content to determine the contribution of this compound. Winter indoor geometric mean concentrations of coarse particles exceeded outdoor concentrations (3.73 μg m -3 vs 2.49 μg m -3; paired t-test p < 0.0001); however the reverse was found in summer (4.34 μg m -3 vs 8.82 μg m -3; paired t-test p < 0.0001). Linear regression indicated that winter predictors of indoor coarse particles were outdoor coarse particles, ventilation and presence of at least two or more occupants. During the summer, increased use of central air conditioning was associated with reduced coarse particles, while smoking and the presence of two or more occupants resulted in increased coarse particles. Endotoxin concentrations (EU μg -1) were lower indoors than outdoors in both seasons. Spatial variability of ambient coarse particles was assessed to determine the suitability of using a single monitoring station within a city to estimate exposure. The coefficients of variation between homes sampled simultaneously and the central monitoring station were calculated (median COV in summer = 15% and winter = 24%) and showed significant variability by week, especially during the summer months, suggesting a single site may be insufficient for characterizing exposure. Future studies should consider daily measurements per home to understand shorter term exposures and day to day

  19. Protein aggregation and prionopathies.

    PubMed

    Renner, M; Melki, R

    2014-06-01

    Prion protein and prion-like proteins share a number of characteristics. From the molecular point of view, they are constitutive proteins that aggregate following conformational changes into insoluble particles. These particles escape the cellular clearance machinery and amplify by recruiting the soluble for of their constituting proteins. The resulting protein aggregates are responsible for a number of neurodegenerative diseases such as Creutzfeldt-Jacob, Alzheimer, Parkinson and Huntington diseases. In addition, there are increasing evidences supporting the inter-cellular trafficking of these aggregates, meaning that they are "transmissible" between cells. There are also evidences that brain homogenates from individuals developing Alzheimer and Parkinson diseases propagate the disease in recipient model animals in a manner similar to brain extracts of patients developing Creutzfeldt-Jacob's disease. Thus, the propagation of protein aggregates from cell to cell may be a generic phenomenon that contributes to the evolution of neurodegenerative diseases, which has important consequences on human health issues. Moreover, although the distribution of protein aggregates is characteristic for each disease, new evidences indicate the possibility of overlaps and crosstalk between the different disorders. Despite the increasing evidences that support prion or prion-like propagation of protein aggregates, there are many unanswered questions regarding the mechanisms of toxicity and this is a field of intensive research nowadays. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  20. Study on conversion relationships of compressive strength indexes for recycled lightweight aggregate concrete

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang-gang; Yang, Jian-hui; Kuang, Xiao-mei

    2017-01-01

    In order to study cube compressive strength and axial compressive strength of recycled lightweight aggregate concrete(RLAC), and conversion relationship between the two, with the replacement rate of recycled lightweight coarse aggregate as change parameters, 15 standard cube test specimens and 15 standard prism test specimens were produced to carry out the test. Then compressive strength of test specimens were measured, and the law of different replacement rate of recycled lightweight coarse aggregate influencing compressive strength of RLAC was analyzed, as the method of statistical regression adopted, the conversion relationships between of cube compressive strength and axial compressive strength of RLAC was obtained. It is shown that compressive strength of RLAC are lower than compressive strength of ordinary concrete; and that compressive strength of RLAC gradually decreases as replacement rate of recycled lightweight coarse aggregate increases; as well as, the conversion relationship between axial compressive strength and cube compressive strength of RLAC is different from ordinary concrete; based on the experimental data, conversion relationship formula between compressive strength indexes of RLAC was established. It is suggested that the replacement rate of recycled lightweight aggregate should be controlled within 25%.

  1. A coarse-grained model for PETN crystals

    SciTech Connect

    Gee, R; Wu, C; Maiti, A

    2006-02-10

    Using the energetic material Pentaerythritol Tetranitrate (PETN) as a specific example of molecular crystal, we describe the development of a simple coarse-graining procedure by grouping several atoms or whole functional groups into single charge-neutral beads. As compared to fully atomistic calculations the coarse-grained model speeds up simulations by more than two orders of magnitude. Yet, by adjusting only two parameters in the coarse-grained interaction, the model accurately predicts the lattice constants, sublimation energy, pressure-volume curve up to P=10 GPa, and energetically the most stable facets. Computed surface and desorption energies, bulk modulus, and equilibrium morphology are reported as well.

  2. Evaluation of recycled concrete aggregates for their suitability in construction activities: An experimental study.

    PubMed

    Puthussery, Joseph V; Kumar, Rakesh; Garg, Anurag

    2017-02-01

    Construction and demolition waste disposal is a major challenge in developing nations due to its ever increasing quantities. In this study, the recycling potential of waste concrete as aggregates in construction activities was studied. The metal leaching from the recycled concrete aggregates (RCA) collected from the demolition site of a 50year old building, was evaluated by performing three different leaching tests (compliance, availability and Toxic Characteristic Leaching Procedure). The metal leaching was found mostly within the permissible limit except for Hg. Several tests were performed to determine the physical and mechanical properties of the fine and coarse aggregates produced from recycled concrete. The properties of recycled aggregates were found to be satisfactory for their utilization in road construction activities. The suitability of using recycled fine and coarse aggregates with Portland pozzolanic cement to make a sustainable and environmental friendly concrete mix design was also analyzed. No significant difference was observed in the compressive strength of various concrete mixes prepared by natural and recycled aggregates. However, only the tensile strength of the mix prepared with 25% recycled fine aggregates was comparable to that of the control concrete. For other mixes, the tensile strength of the concrete was found to drop significantly. In summary, RCA should be considered seriously as a building material for road construction, mass concrete works, lightly reinforced sections, etc. The present work will be useful for the waste managers and policy makers particularly in developing nations where proper guidelines are still lacking. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. 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

  4. Mineralogical and microscopic evaluation of coarse taconite tailings from Minnesota taconite operations.

    PubMed

    Zanko, Lawrence M; Niles, Harlan B; Oreskovich, Julie A

    2008-10-01

    Eighteen coarse taconite tailings samples were collected in 2000-2001 from five western Mesabi Range taconite (iron ore) operations located in northern Minnesota, i.e., EVTAC, Hibbing Taconite (Hibtac), USX Minntac, Ispat Inland (Minorca), and National Steel Pellet Company (NSPC), to test their physical, geological, chemical, and mineralogical properties [Zanko, L.M., Niles, H.B., Oreskovich, J.A., 2003. Properties and aggregate potential of coarse taconite tailings from five Minnesota taconite operations, Minnesota Department of Transportation, Local Road Research Board, St. Paul, MN, Report No. 2004-06 (also as Natural Resources Research Institute technical report, NRRI/TR-2003/44)]. The goal was to assemble a body of technical data that could be used to better assess the potential of using a crushed taconite mining byproduct like coarse tailings for more widespread construction aggregate purposes, primarily in roads and highways. An important part of the mineralogical assessment included X-ray diffraction (XRD) analyses and microscopic (polarized light microscopy, scanning electron microscopy, and transmission electron microscopy, i.e., PLM, SEM, and TEM, respectively) evaluation of the size and shape (morphological) characteristics of potentially respirable microscopic mineral particles and fragments. Quantitative mineralogy, based on XRD analyses, showed that the dominant mineral in all samples was quartz (55-60%), followed by much smaller amounts of iron oxides, carbonates, and silicates. Specialized microscopic analyses and testing performed by the RJ Lee Group, Monroeville, PA, on both pulverized (-200 mesh, or 0.075mm) and as-is sample composites showed that no regulated asbestos minerals or amphibole minerals were detected in the western Mesabi Range samples. A small number (26) of non-asbestos and non-amphibole mineral cleavage fragments/mineral fibers were detected by SEM out of 1000 fields analyzed, but most were identified as minnesotaite and talc

  5. Fibronectin Aggregation and Assembly

    PubMed Central

    Ohashi, Tomoo; Erickson, Harold P.

    2011-01-01

    The mechanism of fibronectin (FN) assembly and the self-association sites are still unclear and contradictory, although the N-terminal 70-kDa region (I1–9) is commonly accepted as one of the assembly sites. We previously found that I1–9 binds to superfibronectin, which is an artificial FN aggregate induced by anastellin. In the present study, we found that I1–9 bound to the aggregate formed by anastellin and a small FN fragment, III1–2. An engineered disulfide bond in III2, which stabilizes folding, inhibited aggregation, but a disulfide bond in III1 did not. A gelatin precipitation assay showed that I1–9 did not interact with anastellin, III1, III2, III1–2, or several III1–2 mutants including III1–2KADA. (In contrast to previous studies, we found that the III1–2KADA mutant was identical in conformation to wild-type III1–2.) Because I1–9 only bound to the aggregate and the unfolding of III2 played a role in aggregation, we generated a III2 domain that was destabilized by deletion of the G strand. This mutant bound I1–9 as shown by the gelatin precipitation assay and fluorescence resonance energy transfer analysis, and it inhibited FN matrix assembly when added to cell culture. Next, we introduced disulfide mutations into full-length FN. Three disulfide locks in III2, III3, and III11 were required to dramatically reduce anastellin-induced aggregation. When we tested the disulfide mutants in cell culture, only the disulfide bond in III2 reduced the FN matrix. These results suggest that the unfolding of III2 is one of the key factors for FN aggregation and assembly. PMID:21949131

  6. Mimicking coarse-grained simulations without coarse-graining: Enhanced sampling by damping short-range interactions

    NASA Astrophysics Data System (ADS)

    Wei, Dongshan; Wang, Feng

    2010-08-01

    The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

  7. 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.

  8. Spectral coarse graining for random walks in bipartite networks.

    PubMed

    Wang, Yang; Zeng, An; Di, Zengru; Fan, Ying

    2013-03-01

    Many real-world networks display a natural bipartite structure, yet analyzing and visualizing large bipartite networks is one of the open challenges in complex network research. A practical approach to this problem would be to reduce the complexity of the bipartite system while at the same time preserve its functionality. However, we find that existing coarse graining methods for monopartite networks usually fail for bipartite networks. In this paper, we use spectral analysis to design a coarse graining scheme specific for bipartite networks, which keeps their random walk properties unchanged. Numerical analysis on both artificial and real-world networks indicates that our coarse graining can better preserve most of the relevant spectral properties of the network. We validate our coarse graining method by directly comparing the mean first passage time of the walker in the original network and the reduced one.

  9. Innovations in the flotation of fine and coarse particles

    NASA Astrophysics Data System (ADS)

    Fornasiero, D.; Filippov, L. O.

    2017-07-01

    Research on the mechanisms of particle-bubble interaction has provided valuable information on how to improve the flotation of fine (<20 µm) and coarse particles (>100 µm) with novel flotation machines which provide higher collision and attachment efficiencies of fine particles with bubbles and lower detachment of the coarse particles. Also, new grinding methods and technologies have reduced energy consumption in mining and produced better mineral liberation and therefore flotation performance.

  10. 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.

  11. Observing Convective Aggregation

    NASA Astrophysics Data System (ADS)

    Holloway, Christopher E.; Wing, Allison A.; Bony, Sandrine; Muller, Caroline; Masunaga, Hirohiko; L'Ecuyer, Tristan S.; Turner, David D.; Zuidema, Paquita

    2017-06-01

    Convective self-aggregation, the spontaneous organization of initially scattered convection into isolated convective clusters despite spatially homogeneous boundary conditions and forcing, was first recognized and studied in idealized numerical simulations. While there is a rich history of observational work on convective clustering and organization, there have been only a few studies that have analyzed observations to look specifically for processes related to self-aggregation in models. Here we review observational work in both of these categories and motivate the need for more of this work. We acknowledge that self-aggregation may appear to be far-removed from observed convective organization in terms of time scales, initial conditions, initiation processes, and mean state extremes, but we argue that these differences vary greatly across the diverse range of model simulations in the literature and that these comparisons are already offering important insights into real tropical phenomena. Some preliminary new findings are presented, including results showing that a self-aggregation simulation with square geometry has too broad distribution of humidity and is too dry in the driest regions when compared with radiosonde records from Nauru, while an elongated channel simulation has realistic representations of atmospheric humidity and its variability. We discuss recent work increasing our understanding of how organized convection and climate change may interact, and how model discrepancies related to this question are prompting interest in observational comparisons. We also propose possible future directions for observational work related to convective aggregation, including novel satellite approaches and a ground-based observational network.

  12. Observing convective aggregation

    NASA Astrophysics Data System (ADS)

    Holloway, Christopher; Wing, Allison; Bony, Sandrine; Muller, Caroline; Masunaga, Hirohiko; L'Ecuyer, Tristan; Turner, David; Zuidema, Paquita

    2017-04-01

    Convective self-aggregation was first recognized and studied in idealized numerical simulations. While there is a rich history of observational work on convective clustering and organization, there have been only a few studies that have analyzed observations to look specifically for processes related to self-aggregation in models. Here we review observational work in both of these categories and motivate the need for more of this work. We acknowledge that self-aggregation may appear to be far-removed from observed convective organization in terms of time scales, initial conditions, initiation processes, and mean state extremes, but we argue that these differences vary greatly across the diverse range of model simulations in the literature and that these comparisons are already offering important insights into real tropical phenomena. Some preliminary new findings are presented, including results showing that a self-aggregation simulation with square geometry has too broad a distribution of humidity and is too dry in the driest regions when compared with radiosonde records from Nauru, while an elongated channel simulation has realistic representations of atmospheric humidity and its variability. We discuss recent work increasing our understanding of how organized convection and climate change may interact, and how model discrepancies related to this question are prompting interest in observational comparisons. We also propose possible future directions for observational work related to convective aggregation, including novel satellite approaches and a ground-based observational network.

  13. Highly Coarse-Grained Representations of Transmembrane Proteins

    PubMed Central

    2017-01-01

    Numerous biomolecules and biomolecular complexes, including transmembrane proteins (TMPs), are symmetric or at least have approximate symmetries. Highly coarse-grained models of such biomolecules, aiming at capturing the essential structural and dynamical properties on resolution levels coarser than the residue scale, must preserve the underlying symmetry. However, making these models obey the correct physics is in general not straightforward, especially at the highly coarse-grained resolution where multiple (∼3–30 in the current study) amino acid residues are represented by a single coarse-grained site. In this paper, we propose a simple and fast method of coarse-graining TMPs obeying this condition. The procedure involves partitioning transmembrane domains into contiguous segments of equal length along the primary sequence. For the coarsest (lowest-resolution) mappings, it turns out to be most important to satisfy the symmetry in a coarse-grained model. As the resolution is increased to capture more detail, however, it becomes gradually more important to match modular repeats in the secondary structure (such as helix-loop repeats) instead. A set of eight TMPs of various complexity, functionality, structural topology, and internal symmetry, representing different classes of TMPs (ion channels, transporters, receptors, adhesion, and invasion proteins), has been examined. The present approach can be generalized to other systems possessing exact or approximate symmetry, allowing for reliable and fast creation of multiscale, highly coarse-grained mappings of large biomolecular assemblies. PMID:28043122

  14. 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.

  15. 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.

  16. 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.

  17. Source identification of coarse particles in the Desert ...

    EPA Pesticide Factsheets

    The Desert Southwest Coarse Particulate Matter Study was undertaken to further our understanding of the spatial and temporal variability and sources of fine and coarse particulate matter (PM) in rural, arid, desert environments. Sampling was conducted between February 2009 and February 2010 in Pinal County, AZ near the town of Casa Grande where PM concentrations routinely exceed the U.S. National Ambient Air Quality Standards (NAAQS) for both PM10 and PM2.5. In this desert region, exceedances of the PM10 NAAQS are dominated by high coarse particle concentrations, a common occurrence in this region of the United States. This work expands on previously published measurements of PM mass and chemistry by examining the sources of fine and coarse particles and the relative contribution of each to ambient PM mass concentrations using the Positive Matrix Factorization receptor model (Clements et al., 2014). Highlights • Isolation of coarse particles from fine particle sources. • Unique chemical composition of coarse particles. • Role of primary biological particles on aerosol loadings.

  18. 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.

  19. Study on performance of concrete with over-burnt bricks aggregates and micro-silica admixture

    NASA Astrophysics Data System (ADS)

    Praveen, K.; Sathyan, Dhanya; Mini, K. M.

    2016-09-01

    Concrete is made by mixing cement, sand, aggregates and water in required proportion, where aggregates occupy the major volume. Addition of aggregates in concrete improves properties of concrete. With the natural resources depleting rapidly, limiting the use of natural resources and enhancing the use of waste materials is very important for sustainable development. Over-burnt bricks are a waste material which cannot be used in construction directly because of their irregular shape and dark colour. Use of over-burnt bricks helps to preserve natural aggregate source. The present study focuses on the effects of microsilica at various percentages as a partial cement replacement in concrete with over-burnt bricks as coarse aggregates. The mechanical properties of hardened concrete such as splitting tensile strength, flexural strength and compressive strength are studied and analyzed.

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

    SciTech Connect

    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.

  1. 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.

  2. 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.

  3. Systematic Coarse-graining of Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Voth, Gregory

    2015-03-01

    Coarse-grained (CG) models can provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms that are correlated over distance scales of many covalent bond lengths and at long time scales. Systematic variational coarse-graining methods based on information from molecular dynamics simulations of finer-grained (e.g., all-atom) models provide attractive tools for the systematic development of CG models. Examples include the multiscale coarse-graining (MS-CG) and relative entropy minimization methods, and results from the former theory will be presented in this talk. In addition, a new approach will be presented that is appropriate for the ``ultra coarse-grained'' (UCG) regime, e.g., at a coarse-grained resolution that is much coarser than one amino acid residue per CG particle in a protein. At this level of coarse-graining, one is faced with the possible existence of multiple metastable states ``within'' the CG sites for a given UCG model configuration. I will therefore describe newer systematic variational UCG methods specifically designed to CG entire protein domains and subdomains into single effective CG particles. This is accomplished by augmenting existing effective particle CG schemes to allow for discrete state transitions and configuration-dependent resolution. Additionally, certain aspects of this work connect back to single-state force matching and open up new avenues for method development. This general body of theory and algorithm provides a formal statistical mechanical basis for the coarse-graining of fine-grained molecular dynamics simulation data at various levels of CG resolution. Representative applications will be described as time allows.

  4. 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.

  5. 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

  6. Quality control of lightweight aggregate concrete based on initial and final water absorption tests

    NASA Astrophysics Data System (ADS)

    Maghfouri, M.; Shafigh, P.; Ibrahim, Z. Binti; Alimohammadi, V.

    2017-06-01

    Water absorption test is used to evaluate overall performance of concrete in terms of durability. The water absorption of lightweight concrete might be considerably higher than the conventional concrete due to higher rate of pores in concrete and lightweight aggregate. Oil palm shell is a bio-solid waste in palm oil industry, which could be used as lightweight aggregate in the concrete mixture. The present study aims to measure the initial and final water absorption and compressive strength of oil palm shell lightweight concrete in order to evaluation of quality control and durability performance. Total normal coarse aggregates were substituted with coarse oil palm shell in a high strength concrete mixture. The quality of concrete was then evaluated based on the compressive strength and water absorption rates. The results showed that fully substitution of normal coarse aggregates with oil palm shell significantly reduced the compressive strength. However, this concrete with the 28-day compressive strength of 40 MPa still can be used as structural concrete. The initial and final water absorption test results also showed that this concrete is not considered as a good concrete in terms of durability. Therefore, it is recommended that both compressive strength and waster absorption tests must be performed for quality control of oil palm shell concretes.

  7. NONLINEAR MULTIGRID SOLVER EXPLOITING AMGe COARSE SPACES WITH APPROXIMATION PROPERTIES

    SciTech Connect

    Christensen, Max La Cour; Villa, Umberto E.; Engsig-Karup, Allan P.; Vassilevski, Panayot S.

    2016-01-22

    The paper introduces a nonlinear multigrid solver for mixed nite element discretizations based on the Full Approximation Scheme (FAS) and element-based Algebraic Multigrid (AMGe). The main motivation to use FAS for unstruc- tured problems is the guaranteed approximation property of the AMGe coarse spaces that were developed recently at Lawrence Livermore National Laboratory. These give the ability to derive stable and accurate coarse nonlinear discretization problems. The previous attempts (including ones with the original AMGe method, [5, 11]), were less successful due to lack of such good approximation properties of the coarse spaces. With coarse spaces with approximation properties, our FAS approach on un- structured meshes should be as powerful/successful as FAS on geometrically re ned meshes. For comparison, Newton's method and Picard iterations with an inner state-of-the-art linear solver is compared to FAS on a nonlinear saddle point problem with applications to porous media ow. It is demonstrated that FAS is faster than Newton's method and Picard iterations for the experiments considered here. Due to the guaranteed approximation properties of our AMGe, the coarse spaces are very accurate, providing a solver with the potential for mesh-independent convergence on general unstructured meshes.

  8. Coarse graining atomistic simulations of plastically deforming amorphous solids

    NASA Astrophysics Data System (ADS)

    Hinkle, Adam R.; Rycroft, Chris H.; Shields, Michael D.; Falk, Michael L.

    2017-05-01

    The primary mode of failure in disordered solids results from the formation and persistence of highly localized regions of large plastic strains known as shear bands. Continuum-level field theories capable of predicting this mechanical response rely upon an accurate representation of the initial and evolving states of the amorphous structure. We perform molecular dynamics simulations of a metallic glass and propose a methodology for coarse graining discrete, atomistic quantities, such as the potential energies of the elemental constituents. A strain criterion is established and used to distinguish the coarse-grained degrees-of-freedom inside the emerging shear band from those of the surrounding material. A signal-to-noise ratio provides a means of evaluating the strength of the signal of the shear band as a function of the coarse graining. Finally, we investigate the effect of different coarse graining length scales by comparing a two-dimensional, numerical implementation of the effective-temperature description in the shear transformation zone (STZ) theory with direct molecular dynamics simulations. These comparisons indicate the coarse graining length scale has a lower bound, above which there is a high level of agreement between the atomistics and the STZ theory, and below which the concept of effective temperature breaks down.

  9. 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.

  10. Characterizing and contrasting instream and riparian coarse wood in western Montana basins

    Treesearch

    Michael K. Young; Ethan A. Mace; Eric T. Ziegler; Elaine K. Sutherland

    2006-01-01

    The importance of coarse wood to aquatic biota and stream channel structure is widely recognized, yet characterizations of large-scale patterns in coarse wood dimensions and loads are rare. To address these issues, we censused instream coarse wood ( 2 m long and 10 cm minimum diameter) and sampled riparian coarse wood and channel characteristics in and along 13 streams...

  11. A multiscale view of therapeutic protein aggregation: a colloid science perspective.

    PubMed

    Nicoud, Lucrèce; Owczarz, Marta; Arosio, Paolo; Morbidelli, Massimo

    2015-03-01

    The formation of aggregates in protein-based pharmaceuticals is a major issue that can compromise drug safety and drug efficacy. With a view to improving protein stability, considerable effort is put forth to unravel the fundamental mechanisms underlying the aggregation process. However, therapeutic protein aggregation is a complex multistep phenomenon that involves time and length scales spanning several orders of magnitude, and strategies addressing protein aggregation inhibition are currently still largely empirical in practice. Here, we review how key concepts developed in the frame of colloid science can be applied to gain knowledge on the kinetics and thermodynamics of therapeutic protein aggregation across different length scales. In particular, we discuss the use of coarse-grained molecular interaction potentials to quantify protein colloidal stability. We then show how population balance equations simulations can provide insights into the mechanisms of aggregate formation at the mesoscale, and we highlight the strength of the concept of fractal scaling to quantify irregular aggregate morphologies. Finally, we correlate the macroscopic rheological properties of protein solutions with the occupied volume fraction and the aggregate structure. Overall, this work illustrates the power and limitations of colloidal approaches in the multiscale description of the aggregation of therapeutic proteins.

  12. Exploring energy landscapes of protein folding and aggregation.

    PubMed

    Mousseau, Normand; Derreumaux, Philippe

    2008-05-01

    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.

  13. Subphase transitions in first-order aggregation processes

    NASA Astrophysics Data System (ADS)

    Koci, Tomas; Bachmann, Michael

    2017-03-01

    In this paper, we investigate the properties of aggregation transitions in the context of generic coarse-grained homopolymer systems. By means of parallel replica-exchange Monte Carlo methods, we perform extensive simulations of systems consisting of up to 20 individual oligomer chains with five monomers each. Using the tools of the versatile microcanonical inflection-point analysis, we show that the aggregation transition is a first-order process consisting of a sequence of subtransitions between intermediate structural phases. We unravel the properties of these intermediate phases by collecting and analyzing their individual contributions towards the density of states of the system. The central theme of this systematic study revolves around translational entropy and its role in the striking phenomena of missing intermediate phases. We conclude with a brief discussion of the scaling properties of the transition temperature and the latent heat.

  14. 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.

  15. Protein simulations in fluids: coupling the OPEP coarse-grained force field with hydrodynamics

    PubMed Central

    Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone

    2017-01-01

    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 modelling systems made up to thousands of proteins, such as in the case of dense protein suspensions. The future perspectives of the multi-scale approach are also discussed. PMID:26574390

  16. Self-assembly of gold nanorods coated with phospholipids: a coarse-grained molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Wan, Mingwei; Li, Xiaoxu; Gao, Lianghui; Fang, Weihai

    2016-11-01

    The self-assembly of phospholipid-coated gold nanorods (GNRs) was investigated by coarse-grained molecular dynamics simulations. We predict that in addition to the formation of deformed vesicles encapsulating GNRs with diverse orientations, the lipid-coated GNRs can form a semi-ring attached to an excess vesicle phase, a branch with excess vesicle phase, a ring phase, a branch phase, a stack phase, and a vortex phase. The morphologies of the lipid-GNR complexes depend on the lipid/GNR molar ratio and the interaction strength between the nanorod surface and the lipid head groups. At given lipid-nanorod interactions, removing the lipid induces a phase transition from an isolated ring or branch phase to an aggregated vortex or stack phase and vice versa. As the lipid-coated GNRs transit from an isolated phase to an aggregated phase, the structure of the lipid at the nanorod surface converts from a bilayer state to a non-bilayer state.

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

    PubMed

    Poulain, P; Saladin, A; Hartmann, B; Prévost, C

    2008-11-30

    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 acid side chains strengthen the binding. Overall, this work demonstrates that coarse grain modeling can reveal itself a precious auxiliary for a general and complete description and understanding of protein-DNA association mechanisms.

  18. Comparison of iterative inverse coarse-graining methods

    NASA Astrophysics Data System (ADS)

    Rosenberger, David; Hanke, Martin; van der Vegt, Nico F. A.

    2016-10-01

    Deriving potentials for coarse-grained Molecular Dynamics (MD) simulations is frequently done by solving an inverse problem. Methods like Iterative Boltzmann Inversion (IBI) or Inverse Monte Carlo (IMC) have been widely used to solve this problem. The solution obtained by application of these methods guarantees a match in the radial distribution function (RDF) between the underlying fine-grained system and the derived coarse-grained system. However, these methods often fail in reproducing thermodynamic properties. To overcome this deficiency, additional thermodynamic constraints such as pressure or Kirkwood-Buff integrals (KBI) may be added to these methods. In this communication we test the ability of these methods to converge to a known solution of the inverse problem. With this goal in mind we have studied a binary mixture of two simple Lennard-Jones (LJ) fluids, in which no actual coarse-graining is performed. We further discuss whether full convergence is actually needed to achieve thermodynamic representability.

  19. Significance of coarse cereals in health and nutrition: a review.

    PubMed

    Kaur, Kiran Deep; Jha, Alok; Sabikhi, Latha; Singh, A K

    2014-08-01

    This review assesses the nutritional attributes of coarse cereals and also their utilization as food and as formulated foods. These cereals are laden with phytochemicals including phenolic acids, tannins, anthocyanins, phytosterols, avenenathramides and policosanols. They possess high antioxidant properties in vitro than staple cereals and fruits by different purported pathways. There are also some anti-nutritional factors that may be reduced by certain processing treatments. Several epidemiological studies show that these cereals are helpful in reducing several kinds of chronic diseases like cancers, cardiovascular diseases, type II diabetes and various gastrointestinal disorders. Being coarse in nature, they cannot replace our staple cereals, but can be used in different proportions with rice and wheat to formulate various nutritional products. They can be used to make porridges, biscuits, cakes, cookies, tortillas, bread, probiotic drinks, ladoo, ghatta, flakes and several fermented foods. The coarse cereals also have good potential in manufacturing bioethanol, paper, oil and biofilms.

  20. Obtaining fully dynamic coarse-grained models from MD.

    PubMed

    Español, Pep; Zúñiga, Ignacio

    2011-06-14

    We present a general method to obtain parametrised models for the drift and diffusion terms of the Fokker-Planck equation of a coarse-grained description of molecular systems. The method is based on the minimisation of the relative entropy defined in terms of the two-time joint probability and thus captures the full dynamics of the coarse-grained description. In addition, we show an alternative Bayesian argument that starts from the path probability of a diffusion process which allows one to obtain the best parametrised model that fits an actual observed path of the coarse-grained variables. Both approaches lead to exactly the same optimisation function giving strong support to the methodology. We provide an heuristic argument that explains how both approaches are connected.

  1. A Decoupled Finite Element Heterogeneous Coarse Mesh Transport Method.

    SciTech Connect

    Mosher, S. W.; Rahnema, Farzad

    2005-01-01

    In a recent paper, an original finite element (FE) method was presented for solving eigenvalue transport problems on a coarse spatial mesh. The method employed a surface Green's function expansion of the angular flux trial functions, so that heterogeneous coarse-meshes could be treated with relative ease. Numerical problems were solved using the multigroup discrete ordinates approximation in one-dimensional (1-D) slab geometry. Unfortunately, difficulties were encountered in finding solutions to the algebraic finite element equations, which led to sizeable angular flux discontinuities at coarse-mesh interfaces and significant errors. For this reason, a nonvariational iterative technique was ultimately favored for converging the angular flux distribution, and was used in conjunction with a Rayleigh quotient for converging the eigenvalue. In this paper, a new derivation of finite element equations is presented, which seems to offer a remedy for at least some of the numerical ills that plagued the previous work. First, the equations are derived in terms of a generalized response function expansion. This allows a more efficient response basis to be employed and vastly reduces the overall computational effort without a substantial loss of accuracy. Second, the tight coupling between coarse-meshes in the original equations is effectively broken by assuming that an accurate estimate of the flux distribution entering a given coarse-mesh is known. With an additional assumption that an accurate eigenvalue estimate is known, an iterative approach to solving these decoupled finite element (DFE) equations is developed. The DFE method has been applied to both 1- and 2-D heterogeneous coarse-mesh problems with a far greater degree of success than the original FE method. However, some numerical difficulties remain to be overcome before the new approach can be considered robust.

  2. Reversible Aggregation of Albumin

    NASA Astrophysics Data System (ADS)

    Colby, Ralph H.; Oates, Katherine M. N.; Krause, Wendy E.; Jones, Ronald L.

    2004-03-01

    We explore the interactions in synovial fluid involving the polyelectrolyte sodium hyaluronate (NaHA) and plasma proteins in their native state (albumin and globulins). Rheological measurements on synovial fluid show it to be highly viscoelastic and also rheopectic (stress increases with time in steady shear). Equilibrium dialysis confirms the findings of Ogston and Dubin that there is no association between NaHA and albumin at physiological pH and salt. What we find instead is a reversible aggregation of albumin, with an association energy of order 3kT and commensurate association lifetime of order microseconds. Certain anti-inflammatory drugs are shown to prevent this reversible aggregation. The implications of these findings for synovial fluid and blood rheology are discussed.

  3. Tracking protein aggregate interactions

    PubMed Central

    Bartz, Jason C; Nilsson, K Peter R

    2011-01-01

    Amyloid fibrils share a structural motif consisting of highly ordered β-sheets aligned perpendicular to the fibril axis.1, 2 At each fibril end, β-sheets provide a template for recruiting and converting monomers.3 Different amyloid fibrils often co-occur in the same individual, yet whether a protein aggregate aids or inhibits the assembly of a heterologous protein is unclear. In prion disease, diverse prion aggregate structures, known as strains, are thought to be the basis of disparate disease phenotypes in the same species expressing identical prion protein sequences.4–7 Here we explore the interactions reported to occur when two distinct prion strains occur together in the central nervous system. PMID:21597336

  4. Zooplankton Aggregations Near Sills

    DTIC Science & Technology

    2003-09-30

    frequency echo-sounder system. This data were supplemented with multi-net (BIONESS) trawls, bongo nets, and otter trawls (operated by D. Mackas and group...side. The general composition of the zooplankton aggregations can be deduced from the relative levels of the three echo-sounder frequencies; krill ...Nov. 20th, 2002. Krill layer is evident at 66 – 90 m, coincident with BIONESS trawl through the region. 3 Figure 2 shows a comparison between

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. Age-Dependent Protein Aggregation Initiates Amyloid-β Aggregation

    PubMed Central

    Groh, Nicole; Bühler, Anika; Huang, Chaolie; Li, Ka Wan; van Nierop, Pim; Smit, August B.; Fändrich, Marcus; Baumann, Frank; David, Della C.

    2017-01-01

    Aging is the most important risk factor for neurodegenerative diseases associated with pathological protein aggregation such as Alzheimer’s disease. Although aging is an important player, it remains unknown which molecular changes are relevant for disease initiation. Recently, it has become apparent that widespread protein aggregation is a common feature of aging. Indeed, several studies demonstrate that 100s of proteins become highly insoluble with age, in the absence of obvious disease processes. Yet it remains unclear how these misfolded proteins aggregating with age affect neurodegenerative diseases. Importantly, several of these aggregation-prone proteins are found as minor components in disease-associated hallmark aggregates such as amyloid-β plaques or neurofibrillary tangles. This co-localization raises the possibility that age-dependent protein aggregation directly contributes to pathological aggregation. Here, we show for the first time that highly insoluble proteins from aged Caenorhabditis elegans or aged mouse brains, but not from young individuals, can initiate amyloid-β aggregation in vitro. We tested the seeding potential at four different ages across the adult lifespan of C. elegans. Significantly, protein aggregates formed during the early stages of aging did not act as seeds for amyloid-β aggregation. Instead, we found that changes in protein aggregation occurring during middle-age initiated amyloid-β aggregation. Mass spectrometry analysis revealed several late-aggregating proteins that were previously identified as minor components of amyloid-β plaques and neurofibrillary tangles such as 14-3-3, Ubiquitin-like modifier-activating enzyme 1 and Lamin A/C, highlighting these as strong candidates for cross-seeding. Overall, we demonstrate that widespread protein misfolding and aggregation with age could be critical for the initiation of pathogenesis, and thus should be targeted by therapeutic strategies to alleviate neurodegenerative

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

    PubMed

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

    2008-06-28

    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(+)NO(3) (-) ionic liquid are provided to illustrate the method.

  11. 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.

  12. Intrinsic disorder modulates protein self-assembly and aggregation.

    PubMed

    De Simone, Alfonso; Kitchen, Craig; Kwan, Ann H; Sunde, Margaret; Dobson, Christopher M; Frenkel, Daan

    2012-05-01

    Protein molecules have evolved to adopt distinctive and well-defined functional and soluble states under physiological conditions. In some circumstances, however, proteins can self-assemble into fibrillar aggregates designated as amyloid fibrils. In vivo these processes are normally associated with severe pathological conditions but can sometimes have functional relevance. One such example is the hydrophobins, whose aggregation at air-water interfaces serves to create robust protein coats that help fungal spores to resist wetting and thus facilitate their dispersal in the air. We have performed multiscale simulations to address the molecular determinants governing the formation of functional amyloids by the class I fungal hydrophobin EAS. Extensive samplings of full-atom replica-exchange molecular dynamics and coarse-grained simulations have allowed us to identify factors that distinguish aggregation-prone from highly soluble states of EAS. As a result of unfavourable entropic terms, highly dynamical regions are shown to exert a crucial influence on the propensity of the protein to aggregate under different conditions. More generally, our findings suggest a key role that specific flexible structural elements can play to ensure the existence of soluble and functional states of proteins under physiological conditions.

  13. Membrane-mediated aggregation of anisotropically curved nanoparticles.

    PubMed

    Olinger, Alexander D; Spangler, Eric J; Kumar, P B Sunil; Laradji, Mohamed

    2016-01-01

    Using systematic numerical simulations, we study the self-assembly of elongated curved nanoparticles on lipid vesicles. Our simulations are based on molecular dynamics of a coarse-grained implicit-solvent model of self-assembled lipid membranes with a Langevin thermostat. Here we consider only the case wherein the nanoparticle-nanoparticle interaction is repulsive, only the concave surface of the nanoparticle interacts attractively with the lipid head groups and only the outer surface of the vesicle is exposed to the nanoparticles. Upon their adhesion on the vesicle, the curved nanoparticles generate local curvature on the membrane. The resulting nanoparticle-generated membrane curvature leads in turn to nanoparticle self-assembly into two main types of aggregates corresponding to chain aggregates at low adhesion strengths and aster aggregates at high adhesion strength. The chain-like aggregates are due to the fact that at low values of adhesion strength, the nanoparticles prefer to lie parallel to each other. As the adhesion strength is increased, a splay angle between the nanoparticles is induced with a magnitude that increases with increasing adhesion strength. The origin of the splay angles between the nanoparticles is shown to be saddle-like membrane deformations induced by a tilt of the lipids around the nanoparticles. This phenomenon of membrane mediated self-assembly of anisotropically curved nanoparticles is explored for systems with varying nanoparticle number densities, adhesion strength, and nanoparticle intrinsic curvature.

  14. From ribbons to tubules: a computational study of the polymorphism in aggregation of helical filaments.

    PubMed

    Gruziel, Magdalena; Szymczak, Piotr

    2015-08-21

    A simple, coarse-grained model of chiral, helical filaments is used to study the polymorphism of fibrous aggregates. Three generic morphologies of the aggregates are observed: ribbons, in which the filaments are joined side-by-side, twisted, helicoidal fibrils, in which filaments entwine along each other and tubular forms, with filaments wound together around a hollow core of the tube. A relative simplicity of the model allows us to supplement numerical simulations with an analytic description of the elastic properties of the aggregates. The model is capable of predicting geometric and structural characteristics of the composite structures, as well as their relative stabilities. We also investigate in detail the transitions between different morphologies of the aggregates.

  15. Depletion attraction of sheet-like ion aggregates in low-dielectric ionomer melts

    NASA Astrophysics Data System (ADS)

    Lu, Keran; Maranas, Janna K.; Milner, Scott T.

    2017-02-01

    Ionomers are polymers in which an ionic group is covalently bonded to the polymer backbone. Ion aggregates in ionomers have morphologies that allow for the packing of the attached polymer backbone. Using ion-only coarse-grained molecular dynamics, we observe that string-like ion aggregates become flat and sheet-like at lower dielectric constants. A consequence of the changing morphology is that the sheet-like aggregates self-assemble to form ordered, lamellar structures. We use a simple thermodynamic model to demonstrate that depletion attraction mediated by small aggregates can explain the observed order. Our results suggest that depletion attraction can drive ions to form structures that have the size scale suggested by direct visualization, produce the commonly observed experimental correlation peak from X-ray and neutron scattering, and satisfy chain-packing constraints that have been demonstrated to be important in simulations.

  16. Coarse woody debris metrics in a California oak woodland

    Treesearch

    William D. Tietje; Michael A. Hardy; Christopher C. Yim

    2015-01-01

    Little information is available on the metrics of coarse woody debris (CWD) in California oak woodland, most notably at the scale of the stand and woodland type. In a remote part of the National Guard Post, Camp Roberts, that has not burned in over a half century, we tallied 314 pieces of CWD in a blue oak (Quercus douglasii)-coast live oak (

  17. Managing coarse woody debris in forests of the Rocky Mountains

    Treesearch

    Russell T. Graham; Alan E. Harvey; Martin F. Jurgensen; Theresa B. Jain; Jonalea R. Tonn; Deborah S. Page-Dumroese

    1994-01-01

    Recommendations for managing coarse woody debris after timber harvest were developed for 14 habitat types, ranging from ponderosa pine (Pinus ponderosa) habitat types of Arizona to subalpine fir (Abies lasiocarpa) habitat types of western Montana. Ectomycorrhizae were used as a bioindicator of healthy, productive forest soils....

  18. 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.

  19. On Coarse Projective Integration for Atomic Deposition in Amorphous Systems

    SciTech Connect

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

    2015-10-02

    Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of timescales 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 gradients 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. In conclusion, 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

    DOE PAGES

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

    2015-10-02

    Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of timescales 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 gradients 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 thismore » 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. In conclusion, 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.« less

  1. 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...

  2. Coarse woody debris in oak woodlands of California.

    Treesearch

    William D. Tietje; Karen L. Waddell; Justin K. Vreeland; Charles L. Bolsinger

    2002-01-01

    An extensive forest inventory was conducted to estimate the amount and distribution of coarse woody debris (CWD) on 5.6 million ac of woodlands in California that are outside of national forests and reserved areas. Woodlands consist primarily of oak (Quercus spp.) types and are defined as forestland incapable of producing commercial quantities of...

  3. Improving coarse woody debris measurements: a taper-based technique

    Treesearch

    Christopher W. Woodall; James A. Westfall

    2007-01-01

    Coarse woody debris (CWD) are dead and down trees of a certain minimum size that are an important forest ecosystem component (e.g., wildlife habitat, carbon stocks, and fuels). Accurately measuring the dimensions of CWD is important for ensuring the quality of CWD estimates and hence for accurately assessing forest ecosystem attributes. To improve the quality of CWD...

  4. 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.

  5. 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.

  6. 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

  7. Subsurface Optical Microscopy of Coarse Grain Spinels. Phase 1

    DTIC Science & Technology

    2013-12-01

    A 456 nm LED line bar illuminated in figure 15 and a Xenon fiber optic bar illuminator is shown for figure 16. The optical in situ or subsurface ... imaging of coarse grain spinels and AlONs is optically more complex than expected. An overhead view of the side illumination field is shown in figure 20

  8. Exploration of scaling effects on coarse resolution land surface phenology

    USDA-ARS?s Scientific Manuscript database

    A great number of land surface phenoloy (LSP) data have been produced from various coarse resolution satellite datasets and detection algorithms across regional and global scales. Unlike field- measured phenological events which are quantitatively defined with clear biophysical meaning, current LSP ...

  9. A coarse wood dynamics model for the Western Cascades.

    Treesearch

    K. Mellen; A. Ager

    2002-01-01

    The Coarse Wood Dynamics Model (CWDM) analyzes the dynamics (fall, fragmentation, and decomposition) of Douglas-fir (Pseudotsuga menziesii) and western hemlock (Tsuga heterophylla) snags and down logs in forested ecosystems of the western Cascades of Oregon and Washington. The model predicts snag fall, height loss and decay,...

  10. A distance limited method for sampling downed coarse woody debris

    Treesearch

    Jeffrey H. Gove; Mark J. Ducey; Harry T. Valentine; Michael S. Williams

    2012-01-01

    A new sampling method for down coarse woody debris is proposed based on limiting the perpendicular distance from individual pieces to a randomly chosen sample point. Two approaches are presented that allow different protocols to be used to determine field measurements; estimators for each protocol are also developed. Both protocols are compared via simulation against...

  11. 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.

  12. 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...

  13. 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...

  14. 7 CFR 457.113 - Coarse grains crop insurance provisions.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... years are as follows: United States Department of Agriculture Federal Crop Insurance Corporation Coarse.... The crop defined as sorghum under the United States Grain Standards Act. Harvest. Combining, threshing... under the Official United States Standards for Grain, including but not limited to protein and oil, will...

  15. 7 CFR 457.113 - Coarse grains crop insurance provisions.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... years are as follows: United States Department of Agriculture Federal Crop Insurance Corporation Coarse.... The crop defined as sorghum under the United States Grain Standards Act. Harvest. Combining, threshing... under the Official United States Standards for Grain, including but not limited to protein and oil, will...

  16. Non-Arrhenius protein aggregation.

    PubMed

    Wang, Wei; Roberts, Christopher J

    2013-07-01

    Protein aggregation presents one of the key challenges in the development of protein biotherapeutics. It affects not only product quality but also potentially impacts safety, as protein aggregates have been shown to be linked with cytotoxicity and patient immunogenicity. Therefore, investigations of protein aggregation remain a major focus in pharmaceutical companies and academic institutions. Due to the complexity of the aggregation process and temperature-dependent conformational stability, temperature-induced protein aggregation is often non-Arrhenius over even relatively small temperature windows relevant for product development, and this makes low-temperature extrapolation difficult based simply on accelerated stability studies at high temperatures. This review discusses the non-Arrhenius nature of the temperature dependence of protein aggregation, explores possible causes, and considers inherent hurdles for accurately extrapolating aggregation rates from conventional industrial approaches for selecting accelerated conditions and from conventional or more advanced methods of analyzing the resulting rate data.

  17. Characterization of coarse particulate matter in school gyms.

    PubMed

    Braniš, Martin; Šafránek, Jiří

    2011-05-01

    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(10-2.5) and PM(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(10-2.5) 4.1-7.4 μg m(-3) and PM(2.5-1.0) 2.0-3.3 μg m(-3)) than indoors (average PM(10-2.5) 13.6-26.7 μg m(-3) and PM(2.5-1.0) 3.7-7.4 μg m(-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(10-2.5) and 1.4-4.8 for the PM(2.5-1.0) values. Under extreme conditions, the I/O ratios reached 180 (PM(10-2.5)) and 19.1 (PM(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 gyms were found to be indoor microenvironments with high

  18. Ultrastructure of acetylcholine receptor aggregates parallels mechanisms of aggregation

    PubMed Central

    Kunkel, Dennis D; Lee, Lara K; Stollberg, Jes

    2001-01-01

    Background Acetylcholine receptors become aggregated at the developing neuromuscular synapse shortly after contact by a motorneuron in one of the earliest manifestations of synaptic development. While a major physiological signal for receptor aggregation (agrin) is known, the mechanism(s) by which muscle cells respond to this and other stimuli have yet to be worked out in detail. The question of mechanism is addressed in the present study via a quantitative examination of ultrastructural receptor arrangement within aggregates. Results In receptor rich cell membranes resulting from stimulation by agrin or laminin, or in control membrane showing spontaneous receptor aggregation, receptors were found to be closer to neighboring receptors than would be expected at random. This indicates that aggregation proceeds heterogeneously: nanoaggregates, too small for detection in the light microscope, underlie developing microaggregates of receptors in all three cases. In contrast, the structural arrangement of receptors within nanoaggregates was found to depend on the aggregation stimulus. In laminin induced nanoaggregates receptors were found to be arranged in an unstructured manner, in contrast to the hexagonal array of about 10 nm spacing found for agrin induced nanoaggregates. Spontaneous aggregates displayed an intermediate amount of order, and this was found to be due to two distinct population of nanoaggregates. Conclusions The observations support earlier studies indicating that mechanisms by which agrin and laminin-1 induced receptor aggregates form are distinct and, for the first time, relate mechanisms underlying spontaneous aggregate formation to aggregate structure. PMID:11749670

  19. The influence of erythrocyte aggregation on induced platelet aggregation.

    PubMed

    Ott, C; Lardi, E; Schulzki, T; Reinhart, W H

    2010-01-01

    Red blood cells (RBCs) affect platelet aggregation in flowing blood (primary hemostasis). We tested the hypothesis that RBC aggregation could influence platelet aggregation. RBC aggregation was altered in vitro by: (i) changing plasma aggregatory properties with 3.7 g% dextran 40 (D40), 3.0 g% dextran 70 (D70) or 1.55 g% dextran 500 (D500); (ii) changing RBC aggregatory properties by incubating RBCs in 50 mU/ml neuraminidase for 60 min (reduction of the surface sialic acid content, thus reducing electrostatic repulsion) and subsequent RBC resuspension in platelet rich plasma (PRP) containing 1 g% dextran 70. RBC aggregation was assessed with the sedimentation rate (ESR). Platelet aggregation was measured: (i) in flowing whole blood with a platelet function analyzer PFA-100(R), which simulates in vivo conditions with RBCs flowing in the center and platelets along the wall, where they adhere to collagen and aggregate; and (ii) in a Chrono-log 700 Aggregometer, which measures changes of impedance by platelet aggregation in whole blood or changes in light transmission in PRP. We found that RBC aggregation increased with increasing molecular weight of dextran (ESR: 4 +/- 3 mm/h, 34 +/- 14 mm/h and 89 +/- 23 mm/hfor D40, D70 and D500, respectively, p < 0.0001) and with neuraminidase-treated RBCs (76 +/- 27 mm/h vs 27 +/- 8 mm/h, respectively, p < 0.0001). Platelet aggregation measured in whole blood under flow conditions (PFA-100) and without flow (Chronolog Aggregometer) was not affected by RBC aggregation. Our data suggest that RBC aggregation does not affect platelet aggregation in vitro and plays no role in primary hemostasis.

  20. Aggregation of polymer-grafted nanoparticles in good solvents: A hierarchical modeling method

    NASA Astrophysics Data System (ADS)

    Cheng, Lisheng; Cao, Dapeng

    2011-09-01

    Brownian dynamics simulations are carried out to study the aggregation behavior of polymer-grafted nanoparticles (NPs) in good solvents by using the coarse-grained model derived from the all-atom force field, according to the hierarchical modeling strategy, and here PEG-grafted gold nanoparticles (GNPs) were taken as an example. Generally, grafting PEG to the surface of GNPs is to protect them from aggregation in the solution. However, our results reveal that PEG-grafted GNPs may also aggregate when concentration increases. Our simulations indicate that there exists a critical aggregating concentration (CAC), beyond which the PEG-grafted GNPs will aggregate. We further check the effects of grafting density and the length of grafted chains on the aggregation behavior of the grafted GNPs, and find that there exists an optimized length of grafted chain, at which the system has the maximal CAC. Furthermore, the aggregate size of self-assembled mesostructures formed by the grafted GNPs increases with the concentration. Interestingly, it is observed that the aggregation favors to form linear gold nanowires rather than compact gold nanoclusters, and the corresponding mechanism is also addressed. It is expected that this work would provide useful information for the fabrication of metal nanowires and the surface modification of metal nanoparticles.

  1. Aggregation of polymer-grafted nanoparticles in good solvents: a hierarchical modeling method.

    PubMed

    Cheng, Lisheng; Cao, Dapeng

    2011-09-28

    Brownian dynamics simulations are carried out to study the aggregation behavior of polymer-grafted nanoparticles (NPs) in good solvents by using the coarse-grained model derived from the all-atom force field, according to the hierarchical modeling strategy, and here PEG-grafted gold nanoparticles (GNPs) were taken as an example. Generally, grafting PEG to the surface of GNPs is to protect them from aggregation in the solution. However, our results reveal that PEG-grafted GNPs may also aggregate when concentration increases. Our simulations indicate that there exists a critical aggregating concentration (CAC), beyond which the PEG-grafted GNPs will aggregate. We further check the effects of grafting density and the length of grafted chains on the aggregation behavior of the grafted GNPs, and find that there exists an optimized length of grafted chain, at which the system has the maximal CAC. Furthermore, the aggregate size of self-assembled mesostructures formed by the grafted GNPs increases with the concentration. Interestingly, it is observed that the aggregation favors to form linear gold nanowires rather than compact gold nanoclusters, and the corresponding mechanism is also addressed. It is expected that this work would provide useful information for the fabrication of metal nanowires and the surface modification of metal nanoparticles. © 2011 American Institute of Physics

  2. Corrosion Behavior of Steel Reinforcement in Concrete with Recycled Aggregates, Fly Ash and Spent Cracking Catalyst

    PubMed Central

    Gurdián, Hebé; García-Alcocel, Eva; Baeza-Brotons, Francisco; Garcés, Pedro; Zornoza, Emilio

    2014-01-01

    The main strategy to reduce the environmental impact of the concrete industry is to reuse the waste materials. This research has considered the combination of cement replacement by industrial by-products, and natural coarse aggregate substitution by recycled aggregate. The aim is to evaluate the behavior of concretes with a reduced impact on the environment by replacing a 50% of cement by industrial by-products (15% of spent fluid catalytic cracking catalyst and 35% of fly ash) and a 100% of natural coarse aggregate by recycled aggregate. The concretes prepared according to these considerations have been tested in terms of mechanical strengths and the protection offered against steel reinforcement corrosion under carbonation attack and chloride-contaminated environments. The proposed concrete combinations reduced the mechanical performance of concretes in terms of elastic modulus, compressive strength, and flexural strength. In addition, an increase in open porosity due to the presence of recycled aggregate was observed, which is coherent with the changes observed in mechanical tests. Regarding corrosion tests, no significant differences were observed in the case of the resistance of these types of concretes under a natural chloride attack. In the case of carbonation attack, although all concretes did not stand the highly aggressive conditions, those concretes with cement replacement behaved worse than Portland cement concretes. PMID:28788613

  3. Atmospheric PAH concentrations in fine and coarse particles.

    PubMed

    Vardar, Nedim; Noll, Kenneth E

    2003-09-01

    Measurements of the urban air concentrations of PAHs associated with PM2.5-fine and PM 10-coarse particles in Chicago on the campus of IIT were achieved using a Universal Air Sampler. Short sampling time (12 hr) and high flow rates were used to measure the PAH concentrations in fine and coarse particles. Measured ambient concentrations of PAHs were classified based on wind direction and back trajectory calculations as Land and Lake samples. Differences in ambient concentrations of PAHs were observed between Land and Lake samples. Fine particle concentrations varied from 9.5 to 25.7 ng m(-3) and averaged 18.2 ng m(-3) for the Land samples, while they ranged from 4.2 to 31.5 ng m(-3) and averaged 13.4 ng m(-3) for the Lake samples. The measured PAH concentrations in coarse particles varied from 6.2 to 22.1 ng m(-3) and averaged 12.9 ng m(-3) for the Land samples, and they ranged from 2.4 to 13.0 ng m(-3) with an average value of 7.3 ng m(-3) for the Lake samples. The fine/coarse ratio of each individual PAH compound varied between 1.3 and 2.7 for the Land samples: it varied between 1.6 and 4.2 for the Lake samples. There was an increase in the fine/coarse ratio of PAH as molecular weight of the compound increases for both Land and Lake samples.

  4. 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

  5. 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.

  6. Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds.

    PubMed

    Fall, S; Nazaret, S; Chotte, J L; Brauman, A

    2004-08-01

    The building and foraging activities of termites are known to modify soil characteristics such as the heterogeneity. In tropical savannas the impact of the activity of soil-feeding termites ( Cubitermes niokoloensis) has been shown to affect the properties of the soil at the aggregate level by creating new soil microenvironments (aggregate size fractions) [13]. These changes were investigated in greater depth by looking at the microbial density (AODC) and the genetic structure (automated rRNA intergenic spacer analysis: ARISA) of the communities in the different aggregate size fractions (i.e., coarse sand, fine sand, coarse silt, fine silt, and dispersible clays) separated from compartments (internal and external wall) of three Cubitermes niokoloensis mounds. The bacterial density of the mounds was significantly higher (1.5 to 3 times) than that of the surrounding soil. Within the aggregate size fractions, the termite building activity resulted in a significant increase in bacterial density within the coarser fractions (>20 mum). Multivariate analysis of the ARISA profiles revealed that the bacterial genetic structures of unfractionated soil and soil aggregate size fractions of the three mounds was noticeably different from the savanna soil used as a reference. Moreover, the microbial community associated with the different microenvironments in the three termite mounds revealed three distinct clusters formed by the aggregate size fractions of each mound. Except for the 2-20 mum fraction, these results suggest that the mound microbial genetic structure is more dependent upon microbial pool affiliation (the termite mound) than on the soil location (aggregate size fraction). The causes of the specificity of the microbial community structure of termite mound aggregate size fractions are discussed.

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

    PubMed

    Kim, Haseog; Park, Sangki; Kim, Hayong

    2016-07-29

    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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  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. 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.

  14. Solving Transportation Problems via Aggregation,

    DTIC Science & Technology

    1984-07-01

    AD-A144 219 SOLVING TRANSPORTATION PROBLEMS VIA AGGREGATION (U) i/l GEORGIA INST OF TECH ATLANTA PRODUCTION AND DISTRIBUTION RESEARCH CENTER R W...10 July 1984 SOLVING TRANSPORTATION PROBLEMS VIA AGGREGATION by" 4 Richard W. Taylort C. M. Shettytt PDRC 84-10 DTIC E L - TE~ School of Business...c UoaOO48--17 Rpouto spritein whol or pr for ny prpos of he U S. overment Abstract Solving Transportation Problems Via Aggregation 0

  15. 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.

  16. Fractal structure of asphaltene aggregates.

    PubMed

    Rahmani, Nazmul H G; Dabros, Tadeusz; Masliyah, Jacob H

    2005-05-15

    A photographic technique coupled with image analysis was used to measure the size and fractal dimension of asphaltene aggregates formed in toluene-heptane solvent mixtures. First, asphaltene aggregates were examined in a Couette device and the fractal-like aggregate structures were quantified using boundary fractal dimension. The evolution of the floc structure with time was monitored. The relative rates of shear-induced aggregation and fragmentation/restructuring determine the steady-state floc structure. The average floc structure became more compact or more organized as the floc size distribution attained steady state. Moreover, the higher the shear rate is, the more compact the floc structure is at steady state. Second, the fractal dimensions of asphaltene aggregates were also determined in a free-settling test. The experimentally determined terminal settling velocities and characteristic lengths of the aggregates were utilized to estimate the 2D and 3D fractal dimensions. The size-density fractal dimension (D(3)) of the asphaltene aggregates was estimated to be in the range from 1.06 to 1.41. This relatively low fractal dimension suggests that the asphaltene aggregates are highly porous and very tenuous. The aggregates have a structure with extremely low space-filling capacity.

  17. Peptide Aggregation in Finite Systems

    PubMed Central

    Singh, Gurpreet; Brovchenko, Ivan; Oleinikova, Alla; Winter, Roland

    2008-01-01

    Universal features of the peptide aggregation process suggest a common mechanism, with a first-order phase transition in aqueous solutions of the peptides being the driving force. Small system sizes strongly affect the stability of the minor phase in the two-phase region. We show manifestations of this effect in aqueous solutions of fragments of the islet amyloid polypeptide, using computer simulation methods and invoking various approaches in characterizing clustering and aggregate formation. These systems with peptide concentrations deeply inside the immiscibility region show two distinct stable states, which interchange with time: one state contains a peptide aggregate; and the other state has an aggregate that is noticeably dissolved. The first state is relevant for macroscopic systems, whereas the second one is artificial. At a fixed concentration, the occurrence probability of the aggregate state vanishes upon decreasing the system size, thus indicating the necessity to apply a finite size-scaling for meaningful studies of peptide aggregation by simulations. The effect observed may be one of the factors responsible for the difference between intracellular and extracellular aggregation and fibrillization of polypeptides. The finite size of biological cells or their compartments may be playing a decisive role in hampering intracellular aggregation of highly insoluble amyloidogenic proteins, whereas aggregation is unavoidable in the extracellular space at the same peptide concentration. PMID:18621830

  18. Molecular Aggregates in Cryogenic Solutions.

    DTIC Science & Technology

    1981-07-07

    of aggregates from solutions of monomers. Rapid deposition into a precooled sample cell is required to generate an aggregate solution. Such a solution...U AU-A11b 490 COLORAO0 STATE UNIV FORT COLLINS DEPT OF CHEMISTRY F/G 20/8 MOLECULAR AGGREGATES IN CRYOGENIC SOLUTIONS.CU) JUL 81 M W SCHAUER- J LEE...MOLECULAR AGGREGATES IN CRYOGENIC SOLUTIONS by M.W. Schauer, J. Lee, and E.R. Bernstein Prepared for Publication in The Journal of Chemical Physics

  19. 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.

  20. Crowding with detection and coarse discrimination of simple visual features.

    PubMed

    Põder, Endel

    2008-04-24

    Some recent studies have suggested that there are actually no crowding effects with detection and coarse discrimination of simple visual features. The present study tests the generality of this idea. A target Gabor patch, surrounded by either 2 or 6 flanker Gabors, was presented briefly at 4 deg eccentricity of the visual field. Each Gabor patch was oriented either vertically or horizontally (selected randomly). Observers' task was either to detect the presence of the target (presented with probability 0.5) or to identify the orientation of the target. The target-flanker distance was varied. Results were similar for the two tasks but different for 2 and 6 flankers. The idea that feature detection and coarse discrimination are immune to crowding may be valid for the two-flanker condition only. With six flankers, a normal crowding effect was observed. It is suggested that the complexity of the full pattern (target plus flankers) could explain the difference.

  1. Coarse-Graining in Simulations of Multicomponent Polymer Systems

    NASA Astrophysics Data System (ADS)

    Sethuraman, Vaidyanathan; Ganesan, Venkat

    2015-03-01

    We investigate the mapping required between the interaction parameters of two different coarse-grained simulation models to ensure a match of the long-range structural characteristics of multicomponent polymeric system. We investigate the extensibility of mapping functions deduced in the context of symmetric block copolymers by Morse and coworkers to other polymeric systems by studying a variety of systems, including, asymmetric diblock copolymers, symmetric triblock copolymers and diblock copolymer-solvent mixtures. We observe excellent agreement for peak in the inverse structure between two popular coarse grained models for all sets of polymeric melt systems investigated, thus showing that the mapping function proposed for diblock copolymer melts is transferable to other polymer melts irrespective of the blockiness or overall composition. We use our findings to propose a methodology to create ordered morphologies in simulations involving hard repulsive potentials in a computationally efficient manner.

  2. 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.

  3. Recent Advances in Transferable Coarse-Grained Modeling of Proteins

    PubMed Central

    Kar, Parimal; Feig, Michael

    2017-01-01

    Computer simulations are indispensable tools for studying the structure and dynamics of biological macromolecules. Biochemical processes occur on different scales of length and time. Atomistic simulations cannot cover the relevant spatiotemporal scales at which the cellular processes occur. To address this challenge, coarse-grained (CG) modeling of the biological systems are employed. Over the last few years, many CG models for proteins continue to be developed. However, many of them are not transferable with respect to different systems and different environments. In this review, we discuss those CG protein models that are transferable and that retain chemical specificity. We restrict ourselves to CG models of soluble proteins only. We also briefly review recent progress made in the multi-scale hybrid all-atom/coarse-grained simulations of proteins. PMID:25443957

  4. Has coarse ocean resolution biased simulations of transient climate sensitivity?

    NASA Astrophysics Data System (ADS)

    Winton, Michael; Anderson, Whit G.; Delworth, Thomas L.; Griffies, Stephen M.; Hurlin, William J.; Rosati, Anthony

    2014-12-01

    We investigate the influence of ocean component resolution on simulation of climate sensitivity using variants of the GFDL CM2.5 climate model incorporating eddy-resolving (1/10°) and eddy-parameterizing (1°) ocean resolutions. Two parameterization configurations of the coarse-resolution model are used yielding a three-model suite with significant variation in the transient climate response (TCR). The variation of TCR in this suite and in an enhanced group of 10 GFDL models is found to be strongly associated with the control climate Atlantic meridional overturning circulation (AMOC) magnitude and its decline under forcing. We find that it is the AMOC behavior rather than resolution per se that accounts for most of the TCR differences. A smaller difference in TCR stems from the eddy-resolving model having more Southern Ocean surface warming than the coarse models.

  5. Salient object detection using coarse-to-fine processing.

    PubMed

    Zhou, Qiangqiang; Zhang, Lin; Zhao, Weidong; Liu, Xianhui; Chen, Yufei; Wang, Zhicheng

    2017-03-01

    In this paper, we propose a salient object detection algorithm that considers both background and foreground cues. It integrates both coarse salient region extraction and a top-down background weight map measure via boundary label propagation into a unified optimization framework to acquire a refined salient map. The coarse saliency map is additionally fused by three prior components: a local contrast map with greater alignment to physiological law, a global focus prior map, and a global color prior map. During the formation of the background weight map, we first construct an affinity matrix and select nodes existing on the border as labels to represent the background. Then we perform a propagation to generate the regional background weight map. Our proposed model was verified on four benchmark datasets, and the experimental results demonstrate that our method has excellent performance.

  6. 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.

  7. 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

  8. Coarse-graining in simulations of multicomponent polymer systems

    NASA Astrophysics Data System (ADS)

    Sethuraman, Vaidyanathan; Nguyen, Bryan H.; Ganesan, Venkat

    2014-12-01

    We investigate the mapping required between the interaction parameters of two different coarse-grained simulation models to ensure a match of the long-range structural characteristics of multicomponent polymeric system. The basis for our studies is the recent work of Morse and workers, which demonstrated the existence of a mapping between the interaction parameters of different coarse-grained simulation models which allow for a matching of the peak of the disordered state structure factor in symmetric diblock copolymers. We investigate the extensibility of their results to other polymeric systems by studying a variety of systems, including, asymmetric diblock copolymers, symmetric triblock copolymers, and diblock copolymer-solvent mixtures. By using the mapping deduced in the context of symmetric diblock copolymers, we observe excellent agreement for peak in the inverse structure between both two popular coarse grained models for all sets of polymeric melt systems investigated, thus showing that the mapping function proposed for diblock copolymer melts is transferable to other polymer melts irrespective of the blockiness or overall composition. Interestingly, for the limited parameter range of polymer-solvent systems investigated in this article, the mapping functions developed for polymer melts are shown to be equally effective in mapping the structure factor of the coarse-grained simulation models. We use our findings to propose a methodology to create ordered morphologies in simulations involving hard repulsive potentials in a computationally efficient manner. We demonstrate the outcomes of methodology by creating lamellar and cylindrical phases of diblock copolymers of long chains in the popularly used Kremer-Grest simulation model.

  9. 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

    2015-03-06

    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.

  10. 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.

  11. Coarse-grained incompressible magnetohydrodynamics: Analyzing the turbulent cascades

    DOE PAGES

    Aluie, Hussein

    2017-02-21

    Here, we formulate a coarse-graining approach to the dynamics of magnetohydrodynamic (MHD) fluids at a continuum of length-scales. In this methodology, effective equations are derived for the observable velocity and magnetic fields spatially-averaged at an arbitrary scale of resolution. The microscopic equations for the bare velocity and magnetic fields are renormalized by coarse-graining to yield macroscopic effective equations that contain both a subscale stress and a subscale electromotive force (EMF) generated by nonlinear interaction of eliminated fields and plasma motions. At large coarse-graining length-scales, the direct dissipation of invariants by microscopic mechanisms (such as molecular viscosity and Spitzer resistivity) ismore » shown to be negligible. The balance at large scales is dominated instead by the subscale nonlinear terms, which can transfer invariants across scales, and are interpreted in terms of work concepts for energy and in terms of topological flux-linkage for the two helicities. An important application of this approach is to MHD turbulence, where the coarse-graining length ℓ lies in the inertial cascade range. We show that in the case of sufficiently rough velocity and/or magnetic fields, the nonlinear inter-scale transfer need not vanish and can persist to arbitrarily small scales. Although closed expressions are not available for subscale stress and subscale EMF, we derive rigorous upper bounds on the effective dissipation they produce in terms of scaling exponents of the velocity and magnetic fields. These bounds provide exact constraints on phenomenological theories of MHD turbulence in order to allow the nonlinear cascade of energy and cross-helicity. On the other hand, we show that the forward cascade of magnetic helicity to asymptotically small scales is impossible unless 3rd-order moments of either velocity or magnetic field become infinite.« less

  12. Coarse semiempirical solution to the protein folding problem

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel; Colubri, Andrés; Appignanesi, Gustavo; Burastero, Teresita

    2001-04-01

    We introduce a semiempirical theory leading to the ab initio prediction of conducive folding pathways and coarsely resolved native backbone geometries of proteins suddenly exposed to in vitro renaturation conditions. The underlying model incorporates a discrete codification of local steric hindrances of the peptide backbone. We first determine a time-evolving finite set of local torsional constraints upon which large-scale organization is built. Thus, the torsional state of the chain is topologically represented by viewing the ( Φ, Ψ)-state of each residue modulo the basin of attraction to which it belongs in the Ramachandran plot. A grammar to combine such coarsely defined torsional states (topologies) and translate them into meaningful patterns of long-range interactions is developed. An algorithm for structure prediction is shown to emerge once this grammar is combined with prescriptions for the time evolution of topological patterns. This algorithm is rooted in the fact that local contributions to the potential energy may be subsumed into time-evolving conformational constraints coarsely defining sets of restricted backbone geometries responsible for framing the patterns of nonbonded interactions. The predictive power of the algorithm is established by obtaining stable topologies of small proteins, which prove to be compatible with their native folds, and computing ab-initio folding pathways for mammalian ubiquitin that ultimately yield a stable structural pattern reproducing its native features.

  13. 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.

  14. 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.

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

    DOE PAGES

    Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; ...

    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

  16. Resuspension of coarse fuel hot particles in the Chernobyl area.

    PubMed

    Wagenpfeil, F; Tschiersch, J

    2001-01-01

    Measurements of resuspended aerosol in the Chernobyl 30-km exclusion zone have shown coarse fuel hot particles in the activity range 1-12 Bq 137Cs per particle. The particles were sampled with newly designed rotating arm impactors which simultaneously collect during the same experiment three samples with fuel particles in the size ranges larger than 3 microns, larger than 6 microns and larger than 9 microns in geometric diameter. The radionuclide ratios, determined after gamma-spectrometry, were in good agreement with the theoretical calculations for the radionuclide-composition of the Chernobyl Nuclear Power Plant at the moment of the accident and the measured hot particles in soil in the early years after the accident. The number concentrations of airborne hot particles were derived from digital autoradiography. For wind resuspension, maximal concentrations of 2.6 coarse hot particles per 1000 m3 and during agricultural activities 36 coarse hot particles per 1000 m3 were measured. The geometric diameter of single hot particles was estimated to be between 6 and 12 microns.

  17. Coarse-graining two-dimensional turbulence via dynamical optimization

    NASA Astrophysics Data System (ADS)

    Turkington, Bruce; Chen, Qian-Yong; Thalabard, Simon

    2016-10-01

    A model reduction technique based on an optimization principle is employed to coarse-grain inviscid, incompressible fluid dynamics in two dimensions. In this reduction the spectrally-truncated vorticity equation defines the microdynamics, while the macroscopic state space consists of quasi-equilibrium trial probability densities on the microscopic phase space, which are parameterized by the means and variances of the low modes of the vorticity. A macroscopic path therefore represents a coarse-grained approximation to the evolution of a nonequilibrium ensemble of microscopic solutions. Closure in terms of the vector of resolved variables, namely, the means and variances of the low modes, is achieved by minimizing over all feasible paths the time integral of their mean-squared residual with respect to the Liouville equation. The equations governing the optimal path are deduced from Hamilton-Jacobi theory. The coarse-grained dynamics derived by this optimization technique contains a scale-dependent eddy viscosity, modified nonlinear interactions between the low mode means, and a nonlinear coupling between the mean and variance of each low mode. The predictive skill of this optimal closure is validated quantitatively by comparing it against direct numerical simulations. These tests show that good agreement is achieved without adjusting any closure parameters.

  18. 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.

  19. 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.

  20. 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

  1. Heterogeneity of coarse particles in an urban area.

    PubMed

    Lagudu, Uma Ramesh K; Raja, Suresh; Hopke, Philip K; Chalupa, David C; Utell, Mark J; Casuccio, Gary; Lersch, Traci L; West, Roger R

    2011-04-15

    The variation in composition and concentration of coarse particles in Rochester, a medium-sized city in western New York, was studied using UNC passive samplers and computer-controlled scanning electron microscopy (CCSEM). The samplers were deployed in a 5 × 5 grid (2 km × 2 km per grid cell) for 2-3 week periods in two seasons (September 2008 and May 2009) at 25 different sites across Rochester. CCSEM analysis yielded size and elemental composition for individual particles and analyzed more than 800 coarse particles per sample. Based on the composition as reflected in the fluoresced X-ray spectrum, the particles were grouped into classes with similar chemical compositions using an adaptive resonance theory (ART) network. The mass fractions of particles in the identified classes were then used to assess the homogeneity of composition and concentration across the measurement domain. These results illustrate how particle sampling using the UNC passive sampler coupled with CCSEM/ART can be used to determine the concentration and source of the coarse particulate matter at multiple sites. The particle compositions were dominated by elements suggesting that the major particle sources are road dust and biological particles. Considerable heterogeneity in both composition and concentration were observed between adjacent sites as indicated by cofficient of divergence analyses.

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

    PubMed

    Choi, Eunsong; Mondal, Jagannath; Yethiraj, Arun

    2014-01-09

    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.

  3. 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

  4. Atomistic and Coarse-grained Simulations of Hexabenzocoronene Crystals

    NASA Astrophysics Data System (ADS)

    Ziogos, G.; Megariotis, G.; Theodorou, D. N.

    2016-08-01

    This study concerns atomistic and coarse-grained Molecular Dynamics simulations of pristine hexabenzocoronene (HBC) molecular crystals. HBC is a symmetric graphene flake of nanometric size that falls in the category of polyaromatic hydrocarbons, finding numerous applications in the field of organic electronics. The HBC molecule is simulated in its crystalline phase initially by means of an all-atom representation, where the molecules self- organize into well aligned molecular stacks, which in turn create a perfect monoclinic molecular crystal. The atomistic model reproduces fairly well the structural experimental properties and thus can be used as a reliable starting point for the development of a coarsegrained model following a bottom-up approach. The coarse-grained model is developed by applying Iterative Boltzmann Inversion, a systematic coarse-graining method which reproduces a set of target atomistic radial distribution functions and intramolecular distributions at the coarser level of description. This model allows the simulation of HBC crystals over longer time and length scales. The crystalline phase is analyzed in terms of the Saupe tensor and thermomechanical properties are probed at the atomistic level.

  5. Effects of Source-Apportioned Coarse Particulate Matter (PM) ...

    EPA Pesticide Factsheets

    The Cleveland Multiple Air Pollutant Study (CMAPS) is one of the first comprehensive studies conducted to evaluate particulate matter (PM) over local and regional scales. Cleveland and the nearby Ohio River Valley impart significant regional sources of air pollution including coal combustion and steel production. Size-fractionated PM (coarse, fine and ultrafine) were collected from an urban site (G.T. Craig (GTC)) and a rural site (Chippewa Lake monitor (CLM) located 53 km southwest of Cleveland) from July 2009 to June 2010. Following collection, resulting speciated PM data were apportioned to identify local industrial emission sources for each size fraction and location, indicating these samples were enriched with resident emission sources. This study was designed to determine whether exposure of the CMAPS coarse PM contributes to the exacerbation of allergic asthma. Non-sensitized and house dust mite (HDM)-sensitized female Balb/cJ mice (n= 8/group) were exposed via oropharyngeal (OP) aspiration to 100 g coarse fractions of one of five source apportioned groups representative of distinct time periods of 4-6 weeks (traffic, coal, steel 1, steel 2, or winter PM) and OP challenge with HDM conducted 2 hr following dosing with PM. Two days later, airway responsiveness to methacholine aerosol was assessed in anesthetized ventilated control and HDM mice. The HDM-allergic mice demonstrated increased airway reactivity in comparison to control mice. Bronchoalveolar l

  6. 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.

  7. Parametrizing coarse grained models for molecular systems at equilibrium

    NASA Astrophysics Data System (ADS)

    Kalligiannaki, E.; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plecháč, P.; Harmandaris, V.

    2016-10-01

    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  8. From Cooperative Self-Assembly to Water-Soluble Supramolecular Polymers Using Coarse-Grained Simulations.

    PubMed

    Bochicchio, Davide; Pavan, Giovanni M

    2017-01-24

    Supramolecular polymers, formed via noncovalent self-assembly of elementary monomers, are extremely interesting for their dynamic bioinspired properties. In order to understand their behavior, it is necessary to access their dynamics while maintaining high resolution in the treatment of the monomer structure and monomer-monomer interactions, which is typically a difficult task, especially in aqueous solution. Focusing on 1,3,5-benzenetricarboxamide (BTA) water-soluble supramolecular polymers, we have developed a transferable coarse-grained model that allows studying BTA supramolecular polymerization in water, while preserving remarkable consistency with the atomistic models in the description of the key interactions between the monomers (hydrophobic, H-bonding, etc.), self-assembly cooperativity, and amplification of order into the growing fibers. This permitted us to monitor the amplification of the key interactions between the monomers (including H-bonding) in the BTA fibers during the dynamic polymerization process. Our molecular dynamics simulations provide a picture of a stepwise cooperative polymerization mechanism, where initial fast hydrophobic aggregation of the BTA monomers in water is followed by the slower reorganization of these disordered aggregates into ordered directional oligomers. Supramolecular polymer growth then proceeds on a slower time scale. We challenged our models via comparison with the experimental evidence, capturing the effect of temperature variations and subtle changes in the monomer structure on the polymerization and on the properties of the fibers seen in the real systems. This work provides a multiscale spatiotemporal characterization of BTA self-assembly in water and a useful platform to study a variety of BTA-based supramolecular polymers toward structure-property relationships.

  9. 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

  10. Coarse woody debris: Managing benefits and fire hazard in the recovering forest

    Treesearch

    James K. Brown; Elizabeth D. Reinhardt; Kylie A. Kramer

    2003-01-01

    Management of coarse woody debris following fire requires consideration of its positive and negative values. The ecological benefits of coarse woody debris and fire hazard considerations are summarized. This paper presents recommendations for desired ranges of coarse woody debris. Example simulations illustrate changes in debris over time and with varying management....

  11. Quantifying the coarse-root biomass of intensively managed loblolly pine plantations

    Treesearch

    Ashley T. Miller; H. Lee Allen; Chris A. Maier

    2006-01-01

    Most of the carbon accumulation during a forest rotation is in plant biomass and the forest floor. Most of the belowground biomass in older loblolly pine (Pinus taeda L.) forests is in coarse roots, and coarse roots ersist longer after harvest than aboveground biomass and fine oots. The main objective was to assess the carbon accumulation in coarse...

  12. Quantifying the coarse-root biomass of intensively managed loblolly pine plantations

    Treesearch

    Ashley T. Miller; H. Lee Allen; Chris A. Maier

    2006-01-01

    Most of the carbon accumulation during a forest rotation is in plant biomass and the forest floor. Most of the belowground biomass in older loblolly pine (Pinus taeda L.) forests is in coarse roots, and coarse roots persist longer after harvest than aboveground biomass and fine roots. The main objective was to assess the carbon accumulation in coarse...

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

    NASA Astrophysics Data System (ADS)

    Cao, Zhen; Voth, Gregory A.

    2015-12-01

    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.

  14. 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.

  15. 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…

  16. 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…

  17. 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.

  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.

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

    PubMed

    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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

    2015-02-05

    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.

  4. A multi-state coarse grained modeling approach for an intrinsically disordered peptide.

    PubMed

    Ramezanghorbani, Farhad; Dalgicdir, Cahit; Sayar, Mehmet

    2017-09-07

    Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LKα14 is disordered in dilute solutions; however, it strictly adopts the α-helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an α-helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.

  5. A multi-state coarse grained modeling approach for an intrinsically disordered peptide

    NASA Astrophysics Data System (ADS)

    Ramezanghorbani, Farhad; Dalgicdir, Cahit; Sayar, Mehmet

    2017-09-01

    Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LKα 14 is disordered in dilute solutions; however, it strictly adopts the α -helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an α -helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.

  6. Premature red blood cells have decreased aggregation and enhanced aggregability.

    PubMed

    Arbell, D; Orkin, B; Bar-Oz, B; Barshtein, G; Yedgar, S

    2008-06-01

    Preterm infants are highly susceptible to ischemic damage. This damage is most obvious in the brain, retina, and gastrointestinal tract. Studies focusing on the rheological properties of premature red blood cells (pRBCs) have consistently shown minimal or no RBC aggregation. Previously, measurements of pRBC aggregation kinetics indicated that specific plasma properties are responsible for the decreased RBC aggregation observed in the neonates, but that their specific RBC properties do not affect it. However, the strength of interaction in the pRBC aggregates as a function of medium composition has not been tested. In our previous research, we described clinically relevant parameters, that is, the aggregate resistance to disaggregation by flow. With the help of a cell flow property analyzer (CFA), we can monitor RBC aggregation by direct visualization of its dynamics during flow. We used the CFA to examine pRBC (from 9 premature babies) in the natural plasma and in PBS buffer supplemented with dextran (500 kDa) to distinguish between RBC intrinsic-cellular and plasma factors. pRBCs suspended in the native plasma showed minimal or no aggregation in comparison to normal adult RBC. When we transferred pRBCs from the same sample to the dextran solution, enhanced resistance to disaggregation by flow was apparent.

  7. Properties of Concrete partially replaced with Coconut Shell as Coarse aggregate and Steel fibres in addition to its Concrete volume

    NASA Astrophysics Data System (ADS)

    Kalyana Chakravarthy, P. R.; Janani, R.; Ilango, T.; Dharani, K.

    2017-03-01

    Cement is a binder material with various composition of Concrete but instantly it posses low tensile strength. The study deals with mechanical properties of that optimized fiber in comparison with conventional and coconut shell concrete. The accumulation of fibers arbitrarily dispersed in the composition increases the resistance to cracking, deflection and other serviceability conditions substantially. The steel fiber in extra is one of the revision in coconut shell concrete and the outcome of steel fiber in coconut shell concrete was to investigate and compare with the conventional concrete. For the given range of steel fibe from 0.5 to 2.0%, 12 beams and 36 cylindrical specimens were cast and tested to find the mechanical properties like flexural strength, split tensile, impact resistance and the modulus of elasticity of both conventional and coconut shell concrete has been studied and the test consequences are compared with the control concrete and coconut shell concrete for M25 Grade. It is fulfilled that, the steel fibers used in this venture has shown significant development in all the properties of conventional and coconut shell concrete while compared to controlled conventional and coconut shell concrete like, Flexural strength by 6.67 % for 1.0 % of steel fiber in conventional concrete and by 5.87 % for 1.5 % of steel fiber in coconut shell concrete.

  8. Orthogonal flexible Rydberg aggregates

    NASA Astrophysics Data System (ADS)

    Leonhardt, K.; Wüster, S.; Rost, J. M.

    2016-02-01

    We study the link between atomic motion and exciton transport in flexible Rydberg aggregates, assemblies of highly excited light alkali-metal atoms, for which motion due to dipole-dipole interaction becomes relevant. In two one-dimensional atom chains crossing at a right angle adiabatic exciton transport is affected by a conical intersection of excitonic energy surfaces, which induces controllable nonadiabatic effects. A joint exciton-motion pulse that is initially governed by a single energy surface is coherently split into two modes after crossing the intersection. The modes induce strongly different atomic motion, leading to clear signatures of nonadiabatic effects in atomic density profiles. We have shown how this scenario can be exploited as an exciton switch, controlling direction and coherence properties of the joint pulse on the second of the chains [K. Leonhardt et al., Phys. Rev. Lett. 113, 223001 (2014), 10.1103/PhysRevLett.113.223001]. In this article we discuss the underlying complex dynamics in detail, characterize the switch, and derive our isotropic interaction model from a realistic anisotropic one with the addition of a magnetic bias field.

  9. Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

    PubMed

    Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

    2013-10-08

    We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

  10. Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation

    PubMed Central

    Sterpone, Fabio; Nguyen, Phuong H.; Kalimeri, Maria; Derreumaux, Philippe

    2014-01-01

    We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions. PMID:25419192

  11. 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.

  12. Evaluation of the environmental, material, and structural performance of recycled aggregate concrete

    NASA Astrophysics Data System (ADS)

    Michaud, Katherine Sarah

    Concrete is the most commonly used building material in the construction industry, and contributes to 52% of construction and demolition waste in Canada. Recycled concrete aggregate (RCA) is one way to reduce this impact. To evaluate the performance of coarse and granular (fine and coarse) RCA in structural concrete applications, four studies were performed: an environmental assessment, a material testing program, a shear performance study, and a flexural performance study. To determine the environmental benefits of recycled aggregate concrete (RAC), three case studies were investigated using different populations and proximities to city centres. Environmental modelling suggested that RCA replacement could result in energy savings and greenhouse gas emission reductions, especially in remote areas. Tests were performed to determine if the volumetric replacement of up to 30% coarse RCA and 20% granular RCA is suitable for structural concrete applications in Canada. Fresh, hardened, and durability properties were evaluated. All five (5) of the RCA mixes showed equivalent material performance to the control mixes and met the requirements for a structural concrete mix. The five (5) RAC mixes were also used in structural testing. One-way reinforced concrete slab specimens were tested to failure to evaluate the shear and flexural performance of the RAC members. Peak capacities of and crack formation within each member were analyzed to evaluate the performance of RAC compared to conventional concrete. The shear capacity of specimens made from four (4) of the five (5) RAC mixtures was higher or equivalent to the control specimens. Specimens of the concrete mixture containing the highest content of recycled aggregate, 20% volumetric replacement of granular RCA, had shear capacities 14.1% lower, and exhibited cracking at lower loads than the control. The average flexural capacities of all RAC specimens were within 3.7% of the control specimens. Results from this research

  13. 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

    2012-05-08

    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.

  14. Patterns of gravity induced aggregate migration during casting of fluid concretes

    SciTech Connect

    Spangenberg, J.; Roussel, N.; Hattel, J.H.; Sarmiento, E.V.; Zirgulis, G.; Geiker, M.R.

    2012-12-15

    In this paper, aggregate migration patterns during fluid concrete castings are studied through experiments, dimensionless approach and numerical modeling. The experimental results obtained on two beams show that gravity induced migration is primarily affecting the coarsest aggregates resulting in a decrease of coarse aggregates volume fraction with the horizontal distance from the pouring point and in a puzzling vertical multi-layer structure. The origin of this multi layer structure is discussed and analyzed with the help of numerical simulations of free surface flow. Our results suggest that it finds its origin in the non Newtonian nature of fresh concrete and that increasing casting rate shall decrease the magnitude of gravity induced particle migration.

  15. 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

  16. Structure and aggregation proclivity of C12E3 in aqueous solution

    NASA Astrophysics Data System (ADS)

    Zahariev, Ts.; Ivanova, A.; Velinova, M.; Tadjer, A.

    2013-01-01

    Olygo(ethylene glycol) alkyl ethers - CxEy are well known for their high surface activity and rich phase behavior. These substances exhibit some unusual aggregation characteristics in aqueous solution even at concentrations well below CMC attributed to the formation of pre-aggregates of small size, e.g., dimers. To verify this, a series of C12E3 dimers with initial geometries taken from coarse-grained molecular dynamics simulations is subject to geometry optimization with two quantum chemical methods: DFT and ONIOM in implicit water solvent. The resulting structures are classified into groups based on structural parameters. Their stability is assessed by relative and binding energy and rationalized in terms of molecular characteristics. All studied dimers are stable and various mutual alignments of the surfactants therein are feasible. The loss of surface area is outlined as the predominant stabilizing factor. Substantial number of the structures is suitable for further aggregation.

  17. 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.

  18. 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.

  19. Kinetics of Aggregation with Choice

    SciTech Connect

    Ben-Naim, Eli; Krapivsky, Paul

    2016-12-01

    Here we generalize the ordinary aggregation process to allow for choice. In ordinary aggregation, two random clusters merge and form a larger aggregate. In our implementation of choice, a target cluster and two candidate clusters are randomly selected and the target cluster merges with the larger of the two candidate clusters.We study the long-time asymptotic behavior and find that as in ordinary aggregation, the size density adheres to the standard scaling form. However, aggregation with choice exhibits a number of different features. First, the density of the smallest clusters exhibits anomalous scaling. Second, both the small-size and the large-size tails of the density are overpopulated, at the expense of the density of moderate-size clusters. Finally, we also study the complementary case where the smaller candidate cluster participates in the aggregation process and find an abundance of moderate clusters at the expense of small and large clusters. Additionally, we investigate aggregation processes with choice among multiple candidate clusters and a symmetric implementation where the choice is between two pairs of clusters.

  20. Kinetics of Aggregation with Choice

    DOE PAGES

    Ben-Naim, Eli; Krapivsky, Paul

    2016-12-01

    Here we generalize the ordinary aggregation process to allow for choice. In ordinary aggregation, two random clusters merge and form a larger aggregate. In our implementation of choice, a target cluster and two candidate clusters are randomly selected and the target cluster merges with the larger of the two candidate clusters.We study the long-time asymptotic behavior and find that as in ordinary aggregation, the size density adheres to the standard scaling form. However, aggregation with choice exhibits a number of different features. First, the density of the smallest clusters exhibits anomalous scaling. Second, both the small-size and the large-size tailsmore » of the density are overpopulated, at the expense of the density of moderate-size clusters. Finally, we also study the complementary case where the smaller candidate cluster participates in the aggregation process and find an abundance of moderate clusters at the expense of small and large clusters. Additionally, we investigate aggregation processes with choice among multiple candidate clusters and a symmetric implementation where the choice is between two pairs of clusters.« less

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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.

  7. A fusion approach for coarse-to-fine target recognition

    NASA Astrophysics Data System (ADS)

    Folkesson, Martin; Grönwall, Christina; Jungert, Erland

    2006-04-01

    A fusion approach in a query based information system is presented. The system is designed for querying multimedia data bases, and here applied to target recognition using heterogeneous data sources. The recognition process is coarse-to-fine, with an initial attribute estimation step and a following matching step. Several sensor types and algorithms are involved in each of these two steps. An independence of the matching results, on the origin of the estimation results, is observed. It allows for distribution of data between algorithms in an intermediate fusion step, without risk of data incest. This increases the overall chance of recognising the target. An implementation of the system is described.

  8. Transferability of coarse-grained force fields: The polymer case

    NASA Astrophysics Data System (ADS)

    Carbone, Paola; Varzaneh, Hossein Ali Karimi; Chen, Xiaoyu; Müller-Plathe, Florian

    2008-02-01

    A key question for all coarse-graining methodologies is the degree of transferability of the resulting force field between various systems and thermodynamic conditions. Here we present a detailed study of the transferability over different thermodynamic states of a coarse-grained (CG) force field developed using the iterative Boltzmann inversion method. The force field is optimized against distribution functions obtained from atomistic simulations. We analyze the polymer case by investigating the bulk of polystyrene and polyamide-6,6 whose coarse-grained models differ in the chain length and in the number of atoms lumped in one bead. The effect of temperature and pressure on static, dynamic, and thermodynamic properties is tested by comparing systematically the coarse-grain results with the atomistic ones. We find that the CG model describing the polystyrene is transferable only in a narrow range of temperature and it fails in describing the change of the bulk density when temperature is 80K lower than the optimization one. Moreover the calculation of the self-diffusion coefficient shows that the CG model is characterized by a faster dynamics than the atomistic one and that it overestimates the isothermal compressibility. On the contrary, the polyamide-6,6 CG model turns out to be fully transferable between different thermodynamic conditions. The transferability is checked by changing either the temperature or the pressure of the simulation. We find that, in this case, the CG model is able to follow all the intra- and interstructural rearrangements caused by the temperature changes. In addition, while at low temperature the difference between the CG and atomistic dynamics is remarkable due to the presence of hydrogen bonds in the atomistic systems, for high temperatures, the speedup of the CG dynamics is strongly reduced, leading to a CG diffusion coefficient only six times bigger than the atomistic one. Moreover, the isothermal compressibility calculated at

  9. Dynamical coarse grained models with realistic time dependence

    NASA Astrophysics Data System (ADS)

    Andersen, Hans

    2015-03-01

    Coarse grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. We consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse Graining (MS-CG) method of Voth and coworkers. We propose a method of converting an MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that was studied by Zwanzig [R. Zwanzig, J. Stat. Phys. 9, 215 (1973)]. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics simulation programs. We present tests of this method on a series of simple examples that demonstrate that the method provides realistic dynamical CG models that have non-Markovian or close to Markovian behavior that is consistent with the actual dynamical behavior of the all-atom system used to construct the CG model. The dynamic CG models have computational requirements that are similar to

  10. Residual gas saturation effects on hydraulic conductivity of coarse sand

    NASA Astrophysics Data System (ADS)

    Princ, Tomas; Reis Fideles, Helena Maria; Snehota, Michal; Sacha, Jan; Cislerova, Milena

    2017-04-01

    The aim of the first part of this study was to experimentally determine the relationship between gas residual saturation (Sgr) and actual hydraulic conductivity (K) of coarse sand. Sgr indicates the ratio of entrapped air volume to pore volume of the sample. The value of residual gas saturation value determined in experiments exhibits temporal variability (due to history of wetting and drying, due to redistribution, air dissolution etc.), but many two-phase models assume value of Sgr to be constant. The K(Sgr) relationship was determined in series of constant head infiltration-outflow experiments. The first runs was performed on fully saturated sample. After the first infiltration run and then after each subsequent infiltration run, sample was drained under tension on a sand tank. Sgr was determined gravimetrically before each infiltration run. The value of K was determined using a Darcy's law from measured steady state flux and each measurement then provided one value of K(Sgr). Several relative hydraulic conductivity models were tested to fit the measured points. In the second part of this study the aim was to compare hydraulic conductivities predicted from the retention curves by Mualem - van Genuchten model and measured K(Sgr). The performance of both concepts was tested in numerical simulation of the complex infiltration-outflow experiment using TOUGH2 multiphase model (Pruess et al., 2012). TOUGH2 model considers Sgr as a point, below which gas phase becomes immobile, but its content still can be reduced by dissolution into water. The simulated infiltration-outflow experiment was previously conducted on a compacted sample composed of fine, medium coarse and coarse sand (Sněhota et al., 2015). The data of water content distribution during various stages of the experiment were determined by means of neutron tomography. The Levenberg-Marquardt algorithm was used for parameter optimization. Four parameters (permeability and residual gas saturation of fine and

  11. Physical property data on coarse anthracite waste. Report of investigations

    SciTech Connect

    Stewart, B.M.; Atkins, L.A.

    1983-07-01

    Since 1974, a large amount of data has been developed concerning the physical properties and stability characteristics of waste generated by the mining and preparation of bituminous coal. However, very little information has been developed on the properties and characteristics of anthracite waste. During this Bureau of Mines research project, coarse anthracite breaker refuse from five sites in eastern Pennsylvania was sampled and the physical properties, which indicate stability characteristics, were determined in the laboratory. Stability analyses were conducted on six theoretical anthracite waste embankments. These analyses show the effects on minimum safety factors of geometry, phreatic surface level, and physical properties.

  12. 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

  13. Coarse-grained incompressible magnetohydrodynamics: analyzing the turbulent cascades

    NASA Astrophysics Data System (ADS)

    Aluie, Hussein

    2017-02-01

    We formulate a coarse-graining approach to the dynamics of magnetohydrodynamic (MHD) fluids at a continuum of length-scales ℓ. In this methodology, effective equations are derived for the observable velocity and magnetic fields spatially-averaged at an arbitrary scale of resolution. The microscopic equations for the ‘bare’ velocity and magnetic fields are ‘renormalized’ by coarse-graining to yield macroscopic effective equations that contain both a subscale stress and a subscale electromotive force (EMF) generated by nonlinear interaction of eliminated fields and plasma motions. Particular attention is given to the effects of these subscale terms on the balances of the quadratic invariants of ideal incompressible MHD—energy, cross-helicity and magnetic helicity. At large coarse-graining length-scales, the direct dissipation of the invariants by microscopic mechanisms (such as molecular viscosity and Spitzer resistivity) is shown to be negligible. The balance at large scales is dominated instead by the subscale nonlinear terms, which can transfer invariants across scales, and are interpreted in terms of work concepts for energy and in terms of topological flux-linkage for the two helicities. An important application of this approach is to MHD turbulence, where the coarse-graining length ℓ lies in the inertial cascade range. We show that in the case of sufficiently rough velocity and/or magnetic fields, the nonlinear inter-scale transfer need not vanish and can persist to arbitrarily small scales. Although closed expressions are not available for subscale stress and subscale EMF, we derive rigorous upper bounds on the effective dissipation they produce in terms of scaling exponents of the velocity and magnetic fields. These bounds provide exact constraints on phenomenological theories of MHD turbulence in order to allow the nonlinear cascade of energy and cross-helicity. On the other hand, we prove a very strong version of the Woltjer-Taylor conjecture

  14. Fractal aggregates in Titan's atmosphere

    NASA Astrophysics Data System (ADS)

    Cabane, M.; Rannou, P.; Chassefiere, E.; Israel, G.

    1993-04-01

    The cluster structure of Titan's atmosphere was modeled by using an Eulerian microphysical model with the specific formulation of microphysical laws applying to fractal particles. The growth of aggregates in the settling phase was treated by introducing the fractal dimension as a parameter of the model. The model was used to obtain a vertical distribution of size and number density of the aggregates for different production altitudes. Results confirm previous estimates of the formation altitude of photochemical aerosols. The vertical profile of the effective radius of aggregates was calculated as a function of the visible optical depth.

  15. Aggregated Computational Toxicology Online Resource

    EPA Pesticide Factsheets

    Aggregated Computational Toxicology Online Resource (AcTOR) is EPA's online aggregator of all the public sources of chemical toxicity data. ACToR aggregates data from over 1,000 public sources on over 500,000 chemicals and is searchable by chemical name, other identifiers and by chemical structure. It can be used to query a specific chemical and find all publicly available hazard, exposure and risk assessment data. It also provides access to EPA's ToxCast, ToxRefDB, DSSTox, Dashboard and DSSTox data.

  16. Upscaling the Use of Mixed Recycled Aggregates in Non-Structural Low Cement Concrete

    PubMed Central

    López-Uceda, Antonio; Ayuso, Jesús; Jiménez, José Ramón; Agrela, Francisco; Barbudo, Auxiliadora; De Brito, Jorge

    2016-01-01

    This research aims to produce non-structural concrete with mixed recycled aggregates (MRA) in upscaled applications with low-cement content. Four slabs were executed with concrete made with different ratios of coarse MRA (0%, 20%, 40% and 100%), using the mix design, the mixing procedures and the facilities from a nearby concrete production plant. The analysis of the long-term compressive and splitting tensile strengths in concrete cores, extracted from the slabs, allowed the highlighting of the long-term high strength development potential of MRA incorporation. The study of cast specimens produced in situ under the same conditions as the slabs showed, firstly, that the use of MRA has a great influence on the properties related to durability, secondly, that the loss of compressive strength for total MRA incorporation relative to control concrete increases proportionally with the class strength, and, thirdly, that the mechanical properties (including Schmidt hammer results) from the concrete slabs showed no significant differences relative to the control concrete for coarse aggregates replacements up to 40%. Therefore, this upscaled experimental study supports the application of concrete with 100% coarse MRA incorporation and low cement content in non-structural civil works such as bike lanes, gutters, ground slabs, leveling surfaces, and subgrades for foundations. To the best of the authors’ knowledge, there have not been any upscaled applications of concrete with MRA and low cement content. PMID:28787892

  17. [Pollutant distribution in organo-mineral aggregates in topsoils from a site contaminated by organochlorine pesticides].

    PubMed

    Cong, Xin; Xue, Nan-dong; Liang, Gang; Wang, Shi-jie; Zhu, Shu-quan; Li, Fa-sheng

    2008-09-01

    Four different soil particle-size fractions that is clay, silt, fine sand and coarse sand ( <2 microm, 2-20 microm, 20-200 microm, > 200 microm) from the topsoils in an organochlorine pesticide (OCP) field were separated by physical method to characterize the OCPs distribution in soils and to study the effect of organic matter and mineral composition in different separates on pollutants distribution. The results show that the concentrations of HCHs and DDTs in silt with 463.1 mg x kg(-1) and 1225.6 mg x kg(-1) are higher than those in coarse sand, 157.8 mg x kg(-1) and 384.5 mg x kg(-1), respectively. There is a significant correlationship between IgKoc. and the contents of HCHs and DDTs in clay. The analysis on X-ray diffraction of organo-mineral aggregates demonstrates that clay and silt have a much higher content of the clay minerals than those in coarse sand within the contaminated soils. There are some differences with different particle-size fractions in the content and composition of the clay minerals in organo-mineral aggregates, which affect the OCP distribution in soils to some extents. The results also suggest that the distribution of HCHs and DDTs in the particle with more pollutants in the site is similar to that in airborne particles. So the environmental behavior of OCPs in topsoils from the contaminated site should be paid more attention especially in ambient air-soil interaction.

  18. Upscaling the Use of Mixed Recycled Aggregates in Non-Structural Low Cement Concrete.

    PubMed

    López-Uceda, Antonio; Ayuso, Jesús; Jiménez, José Ramón; Agrela, Francisco; Barbudo, Auxiliadora; De Brito, Jorge

    2016-02-02

    This research aims to produce non-structural concrete with mixed recycled aggregates (MRA) in upscaled applications with low-cement content. Four slabs were executed with concrete made with different ratios of coarse MRA (0%, 20%, 40% and 100%), using the mix design, the mixing procedures and the facilities from a nearby concrete production plant. The analysis of the long-term compressive and splitting tensile strengths in concrete cores, extracted from the slabs, allowed the highlighting of the long-term high strength development potential of MRA incorporation. The study of cast specimens produced in situ under the same conditions as the slabs showed, firstly, that the use of MRA has a great influence on the properties related to durability, secondly, that the loss of compressive strength for total MRA incorporation relative to control concrete increases proportionally with the class strength, and, thirdly, that the mechanical properties (including Schmidt hammer results) from the concrete slabs showed no significant differences relative to the control concrete for coarse aggregates replacements up to 40%. Therefore, this upscaled experimental study supports the application of concrete with 100% coarse MRA incorporation and low cement content in non-structural civil works such as bike lanes, gutters, ground slabs, leveling surfaces, and subgrades for foundations. To the best of the authors' knowledge, there have not been any upscaled applications of concrete with MRA and low cement content.

  19. Kinetics of amyloid aggregation: a study of the GNNQQNY prion sequence.

    PubMed

    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 μs 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.

  20. 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

  1. Aggregation of thrombin-derived C-terminal fragments as a previously undisclosed host defense mechanism

    PubMed Central

    Petrlova, Jitka; Hansen, Finja C.; van der Plas, Mariena J. A.; Mörgelin, Matthias; Malmsten, Martin; Bond, Peter J.; Schmidtchen, Artur

    2017-01-01

    Effective control of endotoxins and bacteria is crucial for normal wound healing. During injury, the key enzyme thrombin is formed, leading to generation of fibrin. Here, we show that human neutrophil elastase cleaves thrombin, generating 11-kDa thrombin-derived C-terminal peptides (TCPs), which bind to and form amorphous amyloid-like aggregates with both bacterial lipopolysaccharide (LPS) and gram-negative bacteria. In silico molecular modeling using atomic resolution and coarse-grained simulations corroborates our experimental observations, altogether indicating increased aggregation through LPS-mediated intermolecular contacts between clusters of TCP molecules. Upon bacterial aggregation, recombinantly produced TCPs induce permeabilization of Escherichia coli and phagocytic uptake. TCPs of about 11 kDa are present in acute wound fluids as well as in fibrin sloughs from patients with infected wounds. We noted aggregation and colocalization of LPS with TCPs in such fibrin material, which indicates the presence of TCP-LPS aggregates under physiological conditions. Apart from identifying a function of proteolyzed thrombin and its fragments, our findings provide an interesting link between the coagulation system, innate immunity, LPS scavenging, and protein aggregation/amyloid formation. PMID:28473418

  2. 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.

  3. 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.

  4. 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.

  5. Surface fractals in liposome aggregation.

    PubMed

    Roldán-Vargas, Sándalo; Barnadas-Rodríguez, Ramon; Quesada-Pérez, Manuel; Estelrich, Joan; Callejas-Fernández, José

    2009-01-01

    In this work, the aggregation of charged liposomes induced by magnesium is investigated. Static and dynamic light scattering, Fourier-transform infrared spectroscopy, and cryotransmission electron microscopy are used as experimental techniques. In particular, multiple intracluster scattering is reduced to a negligible amount using a cross-correlation light scattering scheme. The analysis of the cluster structure, probed by means of static light scattering, reveals an evolution from surface fractals to mass fractals with increasing magnesium concentration. Cryotransmission electron microscopy micrographs of the aggregates are consistent with this interpretation. In addition, a comparative analysis of these results with those previously reported in the presence of calcium suggests that the different hydration energy between lipid vesicles when these divalent cations are present plays a fundamental role in the cluster morphology. This suggestion is also supported by infrared spectroscopy data. The kinetics of the aggregation processes is also analyzed through the time evolution of the mean diffusion coefficient of the aggregates.

  6. Cell aggregation: Packing soft grains

    NASA Astrophysics Data System (ADS)

    Åström, J. A.; Karttunen, M.

    2006-06-01

    Cellular aggregates may be considered as collections of membrane enclosed units with a pressure difference between the internal and external liquid phases. Cells are kept together by membrane adhesion and/or confined space compression. Pattern formation and, in particular, intercellular spacing have important roles in controlling solvent diffusion within such aggregates. A physical approach is used to study generic aspects of cellular packings in a confined space. Average material properties are derived from the free energy. The appearance of penetrating intercellular void channels is found to be critically governed by the cell wall adhesion mechanisms during the formation of dense aggregates. A fully relaxed aggregate efficiently hinders solvent diffusion at high hydrostatic pressures, while a small fraction (˜0.1) of adhesion related packing frustration is sufficient for breaking such a blockage even at high a pressure.

  7. The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems.

    PubMed

    Das, Avisek; Lu, Lanyuan; Andersen, Hans C; Voth, Gregory A

    2012-05-21

    The multiscale coarse-graining (MS-CG) method uses simulation data for an atomistic model of a system to construct a coarse-grained (CG) potential for a coarse-grained model of the system. The CG potential is a variational approximation for the true potential of mean force of the degrees of freedom retained in the CG model. The variational calculation uses information about the atomistic positions and forces in the simulation data. In principle, the resulting MS-CG potential will be an accurate representation of the true CG potential if the basis set for the variational calculation is complete enough and the canonical distribution of atomistic states is well sampled by the data set. In practice, atomistic configurations that have very high potential energy are not sampled. As a result there usually is a region of CG configuration space that is not sampled and about which the data set contains no information regarding the gradient of the true potential. The MS-CG potential obtained from a variational calculation will not necessarily be accurate in this unsampled region. A priori considerations make it clear that the true CG potential of mean force must be very large and positive in that region. To obtain an MS-CG potential whose behavior in the sampled region is determined by the atomistic data set, and whose behavior in the unsampled region is large and positive, it is necessary to intervene in the variational calculation in some way. In this paper, we discuss and compare two such methods of intervention, which have been used in previous MS-CG calculations for dealing with nonbonded interactions. For the test systems studied, the two methods give similar results and yield MS-CG potentials that are limited in accuracy only by the incompleteness of the basis set and the statistical error of associated with the set of atomistic configurations used. The use of such methods is important for obtaining accurate CG potentials.

  8. 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

  9. 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.

  10. A coarse grain model for protein-surface interactions.

    PubMed

    Wei, Shuai; Knotts, Thomas A

    2013-09-07

    The interaction of proteins with surfaces is important in numerous applications in many fields-such as biotechnology, proteomics, sensors, and medicine--but fundamental understanding of how protein stability and structure are affected by surfaces remains incomplete. Over the last several years, molecular simulation using coarse grain models has yielded significant insights, but the formalisms used to represent the surface interactions have been rudimentary. We present a new model for protein surface interactions that incorporates the chemical specificity of both the surface and the residues comprising the protein in the context of a one-bead-per-residue, coarse grain approach that maintains computational efficiency. The model is parameterized against experimental adsorption energies for multiple model peptides on different types of surfaces. The validity of the model is established by its ability to quantitatively and qualitatively predict the free energy of adsorption and structural changes for multiple biologically-relevant proteins on different surfaces. The validation, done with proteins not used in parameterization, shows that the model produces remarkable agreement between simulation and experiment.

  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. 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.

  13. Interrogating Nucleosome Positioning Through Coarse-Grain Molecular Simulation

    NASA Astrophysics Data System (ADS)

    Freeman, Gordon S.; Hinckley, Daniel M.; Ortiz, Vanessa; de Pablo, Juan J.

    2012-02-01

    Nucleosome positioning plays a crucial role in biology. As the fundamental unit in chromosome structure, the nucleosome core particle (NCP) binds to approximately 147 DNA base pairs. The location of bound NCPs in the genome, therefore, affects gene expression. The specific positioning of NCPs has been experimentally probed and competing viewpoints have been presented in the literature. Models for nucleosome positioning based on sequence-dependent flexibility (a genomic ``code" for nucleosome positioning) have been demonstrated to explain available experimental data. However, so do statistical models with no built-in sequence preference; the driving force for NCP positioning therefore remains an open question. We use a coarse-grain model for the NCP in combination with advanced sampling techniques to probe the sequence preference of NCPs. We present a method for determining the relative affinity of two DNA sequences for the NCP and use this method to compare high- and low-affinity sequences. We discuss several coarse-grain protein models with varying level of detail to examine the impact of model resolution on the agreement of our results with experimental evidence. We also investigate the dynamics of the NCP-DNA complex and their dependence on system characteristics.

  14. 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.

  15. Measurement of coarse aerosols in workplaces. A review.

    PubMed

    Vincent, J H

    1994-01-01

    Coarse aerosol fractions in workplaces are sampled if it is felt that particles of all sizes may pose a risk to health. Although the so-called 'total' aerosol has been widely used to refer to the relevant coarse fraction, practical measurement has been very dependent on the actual sampling instrument used. This in turn has led to great uncertainty about what was being measured. In the 1980s, the concept of inhalability was proposed, based on the aerosol particle size fraction that enters the human head through the nose and/or mouth during breathing. Now there is substantial agreement by most of the world's major criteria-setting bodies on a quantitative definition taking the form of a single curve describing the probability of inhalation as a function of particle aerodynamic diameter. This definition now forms a truly health-related 'yardstick' against which to assess the performances of practical sampling devices. In turn, more and more countries are beginning to adopt the new criterion for health-related aerosol measurement in their standards, replacing the old 'total' aerosol concept. Experiments in wind tunnels to investigate the performances of previous samplers for 'total' aerosol show that most of them do not satisfactorily match the new inhalability criterion. A small number of samplers designed specifically for the inhalable fraction have been proposed and are available commercially. They include samplers for both static (or area) and personal sampling.

  16. 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.

  17. Electronically coarse-grained molecular dynamics using quantum Drude oscillators

    NASA Astrophysics Data System (ADS)

    Jones, A. P.; Crain, J.; Cipcigan, F. S.; Sokhan, V. P.; Modani, M.; Martyna, G. J.

    2013-12-01

    Standard molecular dynamics (MD) simulations generally make use of a basic description of intermolecular forces which consists of fixed, pairwise, atom-centred Coulomb, van der Waals and short-range repulsive terms. Important interactions such as many-body polarisation and many-body dispersion which are sensitive to changes in the environment are usually neglected, and their effects treated effectively within mean-field approximations to reproduce a single thermodynamic state point or physical environment. This leads to difficulties in modelling the complex interfaces of interest today where the behaviour may be quite different from the regime of parameterisation. Here, we describe the construction and properties of a Gaussian coarse-grained electronic structure, which naturally generates many-body polarisation and dispersion interactions. The electronic structure arises from a fully quantum mechanical treatment of a set of distributed quantum Drude oscillators (QDOs), harmonic atoms which interact with each other and other moieties via electrostatic (Coulomb) interactions; this coarse-grained approach is capable of describing many-body polarisation and dispersion but not short-range interactions which must be parametrised. We describe how on-the-fly forces due to this exchange-free Gaussian model may be generated with linear scale in the number of atoms in the system using an adiabatic path integral molecular dynamics for quantum Drude oscillators technique (APIMD-QDO). We demonstrate the applicability of the QDO approach to realistic systems via a study of the liquid-vapour interface of water.

  18. 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.

  19. Coarse atmospheric aerosol: size distributions of trace elements

    NASA Astrophysics Data System (ADS)

    Eleftheriadis, K.; Colbeck, I.

    A sampler, employing nine single stage impactors placed in parallel within a portable wind tunnel, has been used to determine the metal content of coarse atmospheric aerosol. The wind tunnel maintains a constant flow environment for the collectors housed inside it, so that representative sampling conditions are achieved compared to the varied ambient wind conditions. At a flow rate of 8 m s -1 the 50% cut-off diameters of the impactors ranged from 7.8 to 38.8 μm. Measurements were conducted at a rural and urban site near Colchester in south east England. The samplers were analysed by PIXE for P, K, Ca, Fe, Ti, Mn, Cu, V, Co, Cr, Br, Zn, Ni, Sc and Pb. It is found that the sampler can be employed to quantitatively characterise the elemental mass size distribution for aerosol larger than 10 μm. The results indicate that a small fraction of the above earth and trace elements' metal mass is present in particles greater than 10 μm. This fraction for earth metals (Ca, K, Ti) is comparatively greater in the rural site than the urban site, while for trace metals (Mn, V, Cu, Cr) this fraction constitutes a more significant part of the coarse mass at the urban site. Trace element concentrations were of a similar order of magnitude to earlier literature reports. Although the number of measurements was limited it can be concluded that the size distributions obtained were characteristic of an unpolluted area.

  20. A coarse grain model for protein-surface interactions

    NASA Astrophysics Data System (ADS)

    Wei, Shuai; Knotts, Thomas A.

    2013-09-01

    The interaction of proteins with surfaces is important in numerous applications in many fields—such as biotechnology, proteomics, sensors, and medicine—but fundamental understanding of how protein stability and structure are affected by surfaces remains incomplete. Over the last several years, molecular simulation using coarse grain models has yielded significant insights, but the formalisms used to represent the surface interactions have been rudimentary. We present a new model for protein surface interactions that incorporates the chemical specificity of both the surface and the residues comprising the protein in the context of a one-bead-per-residue, coarse grain approach that maintains computational efficiency. The model is parameterized against experimental adsorption energies for multiple model peptides on different types of surfaces. The validity of the model is established by its ability to quantitatively and qualitatively predict the free energy of adsorption and structural changes for multiple biologically-relevant proteins on different surfaces. The validation, done with proteins not used in parameterization, shows that the model produces remarkable agreement between simulation and experiment.

  1. Coarse-grained modeling of RNA 3D structure.

    PubMed

    Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M

    2016-07-01

    Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.

  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. 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.

  4. 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.

  5. Does substrate coarseness matter for foraging ants? An experiment with Lasius niger (Hymenoptera; Formicidae).

    PubMed

    Bernadou, Abel; Fourcassié, Vincent

    2008-03-01

    We investigated whether workers of the ant species Lasius niger are able to sense and discriminate the coarseness of the substrate on which they walk. First, we studied the way in which substrate coarseness affects the ants' locomotory behaviour. Second, we investigated the spontaneous preference of ants for substrates of different coarseness. And third, we tested with a differential conditioning procedure the ants' capacity to learn to associate a given coarseness with a food reward. The locomotory behaviour of ants differed according to substrate coarseness: ants moved significantly faster and had more sinuous trajectories on a fine than on a coarse substrate. No spontaneous preference for a substrate of a given coarseness was observed and, even after 20 successive conditioning trials, there was little evidence of the effect of experience on substrate coarseness discrimination. Overall however, ants trained on fine sand made significantly more correct choice than those trained on coarse sand. We discuss these results and argue that in L. niger substrate coarseness may be more important at the collective level, by interacting with the chemical properties of the pheromone trail used in mass recruitment to food source, than at the individual level.

  6. 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

  7. Labile aggregation stimulating substance, free fatty acids, and platelet aggregation.

    PubMed

    Gerrard, J M; White, J G; Krivit, W

    1976-01-01

    Labile aggregation stimulating substance (LASS), an intermediate produced during platelet biosynthesis of PGE2 and PGF2alpha, acts as a physiologic intercellular messenger to promote platelet aggregation and the release reaction. The activity is formed by intact cells after physiologic stimulation or can be generated from platelet membrane fractions after combination with arachidonate. In the present investigation, small amounts of polyunsaturated fatty acids added to an incubation mixture of platelet microsomes and arachidonate were found to significantly inhibit subsequent platelet aggregation. Saturated and mono-unsaturated fatty acids in the same concentrations were without effect. However, in higher concentrations mono-unsaturated fatty acids were found to be inhibitory and stearic acid was found to enhance subsequent platelet aggregation. The inhibition caused by the polyunsaturated fatty acid, linoleate, was shown to be the result of an effect on the production of LASS through an interaction with the platelet enzyme responsible for conversion of arachidonate to LASS. In contrast, stearic acid was found to enhance platelet aggregation by acting on the platelets and not directly on LASS production. The results suggest that small changes in the fatty acid composition of platelet phospholipids could significantly influence platelet reactivity.

  8. Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

    NASA Astrophysics Data System (ADS)

    Genheden, Samuel

    2017-09-01

    We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

  9. Self-folding and aggregation of amyloid nanofibrils.

    PubMed

    Paparcone, Raffaella; Cranford, Steven W; Buehler, Markus J

    2011-04-01

    Amyloids are highly organized protein filaments, rich in β-sheet secondary structures that self-assemble to form dense plaques in brain tissues affected by severe neurodegenerative disorders (e.g. Alzheimer's Disease). Identified as natural functional materials in bacteria, in addition to their remarkable mechanical properties, amyloids have also been proposed as a platform for novel biomaterials in nanotechnology applications including nanowires, liquid crystals, scaffolds and thin films. Despite recent progress in understanding amyloid structure and behavior, the latent self-assembly mechanism and the underlying adhesion forces that drive the aggregation process remain poorly understood. On the basis of previous full atomistic simulations, here we report a simple coarse-grain model to analyze the competition between adhesive forces and elastic deformation of amyloid fibrils. We use simple model system to investigate self-assembly mechanisms of fibrils, focused on the formation of self-folded nanorackets and nanorings, and thereby address a critical issue in linking the biochemical (Angstrom) to micrometre scales relevant for larger-scale states of functional amyloid materials. We investigate the effect of varying the interfibril adhesion energy on the structure and stability of self-folded nanorackets and nanorings and demonstrate that these aggregated amyloid fibrils are stable in such states even when the fibril-fibril interaction is relatively weak, given that the constituting amyloid fibril length exceeds a critical fibril length-scale of several hundred nanometres. We further present a simple approach to directly determine the interfibril adhesion strength from geometric measures. In addition to providing insight into the physics of aggregation of amyloid fibrils our model enables the analysis of large-scale amyloid plaques and presents a new method for the estimation and engineering of the adhesive forces responsible of the self-assembly process of amyloid

  10. Self-folding and aggregation of amyloid nanofibrils

    NASA Astrophysics Data System (ADS)

    Paparcone, Raffaella; Cranford, Steven W.; Buehler, Markus J.

    2011-04-01

    Amyloids are highly organized protein filaments, rich in β-sheet secondary structures that self-assemble to form dense plaques in brain tissues affected by severe neurodegenerative disorders (e.g. Alzheimer's Disease). Identified as natural functional materials in bacteria, in addition to their remarkable mechanical properties, amyloids have also been proposed as a platform for novel biomaterials in nanotechnology applications including nanowires, liquid crystals, scaffolds and thin films. Despite recent progress in understanding amyloid structure and behavior, the latent self-assembly mechanism and the underlying adhesion forces that drive the aggregation process remain poorly understood. On the basis of previous full atomistic simulations, here we report a simple coarse-grain model to analyze the competition between adhesive forces and elastic deformation of amyloid fibrils. We use simple model system to investigate self-assembly mechanisms of fibrils, focused on the formation of self-folded nanorackets and nanorings, and thereby address a critical issue in linking the biochemical (Angstrom) to micrometre scales relevant for larger-scale states of functional amyloid materials. We investigate the effect of varying the interfibril adhesion energy on the structure and stability of self-folded nanorackets and nanorings and demonstrate that these aggregated amyloid fibrils are stable in such states even when the fibril-fibril interaction is relatively weak, given that the constituting amyloid fibril length exceeds a critical fibril length-scale of several hundred nanometres. We further present a simple approach to directly determine the interfibril adhesion strength from geometric measures. In addition to providing insight into the physics of aggregation of amyloid fibrils our model enables the analysis of large-scale amyloid plaques and presents a new method for the estimation and engineering of the adhesive forces responsible of the self-assembly process of

  11. Coarse mesh transport theory model for heterogeneous systems

    NASA Astrophysics Data System (ADS)

    Ilas, Danut

    To improve fuel utilization, recent reactor cores have become substantially more heterogeneous. In these cores, use of variable fuel enrichments and strong absorbers lead to high neutron flux gradients, which may limit the accuracy (validity) of diffusion theory based methods. In fact, the diffusion equation itself may become a poor approximation of the Boltzmann equation, the exact equation that describes the neutron flux. Therefore, numerical methods to solve the transport equation efficiently over a large heterogeneous region (such as a reactor core) are very desirable in case where the diffusion approximation breaks down. Presently, the only methods capable of computing the power (flux) distributions very accurately throughout a large system such as a nuclear reactor core are the Monte-Carlo or the fine-mesh transport theory methods. Both these methods suffer from the long computational time which makes them useless for routine core calculations. Starting from a variational principle that admits trial functions that can be discontinuous at coarse mesh (assembly) interfaces, we propose a method to solve the transport equation on a spatial grid made up of meshes as large as the size of a fuel assembly. The variational principle is derived for the most general case, but further methods are developed for one-dimensional geometry with the angular variable treated by discrete ordinates. The method uses the finite element approach for the space variable with basis functions precomputed for each element to obtain an algebraic linear system of equations. The eigenvalue of this system is the multiplication constant and the eigenvector represents the incoming angular fluxes for each coarse mesh. The latter allows the reconstruction of the fine mesh solution (angular flux) throughout the domain of interest when used with the basis functions (surface Green's function) for each coarse mesh. The method requires no homogenization procedure that can be a serious source of

  12. 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

  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. 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…

  15. 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.

  16. MARTINI Coarse-Grained Models of Polyethylene and Polypropylene.

    PubMed

    Panizon, Emanuele; Bochicchio, Davide; Monticelli, Luca; Rossi, Giulia

    2015-06-25

    The understanding of the interaction of nanoplastics with living organisms is crucial both to assess the health hazards of degraded plastics and to design functional polymer nanoparticles with biomedical applications. In this paper, we develop two coarse-grained models of everyday use polymers, polyethylene (PE) and polypropylene (PP), aimed at the study of the interaction of hydrophobic plastics with lipid membranes. The models are compatible with the popular MARTINI force field for lipids, and they are developed using both structural and thermodynamic properties as targets in the parametrization. The models are then validated by showing their reliability at reproducing structural properties of the polymers, both linear and branched, in dilute conditions, in the melt, and in a PE-PP blend. PE and PP radius of gyration is correctly reproduced in all conditions, while PE-PP interactions in the blend are slightly overestimated. Partitioning of PP and PE oligomers in phosphatidylcholine membranes as obtained at CG level reproduces well atomistic data.

  17. 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.

  18. Coarse-to-fine three-dimensional digitization system

    NASA Astrophysics Data System (ADS)

    Daval, Vincent; Truchetet, Frederic; Aubreton, Olivier

    2015-11-01

    The three-dimensional (3-D) workflow (acquisition-processing-compression) is, in most cases, sequenced into several independent steps. Such approaches result in an acquisition of an important number of 3-D points. After acquisition, the first processing step is a simplification of the data by suppressing many of the computed points. We propose a coarse-to-fine acquisition system that makes it possible to obtain simplified data directly from the acquisition. By calculating some complementary information from two-dimensional (2-D) images, such as 3-D normals, multiple-homogeneous regions will be segmented and affected for a given primitive class. In contrast to other studies, the whole process is not based on a mesh. The obtained model is simplified directly from the 2-D data acquired by a 3-D scanner.

  19. 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.

  20. 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.

  1. 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.

  2. Predicting the settlement of coarse granular materials under vertical loading.

    PubMed

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

    2014-07-16

    Granular materials are widely used in industrial processes despite their complex and poorly understood mechanical behaviour both in static and dynamic regimes. A prototypical example is the settlement and compaction of a granular bed under vibrational loading. The elementary mechanisms of this process are still unclear and there is presently no established theory or methodology to predict the settlement and its statistical variability. By means of a parametric study, carried out on a full-scale track, and a critical analysis of density relaxation laws, we introduce a novel settlement model in coarse granular materials under cyclic loading. Our extensive experimental data indicate that the settlement process is governed by three independent parameters strongly correlated with the vibration intensity and initial packing fraction. We show that the mean settlement is well predicted by the model with its parameter values extracted from experimental data.

  3. Granular mechanics of the critical state of coarse soils

    NASA Astrophysics Data System (ADS)

    Yanqui, Calixtro

    2013-06-01

    In this paper, coarse soils are modeled by granular packings, because both of them have similar characteristics, such as: gaseousity, duality, dilatancy, fragility and hyperbolicity. By virtue of these properties, it is assumed that the contact force ensemble remains the same, while the packing changes because of its dual character, regarding the compactness of the soil. For the dense state, both assemblages coincide themselves, forming chains of contact forces; the transmission of stresses obeys the Trollope's hypothesis of centroidal reactions; and the volumetric strain increases. For the loose state, the packing adopts a "passive" distribution, yielding a constant angle of internal friction at failure; so that, the strain is contractive and the stress transmission occurs fundamentally by shear, in a similar fashion to the Rowe's mechanism. In the figures, the good correspondence between the results of the theory and the reported experimental data is shown.

  4. Sequence transferable coarse-grained model of amphiphilic copolymers

    NASA Astrophysics Data System (ADS)

    De Silva, Chathuranga C.; Leophairatana, Porakrit; Ohkuma, Takahiro; Koberstein, Jeffrey T.; Kremer, Kurt; Mukherji, Debashish

    2017-08-01

    Polymer properties are inherently multi-scale in nature, where delicate local interaction details play a key role in describing their global conformational behavior. In this context, deriving coarse-grained (CG) multi-scale models for polymeric liquids is a non-trivial task. Further complexities arise when dealing with copolymer systems with varying microscopic sequences, especially when they are of amphiphilic nature. In this work, we derive a segment-based generic CG model for amphiphilic copolymers consisting of repeat units of hydrophobic (methylene) and hydrophilic (ethylene oxide) monomers. The system is a simulation analogue of polyacetal copolymers [S. Samanta et al., Macromolecules 49, 1858 (2016)]. The CG model is found to be transferable over a wide range of copolymer sequences and also to be consistent with existing experimental data.

  5. Coarse-graining RNA nanostructures for molecular dynamics simulations

    PubMed Central

    Paliy, Maxim; Melnik, Roderick; Shapiro, Bruce A

    2013-01-01

    A series of coarse-grained models have been developed for study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in full atomistic modeling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the three-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4′ dihedrals taken from a reference structure are included. These findings are discussed in the context of RNA conformation classes. PMID:20577037

  6. 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.

  7. One-bead coarse-grained model for RNA dynamics.

    PubMed

    Villada-Balbuena, Mario; Carbajal-Tinoco, Mauricio D

    2017-01-28

    We present a revised version of a coarse-grained model for RNA dynamics. In such approach, the description of nucleotides is reduced to single points that interact between them through a series of effective pair potentials that were obtained from an improved analysis of RNA structures from the Protein Data Bank. These interaction potentials are the main constituents of a Brownian dynamics simulation algorithm that allows to perform a variety of tasks by taking advantage of the reduced number of variables. Such tasks include the prediction of the three-dimensional configuration of a series of test molecules. Moreover, the model permits the inclusion of effective magnesium ions and the ends of the RNA chains can be pulled with an external force to study the process of unfolding. In spite of the simplicity of the model, we obtain a good agreement with the experimental results.

  8. Predicting the settlement of coarse granular materials under vertical loading

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    Granular materials are widely used in industrial processes despite their complex and poorly understood mechanical behaviour both in static and dynamic regimes. A prototypical example is the settlement and compaction of a granular bed under vibrational loading. The elementary mechanisms of this process are still unclear and there is presently no established theory or methodology to predict the settlement and its statistical variability. By means of a parametric study, carried out on a full-scale track, and a critical analysis of density relaxation laws, we introduce a novel settlement model in coarse granular materials under cyclic loading. Our extensive experimental data indicate that the settlement process is governed by three independent parameters strongly correlated with the vibration intensity and initial packing fraction. We show that the mean settlement is well predicted by the model with its parameter values extracted from experimental data.

  9. A Novel Demultiplexing Design for Coarse WDM: Exploiting Material Dispersion

    NASA Astrophysics Data System (ADS)

    Salameh, Haythem Bany; Al-Rabaie, Mohammad; Khreishah, Abdallah; Al-Zubi, Raed

    2017-08-01

    In this paper, a compact low-cost simple-to-fabricate demultiplexer is proposed for coarse wavelength division multiplexing (CWDM). The device consists of two layers of the same semiconductor material: the first layer is homogeneous medium with a given refractive index n_2, while the second layer is an inhomogeneous medium, where its refractive index is graded according to a creation profile. The proposed design exploits the ray's spatial shift that results from material dispersion as difference wavelengths propagate through the structure. Through analytical analysis and numerical evaluation, we investigate the effects of the various design parameters on the amount of achieved spatial shift between the adjacent wavelengths and the size of the device. The results show promising results for four- and eight-channel devices operating on the standard CWDM wavelength grid.

  10. One-bead coarse-grained model for RNA dynamics

    NASA Astrophysics Data System (ADS)

    Villada-Balbuena, Mario; Carbajal-Tinoco, Mauricio D.

    2017-01-01

    We present a revised version of a coarse-grained model for RNA dynamics. In such approach, the description of nucleotides is reduced to single points that interact between them through a series of effective pair potentials that were obtained from an improved analysis of RNA structures from the Protein Data Bank. These interaction potentials are the main constituents of a Brownian dynamics simulation algorithm that allows to perform a variety of tasks by taking advantage of the reduced number of variables. Such tasks include the prediction of the three-dimensional configuration of a series of test molecules. Moreover, the model permits the inclusion of effective magnesium ions and the ends of the RNA chains can be pulled with an external force to study the process of unfolding. In spite of the simplicity of the model, we obtain a good agreement with the experimental results.

  11. Acceleration of coarse grain molecular dynamics on GPU architectures.

    PubMed

    Shkurti, Ardita; Orsi, Mario; Macii, Enrico; Ficarra, Elisa; Acquaviva, Andrea

    2013-04-05

    Coarse grain (CG) molecular models have been proposed to simulate complex systems with lower computational overheads and longer timescales with respect to atomistic level models. However, their acceleration on parallel architectures such as graphic processing units (GPUs) presents original challenges that must be carefully evaluated. The objective of this work is to characterize the impact of CG model features on parallel simulation performance. To achieve this, we implemented a GPU-accelerated version of a CG molecular dynamics simulator, to which we applied specific optimizations for CG models, such as dedicated data structures to handle different bead type interactions, obtaining a maximum speed-up of 14 on the NVIDIA GTX480 GPU with Fermi architecture. We provide a complete characterization and evaluation of algorithmic and simulated system features of CG models impacting the achievable speed-up and accuracy of results, using three different GPU architectures as case studies. Copyright © 2012 Wiley Periodicals, Inc.

  12. Variational coarse-graining procedure for dynamic homogenization

    NASA Astrophysics Data System (ADS)

    Liu, Chenchen; Reina, Celia

    2017-07-01

    We present a variational coarse-graining framework for heterogeneous media in the spirit of FE2 methods, that allows for a seamless transition from the traditional static scenario to dynamic loading conditions, while being applicable to general material behavior as well as to discrete or continuous representations of the material and its deformation, e.g., finite element discretizations or atomistic systems. The method automatically delivers the macroscopic equations of motion together with the generalization of Hill's averaging relations to the dynamic setting. These include the expression of the macroscopic stresses and linear momentum as a function of the microscopic fields. We further demonstrate with a proof of concept example, that the proposed theoretical framework can be used to perform multiscale numerical simulations. The results are compared with standard single-scale finite element simulations, showcasing the capability of the method to capture the dispersive nature of the medium in the range of frequencies permitted by the multiscale strategy.

  13. 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.

  14. Self-assembly of the beta2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals a beta-barrel species.

    PubMed

    Song, Wei; Wei, Guanghong; Mousseau, Normand; Derreumaux, Philippe

    2008-04-10

    Although a wide variety of proteins can assemble into amyloid fibrils, the structure of the early oligomeric species on the aggregation pathways remains unknown at an atomic level of detail. In this paper we report, using molecular dynamics simulations with the OPEP coarse-grained force field, the free energy landscape of a tetramer and a heptamer of the beta2-microglobulin NHVTLSQ peptide. On the basis of a total of more than 17 ns trajectories started from various states, we find that both species are in equilibrium between amorphous and well-ordered aggregates with cross-beta-structure, a perpendicular bilayer beta-sheet, and, for the heptamer, six- or seven-stranded closed and open beta-barrels. Moreover, analysis of the heptamer trajectories shows that the perpendicular bilayer beta-sheet is one possible precursor of the beta-barrel, but that this barrel can also be formed from a twisted monolayer beta-sheet with successive addition of chains. Comparison with previous aggregation simulations and the fact that nature constructs transmembrane beta-sheet proteins with pores open the possibility that beta-barrels with small inner diameters may represent a common intermediate during the early steps of aggregation.

  15. Spatial aggregation: Language and applications

    SciTech Connect

    Bailey-Kellogg, C.; Zhao, F.; Yip, K.

    1996-12-31

    Spatial aggregation is a framework for organizing computations around image-like, analogue representations of physical processes in data interpretation and control tasks. It conceptualizes common computational structures in a class of implemented problem solvers for difficult scientific and engineering problems. It comprises a mechanism, a language, and a programming style. The spatial aggregation mechanism transforms a numerical input field to successively higher-level descriptions by applying a small, identical set of operators to each layer given a metric, neighborhood relation and equivalence relation. This paper describes the spatial aggregation language and its applications. The spatial aggregation language provides two abstract data types - neighborhood graph and field - and a set of interface operators for constructing the transformations of the field, together with a library of component implementations from which a user can mix-and-match and specialize for a particular application. The language allows users to isolate and express important computational ideas in different problem domains while hiding low-level details. We illustrate the use of the language with examples ranging from trajectory grouping in dynamics interpretation to region growing in image analysis. Programs for these different task domains can be written in a modular, concise fashion in the spatial aggregation language.

  16. Thermodynamic modeling of asphaltene aggregation.

    PubMed

    Rogel, E

    2004-02-03

    A new molecular thermodynamic model for the description of the aggregation behavior of asphaltenes in different solvents is presented. This new model is relatively simple and strictly predictive and does not use any experimental information from asphaltene solutions. In this model, asphaltene aggregates are described as composed of an aromatic core formed by stacked aromatic sheets surrounded by aliphatic chains. The proposed model qualitatively predicts the asphaltene aggregation behavior in a series of different solvents. In particular, the experimental trends observed for the variation of aggregate size with (1) asphaltene molecular characteristics (condensation index, aromaticity, and chain length), (2) asphaltene concentration, (3) solvent characteristics, and (4) temperature have been successfully reproduced by the proposed model. The model also provides a plausible explanation for the existence or absence of a critical micelle concentration (cmc) for asphaltene solutions. Specifically, the model predicted that the asphaltenes with low aromaticities and low aromatic condensations do not exhibit cmc behavior. Finally, the obtained results clearly support the classical model for asphaltene aggregates.

  17. Leaching behaviour of synthetic aggregates.

    PubMed

    van der Sloot, H A; Hoede, D; Cresswell, D J; Barton, J R

    2001-01-01

    In the framework of EU project "Utilising innovative kiln technology to recycle waste into synthetic aggregate" (BRST-CT98-5234), the leaching behaviour of synthetic aggregates has been studied to assess its environmental compatibility in the various stages of its use. Since the conditions are very different for the different uses, the assessment calls for a variety of different leaching conditions. The pH dependence test is used to cover important differences in pH environment to which the materials are exposed to as well as for an assessment of the buffering capacity of the material. Synthetic aggregate features a low buffer capacity, which makes it sensitive to externally imposed pH conditions. Utilisation and storage exposed to acidic conditions needs to be avoided. The results of the pH dependence test and column leaching test are mutually consistent. The CEN TC 154 method appears to provide systematically low values due to the arbitrary selection of test conditions. Synthetic aggregate studied to date will not adversely affect the concrete in its service life. The main issue for aggregate use is the recycling and the "end of life" condition, when the material becomes construction debris. Not metals, but oxyanions, such as Cr VI and Mo are most relevant under these conditions. A concise test has been applied to assess crucial aspects of leaching for different production mixes.

  18. 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

  19. Application of phased array techniques to coarse grain components inspection.

    PubMed

    Mahaut, Steve; Godefroit, Jean-Louis; Roy, Olivier; Cattiaux, Gérard

    2004-04-01

    Ultrasonic inspection of cast stainless steel components from primary and auxiliary cooling circuits of French Nuclear Power Plant has to face with major difficulties due to the coarse grained structure of these materials. Attenuation losses and structural noise are encountered, which limits the performances of defect detection ability, mostly in terms of degraded signal-to-noise ratio and poor sensitivity. To overcome such problems, theoretical and experimental studies have been achieved at the French Atomic Energy Commission, with support from the French Institute for Radiological Protection and Nuclear Safety. Experimental studies have been performed over stainless steel specimen of known coarse structure (equiaxial grains and/or elongated grains), containing artificial reflectors (cylindrical holes and electro-eroded surface breaking notches). Those mock-ups have been inspected using contact probes of different array designs (linear or matrix splitting), and using pulse echo or dual-element techniques. Such arrays allow to control the ultrasonic beam so as to investigate different inspection angles and focusing depths. Experiments were carried out using oblique longitudinal waves, using delay laws computed by a specific model, taking account of acoustical and geometrical properties of the probes and the inspected component. In addition, specific reconstruction techniques have been investigated to enhance the signal-to-noise ratio as well as spatial resolution. These techniques are based on beam-forming summation and multi-angle inspections. Experimental results show that such techniques allow to reduce the speckle noise and to optimise the beam resolution. Those increased performances allow to detect and to size small planar defects located at the inner wall of a thick specimen, using corner and tip diffraction echoes.

  20. 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.

  1. Adsorption and desorption of Cu(2+) on paddy soil aggregates pretreated with different levels of phosphate.

    PubMed

    Dai, Jun; Wang, Wenqin; Wu, Wenchen; Gao, Jianbo; Dong, Changxun

    2017-05-01

    Interactions between anions and cations are important for understanding the behaviors of chemical pollutants and their potential risks in the environment. Here we prepared soil aggregates of a yellow paddy soil from the Taihu Lake region, and investigated the effects of phosphate (P) pretreatment on adsorption-desorption of Cu(2+) of soil aggregates, free iron oxyhydrates-removed soil aggregates, goethite, and kaolinite with batch adsorption method. The results showed that Cu(2+) adsorption was reduced on the aggregates pretreated with low concentrations of P, and promoted with high concentrations of P, showing a V-shaped change. Compared with the untreated aggregates, the adsorption capacity of Cu(2+) was reduced when P application rates were lower than 260, 220, 130 and 110mg/kg for coarse, clay, silt and fine sand fractions, respectively. On the contrary, the adsorption capacity of Cu(2+) was higher on P-pretreated soil aggregates than on the control ones when P application rates were greater than those values. However, the desorption of Cu(2+) was enhanced at low levels of P, but suppressed at high levels of P, displaying an inverted V-shaped change over P adsorption. The Cu(2+) adsorption by the aggregate particles with and without P pretreatments was well described by the Freundlich equation. Similar results were obtained on P-pretreated goethite. However, such P effects on Cu(2+) adsorption-desorption were not observed on kaolinite and free iron oxyhydrates-removed soil aggregates. The present results indicate that goethite is one of the main soil substances responsible for the P-induced promotion and inhibition of Cu(2+) adsorption. Copyright © 2016. Published by Elsevier B.V.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. Coarse-fine adaptive tuned vibration absorber with high frequency resolution

    NASA Astrophysics Data System (ADS)

    Wang, Xi; Yang, Bintang; You, Jiaxin; Gao, Zhe

    2016-11-01

    The speed fluctuation of satellite-rotary-mechanisms causes vibration of slightly different frequencies. The critical requirements of satellites need a vibration control device with high frequency resolution to suppress the vibration. This paper presents a coarse-fine adaptive tuned vibration absorber (ATVA) with high frequency resolution. The coarse-fine ATVA which simultaneously satisfies the requirements of high resolution and relatively wide effective bandwidth is capable of tracking the variable exciting frequency adaptively to suppress the vibration of the primary system. The coarse-fine ATVA is divided into a coarse tuning segment and a fine tuning segment. The coarse tuning segment is used to tune the required natural frequency in a relatively wide effective bandwidth and the fine tuning segment can achieve precise tune in a tiny-scale bandwidth. The mathematical model of the coarse tuning and the fine tuning is proposed to design the parameters of the coarse-fine ATVA. The experimental test results indicate the coarse tuning bandwidth of the coarse-fine ATVA is 8.7 Hz to 29 Hz and the minimum resolution of the fine tuning is 0.05 Hz. Moreover, a significant vibration attenuation of 15dB is verified in the effective bandwidth.

  7. Properties of Non-Structural Concrete Made with Mixed Recycled Aggregates and Low Cement Content

    PubMed Central

    López-Uceda, Antonio; Ayuso, Jesús; López, Martin; Jimenez, José Ramón; Agrela, Francisco; Sierra, María José

    2016-01-01

    In spite of not being legally accepted in most countries, mixed recycled aggregates (MRA) could be a suitable raw material for concrete manufacturing. The aims of this research were as follows: (i) to analyze the effect of the replacement ratio of natural coarse aggregates with MRA, the amount of ceramic particles in MRA, and the amount of cement, on the mechanical and physical properties of a non-structural concrete made with a low cement content; and (ii) to verify if it is possible to achieve a low-strength concrete that replaces a greater amount of natural aggregate with MRA and that has a low cement content. Two series of concrete mixes were manufactured using 180 and 200 kg/m3 of CEM II/A-V 42.5 R type Portland cement. Each series included seven concrete mixes: one with natural aggregates; two MRA with different ceramic particle contents; and one for each coarse aggregate replacement ratio (20%, 40%, and 100%). To study their properties, compressive and splitting tensile strength, modulus of elasticity, density, porosity, water penetration, and sorptivity, tests were performed. The results confirmed that the main factors affecting the properties analyzed in this research are the amount of cement and the replacement ratio; the two MRAs used in this work presented a similar influence on the properties. A non-structural, low-strength concrete (15 MPa) with an MRA replacement ratio of up to 100% for 200 kg/m3 of cement was obtained. This type of concrete could be applied in the construction of ditches, sidewalks, and other similar civil works. PMID:28787874

  8. 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.

  9. Properties of Non-Structural Concrete Made with Mixed Recycled Aggregates and Low Cement Content.

    PubMed

    López-Uceda, Antonio; Ayuso, Jesús; López, Martin; Jimenez, José Ramón; Agrela, Francisco; Sierra, María José

    2016-01-26

    In spite of not being legally accepted in most countries, mixed recycled aggregates (MRA) could be a suitable raw material for concrete manufacturing. The aims of this research were as follows: (i) to analyze the effect of the replacement ratio of natural coarse aggregates with MRA, the amount of ceramic particles in MRA, and the amount of cement, on the mechanical and physical properties of a non-structural concrete made with a low cement content; and (ii) to verify if it is possible to achieve a low-strength concrete that replaces a greater amount of natural aggregate with MRA and that has a low cement content. Two series of concrete mixes were manufactured using 180 and 200 kg/m³ of CEM II/A-V 42.5 R type Portland cement. Each series included seven concrete mixes: one with natural aggregates; two MRA with different ceramic particle contents; and one for each coarse aggregate replacement ratio (20%, 40%, and 100%). To study their properties, compressive and splitting tensile strength, modulus of elasticity, density, porosity, water penetration, and sorptivity, tests were performed. The results confirmed that the main factors affecting the properties analyzed in this research are the amount of cement and the replacement ratio; the two MRAs used in this work presented a similar influence on the properties. A non-structural, low-strength concrete (15 MPa) with an MRA replacement ratio of up to 100% for 200 kg/m³ of cement was obtained. This type of concrete could be applied in the construction of ditches, sidewalks, and other similar civil works.

  10. Channel Aggregation Schemes for Cognitive Radio Networks

    NASA Astrophysics Data System (ADS)

    Lee, Jongheon; So, Jaewoo

    This paper proposed three channel aggregation schemes for cognitive radio networks, a constant channel aggregation scheme, a probability distribution-based variable channel aggregation scheme, and a residual channel-based variable channel aggregation scheme. A cognitive radio network can have a wide bandwidth if unused channels in the primary networks are aggregated. Channel aggregation schemes involve either constant channel aggregation or variable channel aggregation. In this paper, a Markov chain is used to develop an analytical model of channel aggregation schemes; and the performance of the model is evaluated in terms of the average sojourn time, the average throughput, the forced termination probability, and the blocking probability. Simulation results show that channel aggregation schemes can reduce the average sojourn time of cognitive users by increasing the channel occupation rate of unused channels in a primary network.

  11. 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.

  12. Fractal aggregates in tennis ball systems

    NASA Astrophysics Data System (ADS)

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

    2009-09-01

    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 images of the cluster of balls, following Forrest and Witten's pioneering studies on the aggregation of smoke particles, to estimate their fractal dimension.

  13. Customer Aggregation: An Opportunity for Green Power?

    SciTech Connect

    Holt, E.; Bird, L.

    2001-02-26

    We undertook research into the experience of aggregation groups to determine whether customer aggregation offers an opportunity to bring green power choices to more customers. The objectives of this report, therefore, are to (1) identify the different types of aggregation that are occurring today, (2) learn whether aggregation offers an opportunity to advance sales of green power, and (3) share these concepts and approaches with potential aggregators and green power advocates.

  14. 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.

  15. Equilibrium structure of ferrofluid aggregates.

    PubMed

    Yoon, Mina; Tománek, David

    2010-11-17

    We study the equilibrium structure of large but finite aggregates of magnetic dipoles, representing a colloidal suspension of magnetite particles in a ferrofluid. With increasing system size, the structural motif evolves from chains and rings to multi-chain and multi-ring assemblies. Very large systems form single- and multi-wall coils, tubes and scrolls. These structural changes result from a competition between various energy terms, which can be approximated analytically within a continuum model. We also study the effect of external parameters such as magnetic field on the relative stability of these structures. Our results may give insight into experimental data obtained during solidification of ferrofluid aggregates at temperatures where thermal fluctuations become negligible in comparison to inter-particle interactions. These data may also help to experimentally control the aggregation of magnetic particles.

  16. Equilibrium structure of ferrofluid aggregates

    SciTech Connect

    Yoon, Mina; Tomanek, David

    2010-01-01

    We study the equilibrium structure of large but finite aggregates of magnetic dipoles, representing a colloidal suspension of magnetite particles in a ferrofluid. With increasing system size, the structural motif evolves from chains and rings to multi-chain and multi-ring assemblies. Very large systems form single- and multi-wall coils, tubes and scrolls. These structural changes result from a competition between various energy terms, which can be approximated analytically within a continuum model. We also study the effect of external parameters such as magnetic field on the relative stability of these structures. Our results may give insight into experimental data obtained during solidification of ferrofluid aggregates at temperatures where thermal fluctuations become negligible in comparison to inter-particle interactions. These data may also help to experimentally control the aggregation of magnetic particles.

  17. Size distribution of chemical elements and their source apportionment in ambient coarse, fine, and ultrafine particles in Shanghai urban summer atmosphere.

    PubMed

    Lü, Senlin; Zhang, Rui; Yao, Zhenkun; Yi, Fei; Ren, Jingjing; Wu, Minghong; Feng, Man; Wang, Qingyue

    2012-01-01

    Ambient coarse particles (diameter 1.8-10 microm), fine particles (diameter 0.1-1.8 microm), and ultrafine particles (diameter < 0.1 microm) in the atmosphere of the city of Shanghai were sampled during the summer of 2008 (from Aug 27 to Sep 08). Microscopic characterization of the particles was investigated by scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM/EDX). Mass concentrations of Si, P, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Ni, Cu, Zn, As, Se, Br, Rb, Sr, and Pb in the size-resolved particles were quantified by using synchrotron radiation X-ray fluorescence (SRXRF). Source apportionment of the chemical elements was analyzed by means of an enrichment factor method. Our results showed that the average mass concentrations of coarse particles, fine particles and ultrafine particles in the summer air were 9.38 +/- 2.18, 8.82 +/- 3.52, and 2.02 +/- 0.41 microg/m3, respectively. The mass percentage of the fine particles accounted for 51.47% in the total mass of PM10, indicating that fine particles are the major component in the Shanghai ambient particles. SEM/EDX results showed that the coarse particles were dominated by minerals, fine particles by soot aggregates and fly ashes, and ultrafine particles by soot particles and unidentified particles. SRXRF results demonstrated that crustal elements were mainly distributed in the coarse particles, while heavy metals were in higher proportions in the fine particles. Source apportionment revealed that Si, K, Ca, Fe, Mn, Rb, and Sr were from crustal sources, and S, Cl, Cu, Zn, As, Se, Br, and Pb from anthropogenic sources. Levels of P, V, Cr, and Ni in particles might be contributed from multi-sources, and need further investigation.

  18. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. A specialist's audit of aggregated occurrence records: An 'aggregator's' perspective.

    PubMed

    Belbin, Lee; Daly, Joanne; Hirsch, Tim; Hobern, Donald; Salle, John La

    2013-01-01

    A recent ZooKeys' paper (Mesibov, 2013: http://www.pensoft.net/journal_home_page.php?journal_id=1&page=article&SESID=df7bcb35b02603283dcb83ee0e0af0c9&type=show&article_id=5111) has highlighted data quality issues in aggregated data sets, but did not provide a realistic way to address these issues. This paper provides an aggregator's perspective including ways that the whole community can help to address data quality issues. The establishment of GBIF and national nodes (national aggregators) such as the Atlas of Living Australia (ALA) have integrated and exposed a huge diversity of biological observations along with many associated issues. Much of the admirable work by Mesibov (2013) was enabled by having the data exposed. Data quality, one of the highest priorities for GBIF, the national nodes and other aggregators, depends on both automatic methods and community experts to detect and correct data issues. Not all issues can however be automatically detected or corrected, so community assistance is needed to help improve the quality of exposed biological data. We do need to improve the infrastructure and associated processes to more easily identify data issues and document all changes to ensure a full record is permanently and publicly available.

  20. 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

  1. Molecular aggregates in cryogenic solutions

    NASA Astrophysics Data System (ADS)

    Schauer, M. W.; Lee, J.; Bernstein, E. R.

    1981-07-01

    In this report, experimental procedures and results concerning the study of aggregates are presented. Absorption spectra of solutions of the following solutes and solvents have been studied: pyrazine/C3H8; benzene/NF3, C3H8, N2, CO, CF4; and osmium tetroxide/NF3, CH4, C3H8. In order to obtain some qualitative estimation of aggregate size light scattering experiments were also performed on solutions of pyrazine/C3H8, benzene/CF4 benzene/NF3, and benzene/C3H8. The nature of these non-equilibrium molecular clusters in solution will be addressed.

  2. Hydrodynamic behavior of fractal aggregates

    NASA Astrophysics Data System (ADS)

    Wiltzius, Pierre

    1987-02-01

    Measurements of the radius of gyration RG and the hydrodynamic radius RH of colloidal silica aggregates are reported. These aggregates have fractal geometry and RH is proportional to RG for 500 Å<=RH<=7000 Å, with a ratio RH/RG=0.72+/-0.02. The results are compared with predictions for macromolecules of various shapes. The proportionality of the two radii can be understood with use of the pair correlation function of fractal objects and hydrodynamic interactions on the Oseen level. The value of the ratio remains to be explained.

  3. 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.

  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.

  5. Primary and Aggregate Size Distributions of PM in Tail Pipe Emissions form Diesel Engines

    NASA Astrophysics Data System (ADS)

    Arai, Masataka; Amagai, Kenji; Nakaji, Takayuki; Hayashi, Shinji

    Particulate matter (PM) emission exhausted from diesel engine should be reduced to keep the clean air environment. PM emission was considered that it consisted of coarse and aggregate particles, and nuclei-mode particles of which diameter was less than 50nm. However the detail characteristics about these particles of the PM were still unknown and they were needed for more physically accurate measurement and more effective reduction of exhaust PM emission. In this study, the size distributions of solid particles in PM emission were reported. PMs in the tail-pipe emission were sampled from three type diesel engines. Sampled PM was chemically treated to separate the solid carbon fraction from other fractions such as soluble organic fraction (SOF). The electron microscopic and optical-manual size measurement procedures were used to determine the size distribution of primary particles those were formed through coagulation process from nuclei-mode particles and consisted in aggregate particles. The centrifugal sedimentation method was applied to measure the Stokes diameter of dry-soot. Aerodynamic diameters of nano and aggregate particles were measured with scanning mobility particle sizer (SMPS). The peak aggregate diameters detected by SMPS were fallen in the same size regime as the Stokes diameter of dry-soot. Both of primary and Stokes diameters of dry-soot decreased with increases of engine speed and excess air ratio. Also, the effects of fuel properties and engine types on primary and aggregate particle diameters were discussed.

  6. Gelation by phase separation in a whey protein system: in-situ kinetics of aggregation.

    PubMed

    Renard, D; Robert, P; Garnier, C; Dufour, E; Lefebvre, J

    2000-05-26

    The aggregation and gelation properties of beta-lactoglobulin (BLG), a globular protein from milk, was studied in aqueous ethanol solutions at room temperature. The phase state diagrams as a function of pH and ethanol concentration showed that a gel structure appeared after a period ranging from 1 min to 1 week, depending on the physico-chemical conditions. The in-situ kinetics of aggregation were followed by several methods in order to obtain a better understanding of the building of aggregates by the addition of ethanol. It was shown that the aggregation kinetics highly depended upon the pH, the process being fastest at pH 7. Viscoelasticity and infrared measurements indicated that alcohol-induced gelation would proceed via a two-step mechanism: small aggregates loosely connected between them were first built up; a real network took place in a second step. The coarse and irregular structures formed in aqueous ethanol gels revealed by confocal laser scanning microscopy could be analysed in terms of a phase separation. This observation was supported by a syneresis phenomenon visible in the final gel state. BLG in water-ethanol solution would undergo either an inhibition of the demixing by gelation or a binary phase separation accompanied by an irreversible gelation transition.

  7. 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

  8. Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins.

    PubMed

    Emperador, Agustí; Orozco, Modesto

    2017-03-14

    We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.

  9. 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

  10. Studies on recycled aggregates-based concrete.

    PubMed

    Rakshvir, Major; Barai, Sudhirkumar V

    2006-06-01

    Reduced extraction of raw materials, reduced transportation cost, improved profits, reduced environmental impact and fast-depleting reserves of conventional natural aggregates has necessitated the use of recycling, in order to be able to conserve conventional natural aggregate. In this study various physical and mechanical properties of recycled concrete aggregates were examined. Recycled concrete aggregates are different from natural aggregates and concrete made from them has specific properties. The percentages of recycled concrete aggregates were varied and it was observed that properties such as compressive strength showed a decrease of up to 10% as the percentage of recycled concrete aggregates increased. Water absorption of recycled aggregates was found to be greater than natural aggregates, and this needs to be compensated during mix design.

  11. 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. ...

  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. Sequence-dependent internalization of aggregating peptides.

    PubMed

    Couceiro, José R; Gallardo, Rodrigo; De Smet, Frederik; De Baets, Greet; Baatsen, Pieter; Annaert, Wim; Roose, Kenny; Saelens, Xavier; Schymkowitz, Joost; Rousseau, Frederic

    2015-01-02

    Recently, a number of aggregation disease polypeptides have been shown to spread from cell to cell, thereby displaying prionoid behavior. Studying aggregate internalization, however, is often hampered by the complex kinetics of the aggregation process, resulting in the concomitant uptake of aggregates of different sizes by competing mechanisms, which makes it difficult to isolate pathway-specific responses to aggregates. We designed synthetic aggregating peptides bearing different aggregation propensities with the aim of producing modes of uptake that are sufficiently distinct to differentially analyze the cellular response to internalization. We found that small acidic aggregates (≤500 nm in diameter) were taken up by nonspecific endocytosis as part of the fluid phase and traveled through the endosomal compartment to lysosomes. By contrast, bigger basic aggregates (>1 μm) were taken up through a mechanism dependent on cytoskeletal reorganization and membrane remodeling with the morphological hallmarks of phagocytosis. Importantly, the properties of these aggregates determined not only the mechanism of internalization but also the involvement of the proteostatic machinery (the assembly of interconnected networks that control the biogenesis, folding, trafficking, and degradation of proteins) in the process; whereas the internalization of small acidic aggregates is HSF1-independent, the uptake of larger basic aggregates was HSF1-dependent, requiring Hsp70. Our results show that the biophysical properties of aggregates determine both their mechanism of internalization and proteostatic response. It remains to be seen whether these differences in cellular response contribute to the particular role of specific aggregated proteins in disease.

  14. 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

  15. 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

  16. Multistage point relascope and randomized branch sampling for downed coarse woody debris estimation

    Treesearch

    Jeffrey H. Gove; Mark J. Ducey; Harry T. Valentine

    2002-01-01

    New sampling methods have recently been introduced that allow estimation of downed coarse woody debris using an angle gauge, or relascope. The theory behind these methods is based on sampling straight pieces of downed coarse woody debris. When pieces deviate from this ideal situation, auxillary methods must be employed. We describe a two-stage procedure where the...

  17. 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

  18. 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 ...

  19. 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...

  20. Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems

    NASA Astrophysics Data System (ADS)

    Katsoulakis, Markos A.; Plecháč, Petr

    2013-08-01

    In this paper, we focus on the development of new methods suitable for efficient and reliable coarse-graining of non-equilibrium molecular systems. In this context, we propose error estimation and controlled-fidelity model reduction methods based on Path-Space Information Theory, combined with statistical parametric estimation of rates for non-equilibrium stationary processes. The approach we propose extends the applicability of existing information-based methods for deriving parametrized coarse-grained models to Non-Equilibrium systems with Stationary States. In the context of coarse-graining it allows for constructing optimal parametrized Markovian coarse-grained dynamics within a parametric family, by minimizing information loss (due to coarse-graining) on the path space. Furthermore, we propose an asymptotically equivalent method—related to maximum likelihood estimators for stochastic processes—where the coarse-graining is obtained by optimizing the information content in path space of the coarse variables, with respect to the projected computational data from a fine-scale simulation. Finally, the associated path-space Fisher Information Matrix can provide confidence intervals for the corresponding parameter estimators. We demonstrate the proposed coarse-graining method in (a) non-equilibrium systems with diffusing interacting particles, driven by out-of-equilibrium boundary conditions, as well as (b) multi-scale diffusions and the corresponding stochastic averaging limits, comparing them to our proposed methodologies.

  1. The combustion of sound and rotten coarse woody debris: a review

    Treesearch

    Joshua C. Hyde; Alistair M.S. Smith; Roger D. Ottmar; Ernesto C. Alvarado; Penelope. Morgan

    2011-01-01

    Coarse woody debris serves many functions in forest ecosystem processes and has important implications for fire management as it affects air quality, soil heating and carbon budgets when it combusts. There is relatively little research evaluating the physical properties relating to the combustion of this coarse woody debris with even less specifically addressing...

  2. Source identification of coarse particles in the Desert Southwest, USA using Positive Matrix Factorization

    EPA Science Inventory

    The Desert Southwest Coarse Particulate Matter Study was undertaken to further our understanding of the spatial and temporal variability and sources of fine and coarse particulate matter (PM) in rural, arid, desert environments. Sampling was conducted between February 2009 and Fe...

  3. 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 ...

  4. Characterization of coarse woody debris across a 100 year chronosequence of upland oak-hickory forest

    Treesearch

    Travis W. Idol; Phillip E. Pope; Rebecca A. Figler; Felix Ponder Jr.

    1999-01-01

    Coarse woody debris is an important component influencing forest nutrient cycling and contributes to long-term soil productivity. The common practice of classifying coarse woody debris into different decomposition classes has seldom been related to the chemistry/biochemistry of the litter, which is the long term objective of our research. The objective of this...

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

    PubMed

    Zhang, Xinyue; Wang, Wei

    2015-05-05

    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. Modeling respiration from snags and coarse woody debris before and after an invasive gypsy moth disturbance

    Treesearch

    Heidi J. Renninger; Nicholas Carlo; Kenneth L. Clark; Karina V.R. Schäfer

    2014-01-01

    Although snags and coarse woody debris are a small component of ecosystem respiration, disturbances can significantly increase the mass and respiration from these carbon (C) pools. The objectives of this study were to (1) measure respiration rates of snags and coarse woody debris throughout the year in a forest previously defoliated by gypsy moths, (2) develop models...

  7. 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...

  8. Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA

    PubMed Central

    Savelyev, Alexey; Papoian, Garegin A.

    2009-01-01

    Coarse-graining of atomistic force fields allows us to investigate complex biological problems, occurring at long timescales and large length scales. In this work, we have developed an accurate coarse-grained model for double-stranded DNA chain, derived systematically from atomistic simulations. Our approach is based on matching correlators obtained from atomistic and coarse-grained simulations, for observables that explicitly enter the coarse-grained Hamiltonian. We show that this requirement leads to equivalency of the corresponding partition functions, resulting in a one-step renormalization. Compared to prior works exploiting similar ideas, the main novelty of this work is the introduction of a highly compact set of Hamiltonian basis functions, based on molecular interaction potentials. We demonstrate that such compactification allows us to reproduce many-body effects, generated by one-step renormalization, at low computational cost. In addition, compact Hamiltonians greatly increase the likelihood of finding unique solutions for the coarse-grained force-field parameter values. By successfully applying our molecular renormalization group coarse-graining technique to double-stranded DNA, we solved, for the first time, a long-standing problem in coarse-graining polymer systems, namely, how to accurately capture the correlations among various polymeric degrees of freedom. Excellent agreement is found among atomistic and coarse-grained distribution functions for various structural observables, including those not included in the Hamiltonian. We also suggest higher-order generalization of this method, which may allow capturing more subtle correlations in biopolymer dynamics. PMID:19450476

  9. Upper Atmosphere Research Satellite (UARS) attitude accuracy using coarse attitude sensors

    NASA Technical Reports Server (NTRS)

    Krack, K.; Foch, D.; Lambertson, M.; Woolsey, C.; Underwood, S.; Woodruff, C.; Garrick, J.

    1993-01-01

    The Upper Atmosphere Research Satellite (UARS) uses fixed-head star trackers (FHST's) and inertial reference units (IRU's) to determine and control its attitude. This combination of fine sensors results in attitude knowledge accuracies to better than 10 arc-seconds (1 sigma). UARS also has a variety of coarse attitude sensors on board: the three-axis magnetometer (TAM), the coarse Sun sensor (CSS), the fine Sun sensor (FSS), and the Earth sensor assembly (ESA). By comparing attitude solutions using coarse sensors with FHST-determined attitude solutions, estimates can be made of the accuracy of the coarse sensors. This paper presents the results of an analysis that compares attitude solutions using various combinations of UARS coarse attitude sensor data with FHST attitude solutions.

  10. Coarse graining of star-polymer - colloid nanocomposites

    NASA Astrophysics Data System (ADS)

    Marzi, Daniela; Likos, Christos N.; Capone, Barbara

    2012-07-01

    We consider mixtures of self-avoiding multiarm star polymers with hard colloids that are smaller than the star polymer size. By employing computer simulations, and by extending previous theoretical approaches, developed for the opposite limit of small star polymers [A. Jusufi et al., J. Phys.: Condens. Matter 13, 6177 (2001), 10.1088/0953-8984/13/28/303], we coarse-grain the mixture by deriving an effective cross-interaction between the unlike species. The excellent agreement between theory and simulation for all size ratios examined demonstrates that the theoretical approaches developed for the colloidal limit can be successfully modified to maintain their validity also for the present case of the protein limit, in contrast to the situation for mixtures of colloids and linear polymers. We further analyze, on the basis of the derived interactions, the non-additivity parameter of the mixture as a function of size ratio and star functionality and delineate the regions in which we expect mixing as opposed to demixing behavior. Our results are relevant for the study of star-colloid nanocomposites and pave the way for further investigations of the structure and thermodynamics of the same.

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

    SciTech Connect

    Sussman, Roberto A.; Gaspar, I. Delgado; Hidalgo, Juan Carlos E-mail: ismael.delgadog@uaem.edu.mx

    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. Near-road enhancement and solubility of fine and coarse ...

    EPA Pesticide Factsheets

    Communities near major roadways are disproportionately affected by traffic-related air pollution which can contribute to adverse health outcomes. The specific role of particulate matter (PM) from traffic sources is not fully understood due to complex emissions processes and physical/chemical properties of PM in the near-road environment. To investigate the spatial profile and water solubility of elemental PM species near a major roadway, filter-based measurements of fine (PM2.5) and coarse (PM10-2.5) PM were simultaneously collected at multiple distances (10 m, 100 m, and 300 m) from Interstate I-96 in Detroit, Michigan during September–November 2010. Filters were extracted in water, followed by a hot acid extraction, and analyzed by magnetic sector field high resolution inductively coupled plasma mass spectrometry (HR-ICPMS) to quantify water-soluble and acid-soluble trace elements for each PM size fraction. PM2.5 and PM10-2.5 species measured in the near-road samples included elements associated with traffic activity, local industrial sources, and regional pollution. Metals indicative of brake wear (Ba, Cu) were dramatically enriched near the roadway during downwind conditions (factor of 5 concentration increase), with the largest increase within 100 m of the roadway. Moderate near-roadway increases were observed for crustal elements and other traffic-related PM (Fe, Ca), and the lowest increases observed for regional PM species (S). Water solubility varied

  13. Coarse graining approach to First principles modeling of structural materials

    SciTech Connect

    Odbadrakh, Khorgolkhuu; Nicholson, Don M; Rusanu, Aurelian; Samolyuk, German D; Wang, Yang; Stoller, Roger E; Zhang, X.-G.; Stocks, George Malcolm

    2013-01-01

    Classical Molecular Dynamic (MD) simulations characterizing extended defects typically require millions of atoms. First principles calculations employed to understand these defect systems at an electronic level cannot, and should not deal with such large numbers of atoms. We present an e cient coarse graining (CG) approach to calculate local electronic properties of large MD-generated structures from the rst principles. We used the Locally Self-consistent Multiple Scattering (LSMS) method for two types of iron defect structures 1) screw-dislocation dipoles and 2) radiation cascades. The multiple scattering equations are solved at fewer sites using the CG. The atomic positions were determined by MD with an embedded atom force eld. The local moments in the neighborhood of the defect cores are calculated with rst-principles based on full local structure information, while atoms in the rest of the system are modeled by representative atoms with approximated properties. This CG approach reduces computational costs signi cantly and makes large-scale structures amenable to rst principles study. Work is sponsored by the USDoE, O ce of Basic Energy Sciences, Center for Defect Physics, an Energy Frontier Research Center. This research used resources of the Oak Ridge Leadership Computing Facility at the ORNL, which is supported by the O ce of Science of the USDoE under Contract No. DE-AC05-00OR22725.

  14. 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.

  15. Coarse-grained modeling of polyethylene melts: Effect on dynamics

    DOE PAGES

    Peters, Brandon L.; Salerno, K. Michael; Agrawal, Anupriya; ...

    2017-05-23

    The distinctive viscoelastic behavior of polymers results from a coupled interplay of motion on multiple length and time scales. Capturing the broad time and length scales of polymer motion remains a challenge. Using polyethylene (PE) as a model macromolecule, we construct coarse-grained (CG) models of PE with three to six methyl groups per CG bead and probe two critical aspects of the technique: pressure corrections required after iterative Boltzmann inversion (IBI) to generate CG potentials that match the pressure of reference fully atomistic melt simulations and the transferability of CG potentials across temperatures. While IBI produces nonbonded pair potentials thatmore » give excellent agreement between the atomistic and CG pair correlation functions, the resulting pressure for the CG models is large compared with the pressure of the atomistic system. We find that correcting the potential to match the reference pressure leads to nonbonded interactions with much deeper minima and slightly smaller effective bead diameter. However, simulations with potentials generated by IBI and pressure-corrected IBI result in similar mean-square displacements (MSDs) and stress autocorrelation functions G(t) for PE melts. While the time rescaling factor required to match CG and atomistic models is the same for pressure- and non-pressure-corrected CG models, it strongly depends on temperature. Furthermore, transferability was investigated by comparing the MSDs and stress autocorrelation functions for potentials developed at different temperatures.« less

  16. 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.

  17. Coarse particulate matter emissions from cattle feedlots in Australia.

    PubMed

    McGinn, S M; Flesch, T K; Chen, D; Crenna, B; Denmead, O T; Naylor, T; Rowell, D

    2010-01-01

    Open cattle feedlots are a source of air pollutants that include particular matter (PM). Over 24 h, exposure to ambient concentrations of 50 microg m(-3) of the coarse-sized fraction PM (aerodynamic diameter <10 microm [PM(10)]) is recognized as a health concern for humans. The objective of our study was to document PM(10) concentration and emissions at two cattle feedlots in Australia over several days in summer. Two automated samplers were used to monitor the background and in-feedlot PM(10) concentrations. At the in-feedlot location, the PM(10) emission was calculated using a dispersion model. Our measurements revealed that the 24-h PM(10) concentrations on some of the days approached or exceeded the health criteria threshold of 50 microg m(-3) used in Australia. A key factor responsible for the generation of PM(10) was the increased activity of cattle in the evening that coincided with peak concentrations of PM(10) (maximum, 792 microg m(-3)) between 1930 and 2000 h. Rain coincided with a severe decline in PM(10) concentration and emission. A dispersion model used in our study estimated the emission of PM(10) between 31 and 60 g animal(-1) d(-1). These data contribute to needed information on PM(10) associated with livestock to develop results-based environmental policy.

  18. 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

  19. 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.

  20. Coarse cluster enhancing collaborative recommendation for social network systems

    NASA Astrophysics Data System (ADS)

    Zhao, Yao-Dong; Cai, Shi-Min; Tang, Ming; Shang, Min-Sheng

    2017-10-01

    Traditional collaborative filtering based recommender systems for social network systems bring very high demands on time complexity due to computing similarities of all pairs of users via resource usages and annotation actions, which thus strongly suppresses recommending speed. In this paper, to overcome this drawback, we propose a novel approach, namely coarse cluster that partitions similar users and associated items at a high speed to enhance user-based collaborative filtering, and then develop a fast collaborative user model for the social tagging systems. The experimental results based on Delicious dataset show that the proposed model is able to dramatically reduce the processing time cost greater than 90 % and relatively improve the accuracy in comparison with the ordinary user-based collaborative filtering, and is robust for the initial parameter. Most importantly, the proposed model can be conveniently extended by introducing more users' information (e.g., profiles) and practically applied for the large-scale social network systems to enhance the recommending speed without accuracy loss.

  1. 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.

  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. 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.

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

    PubMed

    Deng, Mingsen; Shen, Hujun

    2016-02-04

    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.

  5. Non-conformal coarse-grained potentials for water.

    PubMed

    Rodríguez-López, Tonalli; Khalak, Yuriy; Karttunen, Mikko

    2017-10-07

    Water is a notoriously difficult substance to model both accurately and efficiently. Here, we focus on descriptions with a single coarse-grained particle per molecule using the so-called approximate non-conformal and generalized Stockmayer potentials as the starting points. They are fitted using the radial distribution function and the liquid-gas density profile of the atomistic extended simple point charge (SPC/E) model by downhill simplex optimization. We compare the results with monatomic water (mW), ELBA, and direct iterative Boltzmann inversion of SPC/E. The results show that symmetrical potentials result in non-transferable models, that is, they need to be reparametrized for new state points. This indicates that transferability may require more complex models. Furthermore, the results also show that the addition of a point dipole is not sufficient to make the potentials accurate and transferable to different temperatures (300 K-500 K) and pressures without an appropriate choice of properties as targets during model optimization.

  6. A kinetic chain growth algorithm in coarse-grained simulations.

    PubMed

    Liu, Hong; Zhu, You-Liang; Lu, Zhong-Yuan; Müller-Plathe, Florian

    2016-11-15

    We propose a kinetic chain growth algorithm for coarse-grained (CG) simulations in this work. By defining the reaction probability, it delivers a description of consecutive polymerization process. This algorithm is validated by modeling the process of individual styrene monomers polymerizing into polystyrene chains, which is proved to correctly reproduce the properties of polymers in experiments. By bridging the relationship between the generic chain growth process in CG simulations and the chemical details, the impediment to reaction can be reflected. Regarding to the kinetics, it models a polymerization process with an Arrhenius-type reaction rate coefficient. Moreover, this algorithm can model both the gradual and jump processes of the bond formation, thus it readily encompasses several kinds of previous CG models of chain growth. With conducting smooth simulations, this algorithm can be potentially applied to describe the variable macroscopic features of polymers with the process of polymerization. The algorithm details and techniques are introduced in this article. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. 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.

  8. Coarse Grained Model for Biological Simulations: Recent Refinements and Validation

    PubMed Central

    Vicatos, Spyridon; Rychkova, Anna; Mukherjee, Shayantani; Warshel, Arieh

    2014-01-01

    Exploring the free energy landscape of proteins and modeling the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of various simplified coarse grained (CG) models offers an effective way of sampling the landscape, but most current models are not expected to give a reliable description of protein stability and functional aspects. The main problem is associated with insufficient focus on the electrostatic features of the model. In this respect our recent CG model offers significant advantage as it has been refined while focusing on its electrostatic free energy. Here we review the current state of our model, describing recent refinement, extensions and validation studies while focusing on demonstrating key applications. These include studies of protein stability, extending the model to include membranes and electrolytes and electrodes as well as studies of voltage activated proteins, protein insertion trough the translocon, the action of molecular motors and even the coupling of the stalled ribosome and the translocon. Our example illustrates the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins and large macromolecular complexes. PMID:25050439

  9. 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

  10. Emerging dynamics arising from coarse-grained quantum systems

    NASA Astrophysics Data System (ADS)

    Duarte, Cristhiano; Carvalho, Gabriel Dias; Bernardes, Nadja K.; de Melo, Fernando

    2017-09-01

    The purpose of physics is to describe nature from elementary particles all the way up to cosmological objects like cluster of galaxies and black holes. Although a unified description for all this spectrum of events is desirable, this would be highly impractical. To not get lost in unnecessary details, effective descriptions are mandatory. Here we analyze the dynamics that may emerge from a full quantum description when one does not have access to all the degrees of freedom of a system. More concretely, we describe the properties of the dynamics that arise from quantum mechanics if one has access only to a coarse-grained description of the system. We obtain that the effective maps are not necessarily of Kraus form, due to correlations between accessible and nonaccessible degrees of freedom, and that the distance between two effective states may increase under the action of the effective map. We expect our framework to be useful for addressing questions such as the thermalization of closed quantum systems, as well as the description of measurements in quantum mechanics.

  11. Coarse-grained modeling of protein unspecifically bound to DNA

    NASA Astrophysics Data System (ADS)

    Guardiani, Carlo; Cencini, Massimo; Cecconi, Fabio

    2014-04-01

    There is now a certain consensus that transcription factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D diffusion in solution (jumps), 1D diffusion along DNA (sliding), and small jumps (hopping), achieving association rates higher than for 3D diffusion alone. We investigate the FD phenomenology through molecular dynamics simulations in the framework of coarse-grained modeling. We show that, despite the crude approximations, the model generates, upon varying the equilibrium distance of the DNA-TF interaction, a phenomenology matching a number of experimental and numerical results obtained with more refined models. In particular, focusing on the kinematics of the process, we characterize the geometrical properties of TF trajectories during sliding. We find that sliding occurs via helical paths around the DNA helix, leading to a coupling of translation along the DNA axis with rotation around it. The 1D diffusion constant measured in simulations is found to be interwoven with the geometrical properties of sliding and we develop a simple argument that can be used to quantitatively reproduce the measured values.

  12. Thermodynamics of star polymer solutions: A coarse-grained study

    NASA Astrophysics Data System (ADS)

    Menichetti, Roberto; Pelissetto, Andrea; Randisi, Ferdinando

    2017-06-01

    We consider a coarse-grained (CG) model with pairwise interactions, suitable to describe low-density solutions of star-branched polymers of functionality f. Each macromolecule is represented by a CG molecule with (f + 1) interaction sites, which captures the star topology. Potentials are obtained by requiring the CG model to reproduce a set of distribution functions computed in the microscopic model in the zero-density limit. Explicit results are given for f = 6, 12, and 40. We use the CG model to compute the osmotic equation of state of the solution for concentrations c such that Φp=c /c*≲1 , where c* is the overlap concentration. We also investigate in detail the phase diagram for f = 40, identifying the boundaries of the solid intermediate phase. Finally, we investigate how the polymer size changes with c. For Φp≲0.3 , polymers become harder as f increases at fixed reduced concentration c /c*. On the other hand, for Φp≳0.3 , polymers show the opposite behavior: At fixed Φp, the larger the value of f, the larger their size reduction is.

  13. 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.

  14. CG2AA: backmapping protein coarse-grained structures.

    PubMed

    Lombardi, Leandro E; Martí, Marcelo A; Capece, Luciana

    2016-04-15

    Coarse grain (CG) models allow long-scale simulations with a much lower computational cost than that of all-atom simulations. However, the absence of atomistic detail impedes the analysis of specific atomic interactions that are determinant in most interesting biomolecular processes. In order to study these phenomena, it is necessary to reconstruct the atomistic structure from the CG representation. This structure can be analyzed by itself or be used as an onset for atomistic molecular dynamics simulations. In this work, we present a computer program that accurately reconstructs the atomistic structure from a CG model for proteins, using a simple geometrical algorithm. The software is free and available online at http://www.ic.fcen.uba.ar/cg2aa/cg2aa.py Supplementary data are available at Bioinformatics online. lula@qi.fcen.uba.ar. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. 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

  16. Coarse grained model for calculating the ion mobility of hydrocarbons

    NASA Astrophysics Data System (ADS)

    Kuroboshi, Y.; Takemura, K.

    2016-12-01

    Hydrocarbons are widely used as insulating compounds. However, their fundamental characteristics in conduction phenomena are not completely understood. A great deal of effort is required to determine reasonable ionic behavior from experiments because of their complicated procedures and tight controls of the temperature and the purity of the liquids. In order to understand the conduction phenomena, we have theoretically calculated the ion mobilities of hydrocarbons and investigated their characteristics using the coarse grained model in molecular dynamics simulations. We assumed a molecule of hydrocarbons to be a bead and simulated its dependence on the viscosity, electric field, and temperature. Furthermore, we verified the suitability of the conformation, scale size, and long-range interactions for the ion mobility. The results of the simulations show that the ion mobility values agree reasonably well with the values from Walden's rule and depend on the viscosity but not on the electric field. The ion mobility and self-diffusion coefficient exponentially increase with increasing temperature, while the activation energy decreases with increasing molecular size. These values and characteristics of the ion mobility are in reasonable agreement with experimental results. In the future, we can understand not only the ion mobilies of hydrocarbons in conduction, but also we can predict general phenomena in electrochemistry with molecular dynamics simulations.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Multi-scale simulation of asphaltene aggregation and deposition in capillary flow.

    PubMed

    Boek, Edo S; Headen, Thomas F; Padding, Johan T

    2010-01-01

    Asphaltenes are known as the 'cholesterol' of crude oil. They form nano-aggregates, precipitate, adhere to surfaces, block rock pores and may alter the wetting characteristics of mineral surfaces within the reservoir, hindering oil recovery efficiency. Despite a significant research effort, the structure, aggregation and deposition of asphaltenes under flowing conditions remain poorly understood. For this reason, we have investigated asphaltenes, their aggregation and their deposition in capillary flow using multi-scale simulations and experiments. At the colloid scale, we use a hybrid simulation approach: for the solvent, we used the stochastic rotation dynamics (also known as multi particle collision dynamics) simulation method, which provides both hydrodynamics and Brownian motion. This is coupled to a coarse-grained MD approach for the asphaltene colloids. The colloids interact through a screened Coulomb potential with varying well depth epsilon. We tune the flow rate to obtain Pe(flow) > 1 (hydrodynamic interactions dominate) and Re < 1 (Stokes flow). Imposing a constant pressure drop over the capillary length, we observe that the transient solvent flow rate decreases with increasing well depth epsilon. The interactions between the mesoscopic asphaltene colloids can be related to atomistic MD simulations. Molecular structures for the atomistic calculations were obtained using the quantitative molecular representation approach. Using these structures, we calculate the potential of mean force (PMF) between pairs of asphaltene molecules in an explicit solvent. We obtain a reasonable fit using a -1/r2 attraction for the attractive tail of the PMF at intermediate distances. We speculate that this is due to the two-dimensional nature of the asphaltene molecules. Finally, we discuss how we can relate this interaction to the mesoscopic colloid aggregate interaction. We assume that the colloidal aggregates consist of nano-aggregates. Taking into account observed

  2. Coarse-sediment bands on the inner shelf of southern Monterey Bay, California

    USGS Publications Warehouse

    Hunter, R.E.; Dingler, J.R.; Anima, R.J.; Richmond, B.M.

    1988-01-01

    Bands of coarse sand that trend parallel to the shore, unlike the approximately shore-normal bands found in many inner shelf areas, occur in southern Monterey Bay at water depths of 10-20 m, less than 1 km from the shore. The bands are 20-100 m wide and alternate with bands of fine sand that are of similar width. The coarse-sand bands are as much as 1 m lower than the adjacent fine-sand bands, which have margins inclined at angles of about 20??. The mean grain sizes of the coarse and fine sand are in the range of 0.354-1.0 mm and 0.125-0.354 mm, respectively. Wave ripples that average about 1 m in spacing always occur in the coarse-sand bands. Over a period of 3 yrs, the individual bands moved irregularly and changed in shape, as demonstrated by repeated sidescan sonar surveys and by the monitoring of rods jetted into the sea floor. However, the overall pattern and distribution of the bands remained essentially unchanged. Cores, 0.5-1.0 m long, taken in coarse-sand bands contain 0.2-0.5 m of coarse sand overlying fine sand or interbedded fine and coarse sand. Cores from fine-sand bands have at least one thin coarse sand layer at about the depth of the adjacent coarse-sand band. None of the cores revealed a thick deposit of coarse sand. The shore-parallel bands are of unknown origin. Their origin is especially puzzling because approximately shore-normal bands are present in parts of the study area and immediately to the north. ?? 1988.

  3. Function evaluation of asphalt mixture with industrially produced BOF slag aggregate.

    PubMed

    Zhao, Meiling; Wu, Shaopeng; Chen, Zongwu; Li, Chao

    2016-07-04

    Laboratory research suggested that basic oxygen furnace (BOF) slag-based asphalt mixture was a functional material. However, the BOF slag aggregate's quality was difficult to control when it was heavily used in entity engineering. The primary objective of this research was to evaluate the functional performances of asphalt mixture containing BOF slag coarse aggregate (BSCA), which was from an industrialized production line. Limestone mixture was a control group. The Marshall method was first adopted to design asphalt mixtures. The performances of limestone asphalt mixture and BOF slag asphalt mixture including fatigue failure resistance and moisture stability were then evaluated and compared. Results showed that the asphalt mixture containing BSCA possessed better durability, which meant the quality of BSCA from industrialized production lines was well controlled and this BSCA can be heavily used in entity engineering.

  4. 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.

  5. Role of streams in myxobacteria aggregate formation

    NASA Astrophysics Data System (ADS)

    Kiskowski, Maria A.; Jiang, Yi; Alber, Mark S.

    2004-10-01

    Cell contact, movement and directionality are important factors in biological development (morphogenesis), and myxobacteria are a model system for studying cell-cell interaction and cell organization preceding differentiation. When starved, thousands of myxobacteria cells align, stream and form aggregates which later develop into round, non-motile spores. Canonically, cell aggregation has been attributed to attractive chemotaxis, a long range interaction, but there is growing evidence that myxobacteria organization depends on contact-mediated cell-cell communication. We present a discrete stochastic model based on contact-mediated signaling that suggests an explanation for the initialization of early aggregates, aggregation dynamics and final aggregate distribution. Our model qualitatively reproduces the unique structures of myxobacteria aggregates and detailed stages which occur during myxobacteria aggregation: first, aggregates initialize in random positions and cells join aggregates by random walk; second, cells redistribute by moving within transient streams connecting aggregates. Streams play a critical role in final aggregate size distribution by redistributing cells among fewer, larger aggregates. The mechanism by which streams redistribute cells depends on aggregate sizes and is enhanced by noise. Our model predicts that with increased internal noise, more streams would form and streams would last longer. Simulation results suggest a series of new experiments.

  6. Ash aggregation during the 11 February 2010 partial dome collapse of the Soufrière Hills Volcano, Montserrat

    NASA Astrophysics Data System (ADS)

    Burns, F. A.; Bonadonna, C.; Pioli, L.; Cole, P. D.; Stinton, A.

    2017-04-01

    On 11 February 2010, Soufrière Hills Volcano, Montserrat, underwent a partial dome collapse ( 50 × 106 m3) and a short-lived Vulcanian explosion towards the end. Three main pyroclastic units were identified N and NE of the volcano: dome-collapse pyroclastic density current (PDC) deposits, fountain-collapse PDC deposits formed by the Vulcanian explosion, and tephra-fallout deposits associated with elutriation from the dome-collapse and fountain-collapse PDCs (i.e. co-PDC fallout deposit). The fallout associated with the Vulcanian explosion was mostly dispersed E and SE by high altitude winds. All units N and NE of the volcano contain variable amounts and types of particle aggregates, although the co-PDC fallout deposit is associated with the largest abundance (i.e. up to 24 wt%). The size of aggregates found in the co-PDC fallout deposit increases with distance from the volcano and proximity to the sea, reaching a maximum diameter of 12 mm about 500 m from the coast. The internal grain size of all aggregates have nearly identical distributions (with Mdϕ ≈ 4-5), with particles in the size categories > 3 ϕ (i.e. < 250 μm) being distributed in similar proportions within the aggregates but in different proportions within distinct internal layers. In fact, most aggregates are characterized by a coarse grained central core occupying the main part of the aggregate, coated by a thin layer of finer ash (single-layer aggregates), while others have one or two additional layers accreted over the core (multiple-layer aggregates). Calculated aggregate porosity and settling velocity vary between 0.3 and 0.5 and 11-21 m s- 1, respectively. The aggregate size shows a clear correlation with both the core size and the size of the largest particles found in the core. The large abundance of aggregates in the co-PDC fallout deposits suggests that the buoyant plumes elutriated above PDCs represent an optimal environment for the formation (particle collision) and development

  7. 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

  8. 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.

  9. Virus-induced aggregates in infected cells.

    PubMed

    Moshe, Adi; Gorovits, Rena

    2012-10-17

    During infection, many viruses induce cellular remodeling, resulting in the formation of insoluble aggregates/inclusions, usually containing viral structural proteins. Identification of aggregates has become a useful diagnostic tool for certain viral infections. There is wide variety of viral aggregates, which differ by their location, size, content and putative function. The role of aggregation in the context of a specific virus is often poorly understood, especially in the case of plant viruses. The aggregates are utilized by viruses to house a large complex of proteins of both viral and host origin to promote virus replication, translation, intra- and intercellular transportation. Aggregated structures may protect viral functional complexes from the cellular degradation machinery. Alternatively, the activation of host defense mechanisms may involve sequestration of virus components in aggregates, followed by their neutralization as toxic for the host cell. The diversity of virus-induced aggregates in mammalian and plant cells is the subject of this review.

  10. Platiniferous gold-tourmaline aggregates in the gold-palladium belt of Minas Gerais, Brazil: implications for regional boron metasomatism

    NASA Astrophysics Data System (ADS)

    Cabral, Alexandre Raphael; Tupinambá, Miguel; Zeh, Armin; Lehmann, Bernd; Wiedenbeck, Michael; Brauns, Michael; Kwitko-Ribeiro, Rogerio

    2017-02-01

    The platiniferous gold-palladium belt of Minas Gerais, Brazil, forms an approximately 240-km-long, roughly north-south-trending domain that includes numerous auriferous lodes and platiniferous alluvium. The belt transects two Precambrian terranes, the Quadrilátero Ferrífero in the southern part, and the southern Serra do Espinhaço in the northern part. Both terranes were overprinted by regional fluid flow that led to tourmalinisation, with or without hematitisation, and precious-metal mineralisation. Here, we report the occurrence of coarse-grained gold-tourmaline aggregates and integrate recently obtained ages and tourmaline boron-isotope values published elsewhere. One type of aggregate is unique because it has patches that are close to stoichiometric PdPt, in which gold content varies from 2.5 to 33.5 at.%. The gold-tourmaline aggregates seem to be the ultimate expression of the boron metasomatism.

  11. 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

  12. Aggregation resistant zwitterated superparamagnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Rouhana, Layal L.; Schlenoff, Joseph B.

    2012-05-01

    Superparamagnetic nanoparticles (NPs) are promising for biomedical applications since they can be directed toward the organ of interest using an external magnetic field. They are also good contrast agents for magnetic resonance imaging and have potential for the treatment of malignant tumors (i.e., hyperthermia). Therefore, there is a need to produce stable, non-aggregating superparamagnetic nanomaterials that can withstand the in vivo environment. In this work, the colloidal stability of a dispersion of iron oxide NPs was enhanced by functionalizing them with a short zwitterionic siloxane shell in aqueous media. The stabilization procedure yields superparamagnetic nanomaterials, ca. 10 nm in diameter, with saturation magnetization of about 54 emu/g that resist aggregation at physiological salt concentration, temperature, and pH. The loading of the zwitterionic shell was established with diffuse reflectance infrared spectroscopy and thermal gravimetric analysis. X-ray and electron diffraction verified the starting magnetite phase, and that no change in phase occurred on surface functionalization.

  13. 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.

  14. Texture measurements in fine grained polyphase aggregates

    NASA Astrophysics Data System (ADS)

    Kilian, R.; Heilbronner, R.; Stünitz, H.

    2009-04-01

    When analyzing natural and experimental microstructures, we routinely use the two methods for orientation imaging and texture measurements: (a) the computer-integrated polarization microscopy (CIP, Panozzo Heilbronner & Pauli, 1993) and (b) the electron back scatter diffractometry (EBSD, e.g. Kunze et al., 1994). The CIP method yields orientation maps and pole figures of c-axes (of uni-axial materials), while the EBSD method yields complete textural data for all crystallographic orientations. In order to compare the orientation images the Euler maps (obtained from EBSD) are recalculated and presented with the more intuitive colour look-up tables (CLUTs) of the CIP method. In this contribution we compare and contrast the results achieved by these two methods using two different samples taken from a metagranodiorite (Kilian et al., 2009): (1) a coarse grained mylonitic rock with polycrystalline quartz aggregates and (2) a very fine grained ultramylonitic rock with single quartz grains dispersed in a polymineralic matrix. For the coarse grained sample (1) both methods yield the same (strong) c-axis pole figure: the geometry of the c-axis polefigure as well as the texture intensity (maximum of polefigure) are identical. The texture of sample (2) - where small quartz grains are dispersed in the polymineralic matrix - is very weak to random. The CIP and EBSD c-axis pole figures are different and - as noted previously - these differences arise from a machine specific bias of the EBSD (Schmocker 2002). In addition to texture analysis, both methods are capable of image segmentation (identification and separation of individual grains in the orientation image) as well as shape and grain size analysis. However due to the entirely different approach taken, the results may differ significantly. For example, when deriving the grain size distribution for sample (2) EBSD (combined with with the OIM® analysis software) yields a positively skewed histogram (with the mode occurring

  15. 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.

  16. Locally available aggregate and sediment production

    Treesearch

    Randy B. Foltz; Mark Truebe

    2003-01-01

    Selection of suitable locally available materials to build strong and durable roads with aggregate surfaces is desired to minimize road construction and maintenance costs and to minimize the detrimental effects of sedimentation. Eighteen aggregates were selected from local sources in Idaho, Oregon, South Dakota, and Washington State. Aggregate was placed in shallow...

  17. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 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 § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project all...

  18. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 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 § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project all...

  19. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 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 § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project all...

  20. 24 CFR 58.32 - Project aggregation.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 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 § 58.32 Project aggregation. (a) A responsible entity must group together and evaluate as a single project all...

  1. PRIMO: A Transferable Coarse-grained Force Field for Proteins

    PubMed Central

    Kar, Parimal; Gopal, Srinivasa Murthy; Cheng, Yi-Ming; Predeus, Alexander; Feig, Michael

    2013-01-01

    We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born model. The bonded interactions are either harmonic or distance-based spline interpolated potentials. These potentials are defined on the basis of all-atom molecular dynamics (MD) simulations of dipeptides with the CHARMM22/CMAP force field. The non-bonded parameters are tuned by matching conformational free energies of diverse set of conformations with that of CHARMM all-atom results. PRIMO is designed to provide a correct description of conformational distribution of the backbone (ϕ/ψ) and side chains (χ1) for all amino acids with a CMAP correction term. The CMAP potential in PRIMO is optimized based on the new CHARMM C36 CMAP. The resulting optimized force field has been applied in MD simulations of several proteins of 36–155 amino acids and shown that the root-mean-squared-deviation of the average structure from the corresponding crystallographic structure varies between 1.80 and 4.03 Å. PRIMO is shown to fold several small peptides to their native-like structures from extended conformations. These results suggest the applicability of the PRIMO force field in the study of protein structures in aqueous solution, structure predictions as well as ab initio folding of small peptides. PMID:23997693

  2. Transferable coarse-grained model for perfluorosulfonic acid polymer membranes

    NASA Astrophysics Data System (ADS)

    Kuo, An-Tsung; Okazaki, Susumu; Shinoda, Wataru

    2017-09-01

    Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes.

  3. Coarse-Mode Particle Characterization With Digital Holograph

    NASA Astrophysics Data System (ADS)

    Berg, M.; Subedi, N.

    2015-12-01

    The recent availability of high resolution optoelectronic sensors has revived holography as a useful technique to study aerosol particles. By placing a two-dimensional detector in a collimated laser beam, the interference pattern produced by this light and that forward-scattered by a particle in the beam can be easily measured. This pattern is the particle's in-line hologram and information can be extracted from it directly. For example, applying a Fourier-transform operation to the hologram yields a silhouette-like image of the particle, thus revealing its size and shape without a priori information. In this sense, digital holography "solves" the classic inverse problem in applied light scattering. Moreover, this measurement can be done in situ and applied to flowing aerosol particles using pulsed illumination. In recent work, we have discovered there is also an inherent link between a particle's extinction cross section and the integral of the hologram. Using Mie theory, we have shown this relationship for a variety of spherical particles. The generality of the concept, however, suggests that it applies to nonspherical particles as well. In this presentation we will show that, indeed, the extinction cross section can be extracted from the holograms produced by such particles. Specifically, we investigate prolate and oblate spheroids and cubical particles in the wavelength-size range. Using both the discrete dipole approximation and the T-Matrix method, when applicable, we are able to simulate the holograms and then perform a simple integration to yield the cross sections. We will also present our ongoing experimental work applying this technique to coarse-mode aerosol particles.

  4. California Wildfires of 2008: Coarse and Fine Particulate Matter Toxicity

    PubMed Central

    Wegesser, Teresa C.; Pinkerton, Kent E.; Last, Jerold A.

    2009-01-01

    Background During the last week of June 2008, central and northern California experienced thousands of forest and brush fires, giving rise to a week of severe fire-related particulate air pollution throughout the region. California experienced PM10–2.5 (particulate matter with mass median aerodynamic diameter > 2.5 μm to < 10 μm; coarse ) and PM2.5 (particulate matter with mass median aerodynamic diameter < 2.5 μm; fine) concentrations greatly in excess of the air quality standards and among the highest values reported at these stations since data have been collected. Objectives These observations prompt a number of questions about the health impact of exposure to elevated levels of PM10–2.5 and PM2.5 and about the specific toxicity of PM arising from wildfires in this region. Methods Toxicity of PM10–2.5 and PM2.5 obtained during the time of peak concentrations of smoke in the air was determined with a mouse bioassay and compared with PM samples collected under normal conditions from the region during the month of June 2007. Results Concentrations of PM were not only higher during the wildfire episodes, but the PM was much more toxic to the lung on an equal weight basis than was PM collected from normal ambient air in the region. Toxicity was manifested as increased neutrophils and protein in lung lavage and by histologic indicators of increased cell influx and edema in the lung. Conclusions We conclude that the wildfire PM contains chemical components toxic to the lung, especially to alveolar macrophages, and they are more toxic to the lung than equal doses of PM collected from ambient air from the same region during a comparable season. PMID:19590679

  5. Coarse particulate matter and airborne endotoxin within wood stove homes

    PubMed Central

    McNamara, M.; Thornburg, J.; Semmens, E.; Ward, T.; Noonan, C.

    2015-01-01

    Emissions from indoor biomass burning are a major public health concern in developing areas of the world. Less is known about indoor air quality, particularly airborne endotoxin, in homes burning biomass fuel in residential wood stoves in higher income countries. A filter-based sampler was used to evaluate wintertime indoor coarse particulate matter (PM 10–2.5) and airborne endotoxin (EU/m3, EU/mg) concentrations in 50 homes using wood stoves as their primary source of heat in western Montana. We investigated number of residents, number of pets, dampness (humidity), and frequency of wood stove usage as potential predictors of indoor airborne endotoxin concentrations. Two 48-h sampling events per home revealed a mean winter PM10–2.5 concentration (± s.d.) of 12.9 (± 8.6) μg/m3, while PM2.5 concentrations averaged 32.3 (± 32.6) μg/m3. Endotoxin concentrations measured from PM10–2.5 filter samples were 9.2 (± 12.4) EU/m3 and 1010 (± 1524) EU/mg. PM10–2.5 and PM2.5 were significantly correlated in wood stove homes (r = 0.36, P < 0.05). The presence of pets in the homes was associated with PM10–2.5 but not with endotoxin concentrations. Importantly, none of the other measured home characteristics was a strong predictor of airborne endotoxin, including frequency of residential wood stove usage. PMID:23551341

  6. 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.

  7. Transferable coarse-grained model for perfluorosulfonic acid polymer membranes.

    PubMed

    Kuo, An-Tsung; Okazaki, Susumu; Shinoda, Wataru

    2017-09-07

    Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes.

  8. 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.

  9. 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

  10. PRIMO: A Transferable Coarse-grained Force Field for Proteins.

    PubMed

    Kar, Parimal; Gopal, Srinivasa Murthy; Cheng, Yi-Ming; Predeus, Alexander; Feig, Michael

    2013-08-13

    We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born model. The bonded interactions are either harmonic or distance-based spline interpolated potentials. These potentials are defined on the basis of all-atom molecular dynamics (MD) simulations of dipeptides with the CHARMM22/CMAP force field. The non-bonded parameters are tuned by matching conformational free energies of diverse set of conformations with that of CHARMM all-atom results. PRIMO is designed to provide a correct description of conformational distribution of the backbone (ϕ/ψ) and side chains (χ1) for all amino acids with a CMAP correction term. The CMAP potential in PRIMO is optimized based on the new CHARMM C36 CMAP. The resulting optimized force field has been applied in MD simulations of several proteins of 36-155 amino acids and shown that the root-mean-squared-deviation of the average structure from the corresponding crystallographic structure varies between 1.80 and 4.03 Å. PRIMO is shown to fold several small peptides to their native-like structures from extended conformations. These results suggest the applicability of the PRIMO force field in the study of protein structures in aqueous solution, structure predictions as well as ab initio folding of small peptides.

  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. 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.

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

    DOE PAGES

    Bevc, Staš; Junghans, Christoph; Praprotnik, Matej

    2015-03-15

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

  14. 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.

  15. 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

  16. Alteration of soil carbon and nitrogen pools and enzyme activities as affected by increased soil coarseness

    NASA Astrophysics Data System (ADS)

    Wang, Ruzhen; Lü, Linyou; Creamer, Courtney A.; Dijkstra, Feike A.; Liu, Heyong; Feng, Xue; Yu, Guoqing; Han, Xingguo; Jiang, Yong

    2017-04-01

    Soil coarseness decreases ecosystem productivity, ecosystem carbon (C) and nitrogen (N) stocks, and soil nutrient contents in sandy grasslands subjected to desertification. To gain insight into changes in soil C and N pools, microbial biomass, and enzyme activities in response to soil coarseness, a field experiment was conducted by mixing native soil with river sand in different mass proportions: 0, 10, 30, 50, and 70 % sand addition. Four years after establishing plots and 2 years after transplanting, soil organic C and total N concentrations decreased with increased soil coarseness down to 32.2 and 53.7 % of concentrations in control plots, respectively. Soil microbial biomass C (MBC) and N (MBN) declined with soil coarseness down to 44.1 and 51.9 %, respectively, while microbial biomass phosphorus (MBP) increased by as much as 73.9 %. Soil coarseness significantly decreased the enzyme activities of β-glucosidase, N-acetyl-glucosaminidase, and acid phosphomonoesterase by 20.2-57.5 %, 24.5-53.0 %, and 22.2-88.7 %, used for C, N and P cycling, respectively. However, observed values of soil organic C, dissolved organic C, total dissolved N, available P, MBC, MBN, and MBP were often significantly higher than would be predicted from dilution effects caused by the sand addition. Soil coarseness enhanced microbial C and N limitation relative to P, as indicated by the ratios of β-glucosidase and N-acetyl-glucosaminidase to acid phosphomonoesterase (and MBC : MBP and MBN : MBP ratios). Enhanced microbial recycling of P might alleviate plant P limitation in nutrient-poor grassland ecosystems that are affected by soil coarseness. Soil coarseness is a critical parameter affecting soil C and N storage and increases in soil coarseness can enhance microbial C and N limitation relative to P, potentially posing a threat to plant productivity in sandy grasslands suffering from desertification.

  17. 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

  18. 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.

  19. Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations

    PubMed Central

    2016-01-01

    Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from atomistic simulations are not observed at the CG level based on the Martini model, implying a difference in driving forces for ganglioside interactions in atomistic and CG simulations. For protein-ganglioside interactions, in the atomistic simulations, GM1 lipids bind to specific sites on the AQP1 surface, whereas they are depleted from WALP23. In the CG simulations, the ganglioside binding sites on the AQP1 surface are similar, but ganglioside aggregation and protein-ganglioside interactions are more prevalent than in the atomistic simulations. Using the polarizable Martini water model, results were closer to the atomistic simulations. Although experimental data for validation is lacking, we proposed modified Martini parameters for gangliosides to more closely mimic the sizes and structures of ganglioside clusters observed at the atomistic level. PMID:27610460

  20. 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.