Local-feature analysis for automated coarse-graining of bulk-polymer molecular dynamics simulations.

PubMed

Xue, Y; Ludovice, P J; Grover, M A

2012-12-01

A method for automated coarse-graining of bulk polymers is presented, using the data-mining tool of local feature analysis. Most existing methods for polymer coarse-graining define superatoms based on their covalent bonding topology along the polymer backbone, but here superatoms are defined based only on their correlated motions, as observed in molecular dynamics simulations. Correlated atomic motions are identified in the simulation data using local feature analysis, between atoms in the same or in different polymer chains. Groups of highly correlated atoms constitute the superatoms in the coarse-graining scheme, and the positions of their seed coordinates are then projected forward in time. Based on only the seed positions, local feature analysis enables the full reconstruction of all atomic positions. This reconstruction suggests an iterative scheme to reduce the computation of the simulations to initialize another short molecular dynamic simulation, identify new superatoms, and again project forward in time.

Aspartylglucosaminuria: psychomotor retardation masquerading as a mucopolysaccharidosis.

PubMed

Isenberg, J N; Sharp, H L

1975-05-01

A 5-year-old girl with coarse facies, visceromegaly, and vacuolated lymphocytes is presented as the first case of aspartylglucosaminuria diagnosed in this country. This metabolic defect in glycoprotein catabolism can be clinically confused with other storage diseases such as the mucopolysaccharidoses and mucolipidoses. It is not diagnosed by routine laboratory screening methods. Special studies are required to confirm the diagnosis, but a thin-layer chromatography method for screening urine is presented for use when the diagnosis is suspected. The developmental potential in this inborn error of metabolism is documented.

Radio Frequency Identification (RFID) technology applied to the definition of underwater and subaerial coarse sediment movement

NASA Astrophysics Data System (ADS)

Bertoni, Duccio; Sarti, Giovanni; Benelli, Giuliano; Pozzebon, Alessandro; Raguseo, Gianluca

2010-07-01

In this paper, Radio Frequency Identification technology has been applied to track both underwater and subaerial displacement of pebbles along an artificial coarse beach at Marina di Pisa, Italy. Several preliminary laboratory tests have been performed to adapt the RFID technique for underwater use, which has been the primary impediment to this promising approach to the study of coarse sediment transport and movement. Tests showed the reliability of low frequencies for this kind of work, since they enable good signal transmission and reception through water. Passive ABS plastic transponders were inserted into about 100 pebbles and released onto the beach in March, 2009. A CORE-125 reader was chosen as the operating antenna to continuously transmit low frequency (125 kHz) signals. An acoustic signal toned whenever a pebble was detected while the unambiguous identification code of the pebble is shown immediately on the screen of a laptop connected to the reader. The positions of the pebbles were recorded with a total station. After two months (May, 2009), 74 marked pebbles were retrieved, 77% of the total. The positions of the retrieved pebbles were also recorded with the total station, thus allowing calculation of the coarse sediment transport tendency. About 60% of the recovered pebbles (44 out of 74) were found on the upper shoreface. The analysis of the marked pebble trajectories revealed a divergent transport movement in the northernmost sector of the beach. This movement was probably triggered by an irregularity of the submerged breakwater fronting the shoreline. The southern sector is characterised by chaotic pathways related to the formation and evolution of beach cusps. This outcome highlights and confirms the importance of a complete definition of the beach system, with no separation between the underwater and the subaerial portion of the shore when it comes to sediment transport and movement. This successful application of RFID technology to the underwater environment provides a chance to broaden understanding of a topic in need of further study.

Coarse graining for synchronization in directed networks

NASA Astrophysics Data System (ADS)

Zeng, An; Lü, Linyuan

2011-05-01

Coarse-graining model is a promising way to analyze and visualize large-scale networks. The coarse-grained networks are required to preserve statistical properties as well as the dynamic behaviors of the initial networks. Some methods have been proposed and found effective in undirected networks, while the study on coarse-graining directed networks lacks of consideration. In this paper we proposed a path-based coarse-graining (PCG) method to coarse grain the directed networks. Performing the linear stability analysis of synchronization and numerical simulation of the Kuramoto model on four kinds of directed networks, including tree networks and variants of Barabási-Albert networks, Watts-Strogatz networks, and Erdös-Rényi networks, we find our method can effectively preserve the network synchronizability.

Hyperactivity, unexplained speech delay, and coarse facies--is it Sanfilippo syndrome?

PubMed

Saini, Arushi Gahlot; Singhi, Pratibha; Sahu, Jitendra Kumar; Ganesan, Saptharishi L; Vyas, Sameer; Rao, Sandeep; Sachdeva, Man Updesh Singh

2014-08-01

Mucopolysaccharidosis-IIIB or Sanfilippo-B syndrome is caused by deficiency of lysosomal α-N-acetylglucosaminidase that leads to accumulation of heparan-sulphate and degeneration of central nervous system with progressive dementia, hyperactivity, and aggressive behavior. Mucopolysaccharidosis-III remains underdiagnosed as a cause of developmental delay and hyperactivity both in adults and children because in contrast to other mucopolysaccharidoses, they have little somatic disease, coarse facial features, hepatosplenomegaly or skeletal changes, and a high incidence of false-negative results on the urinary screening tests. We describe here a girl with the classic phenotype of mucopolysaccharidosis-IIIB to alert pediatricians to the possibility of this disorder in children with unexplained speech delay and hyperactivity and prevent unnecessary investigations. © The Author(s) 2013.

Multi-modality image registration for effective thermographic fever screening

NASA Astrophysics Data System (ADS)

Dwith, C. Y. N.; Ghassemi, Pejhman; Pfefer, Joshua; Casamento, Jon; Wang, Quanzeng

2017-02-01

Fever screening based on infrared thermographs (IRTs) is a viable mass screening approach during infectious disease pandemics, such as Ebola and Severe Acute Respiratory Syndrome (SARS), for temperature monitoring in public places like hospitals and airports. IRTs have been found to be powerful, quick and non-invasive methods for detecting elevated temperatures. Moreover, regions medially adjacent to the inner canthi (called the canthi regions in this paper) are preferred sites for fever screening. Accurate localization of the canthi regions can be achieved through multi-modality registration of infrared (IR) and white-light images. Here we propose a registration method through a coarse-fine registration strategy using different registration models based on landmarks and edge detection on eye contours. We have evaluated the registration accuracy to be within +/- 2.7 mm, which enables accurate localization of the canthi regions.

Coarse analysis of collective behaviors: Bifurcation analysis of the optimal velocity model for traffic jam formation

NASA Astrophysics Data System (ADS)

Miura, Yasunari; Sugiyama, Yuki

2017-12-01

We present a general method for analyzing macroscopic collective phenomena observed in many-body systems. For this purpose, we employ diffusion maps, which are one of the dimensionality-reduction techniques, and systematically define a few relevant coarse-grained variables for describing macroscopic phenomena. The time evolution of macroscopic behavior is described as a trajectory in the low-dimensional space constructed by these coarse variables. We apply this method to the analysis of the traffic model, called the optimal velocity model, and reveal a bifurcation structure, which features a transition to the emergence of a moving cluster as a traffic jam.

Debye screening of dislocations.

PubMed

Groma, I; Györgyi, G; Kocsis, B

2006-04-28

Debye-like screening by edge dislocations of some externally given stress is studied by means of a variational approach to coarse grained field theory. Explicitly given are the force field and the induced geometrically necessary dislocation (GND) distribution, in the special case of a single glide axis in 2D, for (i) a single edge dislocation and (ii) a dislocation wall. Numerical simulation demonstrates that the correlation in relaxed dislocation configurations is in good agreement with the induced GND in case (i). Furthermore, the result (ii) well predicts the experimentally observed decay length for the GND developing close to grain boundaries.

Single Particulate SEM-EDX Analysis of Iron-Containing Coarse Particulate Matter in an Urban Environment: Sources and Distribution of Iron within Cleveland, Ohio

EPA Science Inventory

The physicochemical properties of coarse-mode, iron-containing particles, and their temporal and spatial distributions are poorly understood. Single particle analysis combining x-ray elemental mapping and computer-controlled scanning electron microscopy (CCSEM-EDX) of passively ...

A Guide for Developing Standard Operating Job Procedures for the Sludge Thickening Process Wastewater Treatment Facility. SOJP No. 9.

ERIC Educational Resources Information Center

Schwing, Carl M.

This guide describes standard operating job procedures for the screening and grinding process of wastewater treatment facilities. The objective of this process is the removal of coarse materials from the raw waste stream for the protection of subsequent equipment and processes. The guide gives step-by-step instructions for safety inspection,…

Root-cause analysis of the better performance of the coarse-mesh finite-difference method for CANDU-type reactors

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

Shen, W.

2012-07-01

Recent assessment results indicate that the coarse-mesh finite-difference method (FDM) gives consistently smaller percent differences in channel powers than the fine-mesh FDM when compared to the reference MCNP solution for CANDU-type reactors. However, there is an impression that the fine-mesh FDM should always give more accurate results than the coarse-mesh FDM in theory. To answer the question if the better performance of the coarse-mesh FDM for CANDU-type reactors was just a coincidence (cancellation of errors) or caused by the use of heavy water or the use of lattice-homogenized cross sections for the cluster fuel geometry in the diffusion calculation, threemore » benchmark problems were set up with three different fuel lattices: CANDU, HWR and PWR. These benchmark problems were then used to analyze the root cause of the better performance of the coarse-mesh FDM for CANDU-type reactors. The analyses confirm that the better performance of the coarse-mesh FDM for CANDU-type reactors is mainly caused by the use of lattice-homogenized cross sections for the sub-meshes of the cluster fuel geometry in the diffusion calculation. Based on the analyses, it is recommended to use 2 x 2 coarse-mesh FDM to analyze CANDU-type reactors when lattice-homogenized cross sections are used in the core analysis. (authors)« less

Relation between aerosol sources and meteorological parameters for inhalable atmospheric particles in Sao Paulo City, Brazil

NASA Astrophysics Data System (ADS)

Andrade, Fatima; Orsini, Celso; Maenhaut, Willy

Stacked filter units were used to collect atmospheric particles in separate coarse and fine fractions at the Sao Paulo University Campus during the winter of 1989. The samples were analysed by particle-induced X-ray emission (PIXE) and the data were subjected to an absolute principal component analysis (APCA). Five sources were identified for the fine particles: industrial emissions, which accounted for 13% of the fine mass; emissions from residual oil and diesel, explaining 41%; resuspended soil dust, with 28%; and emissions of Cu and of Mg, together with 18%. For the coarse particles, four sources were identified: soil dust, accounting for 59% of the coarse mass; industrial emissions, with 19%; oil burning, with 8%; and sea salt aerosol, with 14% of the coarse mass. A data set with various meteorological parameters was also subjected to APCA, and a correlation analysis was performed between the meteorological "absolute principal component scores" (APCS) and the APCS from the fine and coarse particle data sets. The soil dust sources for the fine and coarse aerosol were highly correlated with each other and were anticorrelated with the sea breeze component. The industrial components in the fine and coarse size fractions were also highly positively correlated. Furthermore, the industrial component was related with the northeasterly wind direction and, to a lesser extent, with the sea breeze component.

Protein-protein interaction specificity is captured by contact preferences and interface composition.

PubMed

Nadalin, Francesca; Carbone, Alessandra

2018-02-01

Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair potential combining interface composition with residue-residue contact preference. CIPS outperforms several other methods on screening docking solutions obtained either with all-atom or with coarse-grain rigid docking. Further testing on 28 CAPRI targets corroborates CIPS predictive power over existing methods. By combining CIPS with atomic potentials, discrimination of correct conformations in all-atom structures reaches optimal accuracy. The drastic reduction of candidate solutions produced by thousands of proteins docked against each other makes large-scale docking accessible to analysis. CIPS source code is freely available at http://www.lcqb.upmc.fr/CIPS. alessandra.carbone@lip6.fr. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices.

PubMed

Lindsay, Richard J; Siess, Jan; Lohry, David P; McGee, Trevor S; Ritchie, Jordan S; Johnson, Quentin R; Shen, Tongye

2018-01-14

We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

NASA Astrophysics Data System (ADS)

Lindsay, Richard J.; Siess, Jan; Lohry, David P.; McGee, Trevor S.; Ritchie, Jordan S.; Johnson, Quentin R.; Shen, Tongye

2018-01-01

We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

Coarse-grained Mineral Dust Deposition in Alpine Lake Sediments: Implications for Regional Drought Patterns and Land-use Changes in the Southwest USA

NASA Astrophysics Data System (ADS)

Pedraza, A.; Kingsley, C.; Marchitto, T. M., Jr.; Lora, J. M.; Pollen, A.; Vollmer, T.; Leithold, E. L.; Mitchell, J.; Tripati, A. K.; Bhattacharya, A.

2017-12-01

Mineral dust accumulation is often causally associated with aridity. However, the relation might not be as straightforward. Consideration of grain sizes and geochemical fingerprinting of the coarse grain fraction will clearly have an impact on how we interpret the sedimentary record of mineral dust in depositional environments e.g. coarse grain fractions of mineral dust would most certainly be transported over relatively short distances and as such in depositional environments, the depositional rate of coarse grains must be determined in order to reliably understand erosional patterns associated with meteorological events (such as frequency of intense wind events such as tornadoes), climatological phenomenon (such as regional droughts) as well as more recently land-use changes. In this study we separate the two size fractions of mineral dust accumulation- fine fraction (typically <4 microns) and coarse fraction (typically >25 microns using grain size analysis from well-studied cores collected from several lake sites distributed across the western southwestern and the Great Plain regions; furthermore we use trace element analysis in each size fraction to identify contributing source regions. We find evidence that the coarser-grain size fraction in the studied lake cores could be of regional origin (and not just local in orgin);. the coarser fraction also appears to be related to intense meteorological events (i.e., the occurrence of cyclones). Analysis is underway to understand the impact of land-use changes on coarse grain fraction

The application and use of chemical space mapping to interpret crystallization screening results

PubMed Central

Snell, Edward H.; Nagel, Ray M.; Wojtaszcyk, Ann; O’Neill, Hugh; Wolfley, Jennifer L.; Luft, Joseph R.

2008-01-01

Macromolecular crystallization screening is an empirical process. It often begins by setting up experiments with a number of chemically diverse cocktails designed to sample chemical space known to promote crystallization. Where a potential crystal is seen a refined screen is set up, optimizing around that condition. By using an incomplete factorial sampling of chemical space to formulate the cocktails and presenting the results graphically, it is possible to readily identify trends relevant to crystallization, coarsely sample the phase diagram and help guide the optimization process. In this paper, chemical space mapping is applied to both single macromolecules and to a diverse set of macromolecules in order to illustrate how visual information is more readily understood and assimilated than the same information presented textually. PMID:19018100

The application and use of chemical space mapping to interpret crystallization screening results.

PubMed

Snell, Edward H; Nagel, Ray M; Wojtaszcyk, Ann; O'Neill, Hugh; Wolfley, Jennifer L; Luft, Joseph R

2008-12-01

Macromolecular crystallization screening is an empirical process. It often begins by setting up experiments with a number of chemically diverse cocktails designed to sample chemical space known to promote crystallization. Where a potential crystal is seen a refined screen is set up, optimizing around that condition. By using an incomplete factorial sampling of chemical space to formulate the cocktails and presenting the results graphically, it is possible to readily identify trends relevant to crystallization, coarsely sample the phase diagram and help guide the optimization process. In this paper, chemical space mapping is applied to both single macromolecules and to a diverse set of macromolecules in order to illustrate how visual information is more readily understood and assimilated than the same information presented textually.

Correlations between the Signal Complexity of Cerebral and Cardiac Electrical Activity: A Multiscale Entropy Analysis

PubMed Central

Lin, Pei-Feng; Lo, Men-Tzung; Tsao, Jenho; Chang, Yi-Chung; Lin, Chen; Ho, Yi-Lwun

2014-01-01

The heart begins to beat before the brain is formed. Whether conventional hierarchical central commands sent by the brain to the heart alone explain all the interplay between these two organs should be reconsidered. Here, we demonstrate correlations between the signal complexity of brain and cardiac activity. Eighty-seven geriatric outpatients with healthy hearts and varied cognitive abilities each provided a 24-hour electrocardiography (ECG) and a 19-channel eye-closed routine electroencephalography (EEG). Multiscale entropy (MSE) analysis was applied to three epochs (resting-awake state, photic stimulation of fast frequencies (fast-PS), and photic stimulation of slow frequencies (slow-PS)) of EEG in the 1–58 Hz frequency range, and three RR interval (RRI) time series (awake-state, sleep and that concomitant with the EEG) for each subject. The low-to-high frequency power (LF/HF) ratio of RRI was calculated to represent sympatho-vagal balance. With statistics after Bonferroni corrections, we found that: (a) the summed MSE value on coarse scales of the awake RRI (scales 11–20, RRI-MSE-coarse) were inversely correlated with the summed MSE value on coarse scales of the resting-awake EEG (scales 6–20, EEG-MSE-coarse) at Fp2, C4, T6 and T4; (b) the awake RRI-MSE-coarse was inversely correlated with the fast-PS EEG-MSE-coarse at O1, O2 and C4; (c) the sleep RRI-MSE-coarse was inversely correlated with the slow-PS EEG-MSE-coarse at Fp2; (d) the RRI-MSE-coarse and LF/HF ratio of the awake RRI were correlated positively to each other; (e) the EEG-MSE-coarse at F8 was proportional to the cognitive test score; (f) the results conform to the cholinergic hypothesis which states that cognitive impairment causes reduction in vagal cardiac modulation; (g) fast-PS significantly lowered the EEG-MSE-coarse globally. Whether these heart-brain correlations could be fully explained by the central autonomic network is unknown and needs further exploration. PMID:24498375

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....

Sediment transport processes in the Pearl River Estuary as revealed by grain-size end-member modeling and sediment trend analysis

NASA Astrophysics Data System (ADS)

Li, Tao; Li, Tuan-Jie

2018-04-01

The analysis of grain-size distribution enables us to decipher sediment transport processes and understand the causal relations between dynamic processes and grain-size distributions. In the present study, grain sizes were measured from surface sediments collected in the Pearl River Estuary and its adjacent coastal areas. End-member modeling analysis attempts to unmix the grain sizes into geologically meaningful populations. Six grain-size end-members were identified. Their dominant modes are 0 Φ, 1.5 Φ, 2.75 Φ, 4.5 Φ, 7 Φ, and 8 Φ, corresponding to coarse sand, medium sand, fine sand, very coarse silt, silt, and clay, respectively. The spatial distributions of the six end-members are influenced by sediment transport and depositional processes. The two coarsest end-members (coarse sand and medium sand) may reflect relict sediments deposited during the last glacial period. The fine sand end-member would be difficult to transport under fair weather conditions, and likely indicates storm deposits. The three remaining fine-grained end-members (very coarse silt, silt, and clay) are recognized as suspended particles transported by saltwater intrusion via the flood tidal current, the Guangdong Coastal Current, and riverine outflow. The grain-size trend analysis shows distinct transport patterns for the three fine-grained end-members. The landward transport of the very coarse silt end-member occurs in the eastern part of the estuary, the seaward transport of the silt end-member occurs in the western part, and the east-west transport of the clay end-member occurs in the coastal areas. The results show that grain-size end-member modeling analysis in combination with sediment trend analysis help to better understand sediment transport patterns and the associated transport mechanisms.

High-throughput single-molecule force spectroscopy for membrane proteins

NASA Astrophysics Data System (ADS)

Bosshart, Patrick D.; Casagrande, Fabio; Frederix, Patrick L. T. M.; Ratera, Merce; Bippes, Christian A.; Müller, Daniel J.; Palacin, Manuel; Engel, Andreas; Fotiadis, Dimitrios

2008-09-01

Atomic force microscopy-based single-molecule force spectroscopy (SMFS) is a powerful tool for studying the mechanical properties, intermolecular and intramolecular interactions, unfolding pathways, and energy landscapes of membrane proteins. One limiting factor for the large-scale applicability of SMFS on membrane proteins is its low efficiency in data acquisition. We have developed a semi-automated high-throughput SMFS (HT-SMFS) procedure for efficient data acquisition. In addition, we present a coarse filter to efficiently extract protein unfolding events from large data sets. The HT-SMFS procedure and the coarse filter were validated using the proton pump bacteriorhodopsin (BR) from Halobacterium salinarum and the L-arginine/agmatine antiporter AdiC from the bacterium Escherichia coli. To screen for molecular interactions between AdiC and its substrates, we recorded data sets in the absence and in the presence of L-arginine, D-arginine, and agmatine. Altogether ~400 000 force-distance curves were recorded. Application of coarse filtering to this wealth of data yielded six data sets with ~200 (AdiC) and ~400 (BR) force-distance spectra in each. Importantly, the raw data for most of these data sets were acquired in one to two days, opening new perspectives for HT-SMFS applications.

Size distributions of ambient air particles and enrichment factor analyses of metallic elements at Taichung Harbor near the Taiwan Strait

NASA Astrophysics Data System (ADS)

Fang, Guor-Cheng; Wu, Yuh-Shen; Chang, Shih-Yu; Huang, Shih-Han; Rau, Jui-Yeh

2006-10-01

This work attempts to characterize metallic elements associated with atmospheric particulate matter on a dry deposition plate, a TE-PUF high-volume air sampler and a universal air sampler. Dry deposition fluxes of particulates and concentrations of total suspended particulate, fine (PM 2.5) and coarse (PM 2.5-10) particulate matters were collected at Taichung harbor sampling sites from August 2004 to January 2005. Chemical analyses of metallic elements were made using a flame atomic absorption spectrophotometer coupled with hollow cathode lamps. Concentrations of metal elements in the forms of coarse particles and fine particles as well as the coarse/fine particulate ratios were presented. Statistical methods such as correlation analysis, principal component analysis and enrichment factor analysis were performed to compare the chemical components and identify possible emission sources at the sampling sites. Metallic elements of Cu, Zn, Pb, Cr, Ni and Mg had higher EF crust ratios in winter and spring than in summer and autumn. Diurnal and nocturnal variations of metallic element concentrations in fine and coarse particles were also discussed.

Optimal Parameter Design of Coarse Alignment for Fiber Optic Gyro Inertial Navigation System.

PubMed

Lu, Baofeng; Wang, Qiuying; Yu, Chunmei; Gao, Wei

2015-06-25

Two different coarse alignment algorithms for Fiber Optic Gyro (FOG) Inertial Navigation System (INS) based on inertial reference frame are discussed in this paper. Both of them are based on gravity vector integration, therefore, the performance of these algorithms is determined by integration time. In previous works, integration time is selected by experience. In order to give a criterion for the selection process, and make the selection of the integration time more accurate, optimal parameter design of these algorithms for FOG INS is performed in this paper. The design process is accomplished based on the analysis of the error characteristics of these two coarse alignment algorithms. Moreover, this analysis and optimal parameter design allow us to make an adequate selection of the most accurate algorithm for FOG INS according to the actual operational conditions. The analysis and simulation results show that the parameter provided by this work is the optimal value, and indicate that in different operational conditions, the coarse alignment algorithms adopted for FOG INS are different in order to achieve better performance. Lastly, the experiment results validate the effectiveness of the proposed algorithm.

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.

PubMed

Riniker, Sereina; van Gunsteren, Wilfred F

2011-02-28

The development of coarse-grained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the electrostatic interactions, however, fails to mimic important properties, e.g., the dielectric screening. Therefore, a coarse-grained model for water is proposed which treats the electrostatic interactions between clusters of water molecules explicitly. Five water molecules are embedded in a spherical CG bead consisting of two oppositely charged particles which represent a dipole. The bond connecting the two particles in a bead is unconstrained, which makes the model polarizable. Experimental and all-atom simulated data of liquid water at room temperature are used for parametrization of the model. The experimental density and the relative static dielectric permittivity were chosen as primary target properties. The model properties are compared with those obtained from experiment, from clusters of simple-point-charge water molecules of appropriate size in the liquid phase, and for other CG water models if available. The comparison shows that not all atomistic properties can be reproduced by a CG model, so properties of key importance have to be selected when coarse graining is applied. Yet, the CG model reproduces the key characteristics of liquid water while being computationally 1-2 orders of magnitude more efficient than standard fine-grained atomistic water models.

Contingency Pest Management Guide. 2010 Edition

DTIC Science & Technology

2010-08-01

indoors as a residual spray to walls, ceilings, window screens and other fly resting areas. Apply outside as a residual ...applications. Cypermethrin (Demon WP) 35.6% 6840-01-390-4822 LB 1 lb jar 1 packet/gal 0.1% Apply indoors as a residual spray to walls, ceilings... indoors as a coarse, low-pressure spray where pests are found. Apply outdoors as a residual spray to lawns, porches and similar areas. May not

Modeling nitrate at domestic and public-supply well depths in the Central Valley, California

USGS Publications Warehouse

Nolan, Bernard T.; Gronberg, JoAnn M.; Faunt, Claudia C.; Eberts, Sandra M.; Belitz, Ken

2014-01-01

Aquifer vulnerability models were developed to map groundwater nitrate concentration at domestic and public-supply well depths in the Central Valley, California. We compared three modeling methods for ability to predict nitrate concentration >4 mg/L: logistic regression (LR), random forest classification (RFC), and random forest regression (RFR). All three models indicated processes of nitrogen fertilizer input at the land surface, transmission through coarse-textured, well-drained soils, and transport in the aquifer to the well screen. The total percent correct predictions were similar among the three models (69–82%), but RFR had greater sensitivity (84% for shallow wells and 51% for deep wells). The results suggest that RFR can better identify areas with high nitrate concentration but that LR and RFC may better describe bulk conditions in the aquifer. A unique aspect of the modeling approach was inclusion of outputs from previous, physically based hydrologic and textural models as predictor variables, which were important to the models. Vertical water fluxes in the aquifer and percent coarse material above the well screen were ranked moderately high-to-high in the RFR models, and the average vertical water flux during the irrigation season was highly significant (p < 0.0001) in logistic regression.

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, Geophys. Res. Lett., 39, L20806, doi:10.1029/2012GL053469.

Development of a LC-MS/MS method for the simultaneous screening of seven water-soluble vitamins in processing semi-coarse wheat flour products.

PubMed

Nurit, Eric; Lyan, Bernard; Piquet, Agnès; Branlard, Gérard; Pujos-Guillot, Estelle

2015-05-01

Wheat is the second largest crop cultivated around the world and constitutes a major part of the daily diet in Europe. It is therefore important to determine the content of micronutrient in wheat and wheat-based food products to define the contribution of wheat-based foods to the nutrition of the consumers. The aim of the present work was to develop a simple and rapid method based on liquid chromatography tandem mass spectrometry (LC-MS/MS) for the simultaneous determination of seven water-soluble vitamins in various wheat-based food materials. The vitamins present in the test material were separated in less than 15 min by using a reverse-phase C18 column, and analyzed by positive ion electrospray selected reaction monitoring MS/MS. The MS response for all the vitamins was linear over the working range (0.05 to 9 μg/mL) with correlation coefficients ranging between 0.991 and 1. Limits of quantification in the different food materials ranged from 0.09 to 3.5 μg/g. Intra-day and inter-day precision were found satisfactory. The developed method was applied for the simultaneous analysis of the water-soluble vitamin natural content of different semi-coarse wheat flours and in their corresponding baking products.

An implicit divalent counterion force field for RNA molecular dynamics

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

Henke, Paul S.; Mak, Chi H., E-mail: cmak@usc.edu; Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089

How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg{sup 2+} screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grainedmore » models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.« less

Analysis Tools for CFD Multigrid Solvers

NASA Technical Reports Server (NTRS)

Mineck, Raymond E.; Thomas, James L.; Diskin, Boris

2004-01-01

Analysis tools are needed to guide the development and evaluate the performance of multigrid solvers for the fluid flow equations. Classical analysis tools, such as local mode analysis, often fail to accurately predict performance. Two-grid analysis tools, herein referred to as Idealized Coarse Grid and Idealized Relaxation iterations, have been developed and evaluated within a pilot multigrid solver. These new tools are applicable to general systems of equations and/or discretizations and point to problem areas within an existing multigrid solver. Idealized Relaxation and Idealized Coarse Grid are applied in developing textbook-efficient multigrid solvers for incompressible stagnation flow problems.

Understanding bulk behavior of particulate materials from particle scale simulations

NASA Astrophysics Data System (ADS)

Deng, Xiaoliang

Particulate materials play an increasingly significant role in various industries, such as pharmaceutical manufacturing, food, mining, and civil engineering. The objective of this research is to better understand bulk behaviors of particulate materials from particle scale simulations. Packing properties of assembly of particles are investigated first, focusing on the effects of particle size, surface energy, and aspect ratio on the coordination number, porosity, and packing structures. The simulation results show that particle sizes, surface energy, and aspect ratio all influence the porosity of packing to various degrees. The heterogeneous force networks within particle assembly under external compressive loading are investigated as well. The results show that coarse-coarse contacts dominate the strong network and coarse-fine contacts dominate the total network. Next, DEM models are developed to simulate the particle dynamics inside a conical screen mill (comil) and magnetically assisted impaction mixer (MAIM), both are important particle processing devices. For comil, the mean residence time (MRT), spatial distribution of particles, along with the collision dynamics between particles as well as particle and vessel geometries are examined as a function of the various operating parameters such as impeller speed, screen hole size, open area, and feed rate. The simulation results can help better understand dry coating experimental results using comil. For MAIM system, the magnetic force is incorporated into the contact model, allowing to describe the interactions between magnets. The simulation results reveal the connections between homogeneity of mixture and particle scale variables such as size of magnets and surface energy of non-magnets. In particular, at the fixed mass ratio of magnets to non-magnets and surface energy the smaller magnets lead to better homogeneity of mixing, which is in good agreement with previously published experimental results. Last but not least, numerical simulations, along with theoretical analysis, are performed to investigate the interparticle force of dry coated particles. A model is derived and can be used to predict the probabilities of hose-host (HH), host-guest (HG), and guest-guest (GG) contacts. The results indicate that there are three different regions dominated by HH, HG, and GG contacts, respectively. Moreover, the critical SAC for the transition of HG to GG contacts is lower than previously estimated value. In summary, particle packing, particle dynamics associated with various particle processing devices, and interparticle force of dry coated particles are investigated in this thesis. The results show that particle scale information such as coordination number, collision dynamics, and contact force between particles from simulation results can help better understand bulk properties of assembly of individual particles.

Estimating the acute health effects of coarse particulate matter accounting for exposure measurement error.

PubMed

Chang, Howard H; Peng, Roger D; Dominici, Francesca

2011-10-01

In air pollution epidemiology, there is a growing interest in estimating the health effects of coarse particulate matter (PM) with aerodynamic diameter between 2.5 and 10 μm. Coarse PM concentrations can exhibit considerable spatial heterogeneity because the particles travel shorter distances and do not remain suspended in the atmosphere for an extended period of time. In this paper, we develop a modeling approach for estimating the short-term effects of air pollution in time series analysis when the ambient concentrations vary spatially within the study region. Specifically, our approach quantifies the error in the exposure variable by characterizing, on any given day, the disagreement in ambient concentrations measured across monitoring stations. This is accomplished by viewing monitor-level measurements as error-prone repeated measurements of the unobserved population average exposure. Inference is carried out in a Bayesian framework to fully account for uncertainty in the estimation of model parameters. Finally, by using different exposure indicators, we investigate the sensitivity of the association between coarse PM and daily hospital admissions based on a recent national multisite time series analysis. Among Medicare enrollees from 59 US counties between the period 1999 and 2005, we find a consistent positive association between coarse PM and same-day admission for cardiovascular diseases.

Size-Differentiated Chemical Composition of Re-Suspended Soil Dust from the Desert Southwest United States

EPA Science Inventory

As part of the Desert Southwest Coarse Particulate Matter Study which characterized the composition of fine and coarse particulate matter in Pinal County, AZ, several source samples were collected from several different soil types to assist in source apportionment analysis of the...

Coarse and fine aerosol source apportionment in Rio de Janeiro, Brazil

NASA Astrophysics Data System (ADS)

Godoy, Maria Luiza D. P.; Godoy, José Marcus; Roldão, Luiz Alfredo; Soluri, Daniela S.; Donagemma, Raquel A.

The metropolitan area of Rio de Janeiro is one of the twenty biggest urban agglomerations in the world, with 11 million inhabitants in the metropolitan area, and has a high population density, with 1700 hab. km -2. For this aerosol source apportionment study, the atmospheric aerosol sampling was performed at ten sites distributed in different locations of the metropolitan area from September/2003 to December/2005, with sampling during 24 h on a weekly basis. Stacked filter units (SFU) were used to collect fine and coarse aerosol particles with a flow rate of 17 L min -1. In both size fractions trace elements were analyzed by Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) as well as water-soluble species by Ion-Chromatography (IC). Also gravimetric analysis and reflectance measurements provided aerosol mass and black carbon concentrations. Very good detection limits for up to 42 species were obtained. Mean annual PM 10 mass concentration ranged from 20 to 37 μg m -3, values that are within the Brazilian air quality standards. Receptor models such as principal factor analysis, cluster analysis and absolute principal factor analysis were applied in order to identify and quantify the aerosol sources. For fine and coarse modes, circa of 100% of the measured mass was quantitatively apportioned to relatively few identified aerosol sources. A very similar and consistent source apportionment was obtained for both fine and coarse modes for all 10 sampling sites. Soil dust is an important component, accounting for 22-72% and for 25-48% of the coarse and fine mass respectively. On the other hand, anthropogenic sources as vehicle traffic and oil combustion represent a relatively high contribution (52-75%) of the fine aerosol mass. The joint use of ICP-MS and IC analysis of species in aerosols has proven to be reliable and feasible for the analysis of large amount of samples, and the coupling with receptor models provided an excellent method for quantitative aerosol source apportionment in large urban areas.

Computationally Guided Design of Polymer Electrolytes for Battery Applications

NASA Astrophysics Data System (ADS)

Wang, Zhen-Gang; Webb, Michael; Savoie, Brett; Miller, Thomas

We develop an efficient computational framework for guiding the design of polymer electrolytes for Li battery applications. Short-times molecular dynamics (MD) simulations are employed to identify key structural and dynamic features in the solvation and motion of Li ions, such as the structure of the solvation shells, the spatial distribution of solvation sites, and the polymer segmental mobility. Comparative studies on six polyester-based polymers and polyethylene oxide (PEO) yield good agreement with experimental data on the ion conductivities, and reveal significant differences in the ion diffusion mechanism between PEO and the polyesters. The molecular insights from the MD simulations are used to build a chemically specific coarse-grained model in the spirit of the dynamic bond percolation model of Druger, Ratner and Nitzan. We apply this coarse-grained model to characterize Li ion diffusion in several existing and yet-to-be synthesized polyethers that differ by oxygen content and backbone stiffness. Good agreement is obtained between the predictions of the coarse-grained model and long-timescale atomistic MD simulations, thus providing validation of the model. Our study predicts higher Li ion diffusivity in poly(trimethylene oxide-alt-ethylene oxide) than in PEO. These results demonstrate the potential of this computational framework for rapid screening of new polymer electrolytes based on ion diffusivity.

Effects of coarse-graining on the scaling behavior of long-range correlated and anti-correlated signals.

PubMed

Xu, Yinlin; Ma, Qianli D Y; Schmitt, Daniel T; Bernaola-Galván, Pedro; Ivanov, Plamen Ch

2011-11-01

We investigate how various coarse-graining (signal quantization) methods affect the scaling properties of long-range power-law correlated and anti-correlated signals, quantified by the detrended fluctuation analysis. Specifically, for coarse-graining in the magnitude of a signal, we consider (i) the Floor, (ii) the Symmetry and (iii) the Centro-Symmetry coarse-graining methods. We find that for anti-correlated signals coarse-graining in the magnitude leads to a crossover to random behavior at large scales, and that with increasing the width of the coarse-graining partition interval Δ, this crossover moves to intermediate and small scales. In contrast, the scaling of positively correlated signals is less affected by the coarse-graining, with no observable changes when Δ < 1, while for Δ > 1 a crossover appears at small scales and moves to intermediate and large scales with increasing Δ. For very rough coarse-graining (Δ > 3) based on the Floor and Symmetry methods, the position of the crossover stabilizes, in contrast to the Centro-Symmetry method where the crossover continuously moves across scales and leads to a random behavior at all scales; thus indicating a much stronger effect of the Centro-Symmetry compared to the Floor and the Symmetry method. For coarse-graining in time, where data points are averaged in non-overlapping time windows, we find that the scaling for both anti-correlated and positively correlated signals is practically preserved. The results of our simulations are useful for the correct interpretation of the correlation and scaling properties of symbolic sequences.

Effects of coarse-graining on the scaling behavior of long-range correlated and anti-correlated signals

PubMed Central

Xu, Yinlin; Ma, Qianli D.Y.; Schmitt, Daniel T.; Bernaola-Galván, Pedro; Ivanov, Plamen Ch.

2014-01-01

We investigate how various coarse-graining (signal quantization) methods affect the scaling properties of long-range power-law correlated and anti-correlated signals, quantified by the detrended fluctuation analysis. Specifically, for coarse-graining in the magnitude of a signal, we consider (i) the Floor, (ii) the Symmetry and (iii) the Centro-Symmetry coarse-graining methods. We find that for anti-correlated signals coarse-graining in the magnitude leads to a crossover to random behavior at large scales, and that with increasing the width of the coarse-graining partition interval Δ, this crossover moves to intermediate and small scales. In contrast, the scaling of positively correlated signals is less affected by the coarse-graining, with no observable changes when Δ < 1, while for Δ > 1 a crossover appears at small scales and moves to intermediate and large scales with increasing Δ. For very rough coarse-graining (Δ > 3) based on the Floor and Symmetry methods, the position of the crossover stabilizes, in contrast to the Centro-Symmetry method where the crossover continuously moves across scales and leads to a random behavior at all scales; thus indicating a much stronger effect of the Centro-Symmetry compared to the Floor and the Symmetry method. For coarse-graining in time, where data points are averaged in non-overlapping time windows, we find that the scaling for both anti-correlated and positively correlated signals is practically preserved. The results of our simulations are useful for the correct interpretation of the correlation and scaling properties of symbolic sequences. PMID:25392599

Hydraulic tests with direct-push equipment

USGS Publications Warehouse

Butler, J.J.; Healey, J.M.; McCall, G.W.; Garnett, E.J.; Loheide, Steven P.

2002-01-01

The potential of direct-push technology for hydraulic characterization of saturated flow systems was investigated at a field site with a considerable degree of subsurface control. Direct-push installations were emplaced by attaching short lengths of screen (shielded and unshielded) to the bottom end of a tool string that was then advanced into the unconsolidated sediments. A series of constant-rate pumping tests were performed in a coarse sand and gravel aquifer using direct-push tool strings as observation wells. Very good agreement (within 4%) was found between hydraulic conductivity (K) estimates from direct-push installations and those from conventional wells. A program of slug tests was performed in direct-push installations using small-diameter adaptations of solid-slug and pneumatic methods. In a sandy silt interval of moderate hydraulic conductivity, K values from tests in a shielded screen tool were in excellent agreement (within 2%) with those from tests in a nearby well. In the coarse sand and gravel aquifer, K values were within 12% of those from multilevel slug tests at a nearby well. However, in the more permeable portions of the aquifer (K > 70 m/day), the smaller-diameter direct-push rods (0.016 m inner diameter [I.D.]) attenuated test responses, leading to an underprediction of K. In those conditions, use of larger-diameter rods (e.g., 0.038 m I.D.) is necessary to obtain K values representative of the formation. This investigation demonstrates that much valuable information can be obtained from hydraulic tests in direct-push installations. As with any type of hydraulic test, K estimates are critically dependent on use of appropriate emplacement and development procedures. In particular, driving an unshielded screen through a heterogeneous sequence will often lead to a buildup of low-K material that can be difficult to remove with standard development procedures.

Investigation of the milling capabilities of the F10 Fine Grind mill using Box-Behnken designs.

PubMed

Tan, Bernice Mei Jin; Tay, Justin Yong Soon; Wong, Poh Mun; Chan, Lai Wah; Heng, Paul Wan Sia

2015-01-01

Size reduction or milling of the active is often the first processing step in the design of a dosage form. The ability of a mill to convert coarse crystals into the target size and size distribution efficiently is highly desirable as the quality of the final pharmaceutical product after processing is often still dependent on the dimensional attributes of its component constituents. The F10 Fine Grind mill is a mechanical impact mill designed to produce unimodal mid-size particles by utilizing a single-pass two-stage size reduction process for fine grinding of raw materials needed in secondary processing. Box-Behnken designs were used to investigate the effects of various mill variables (impeller, blower and feeder speeds and screen aperture size) on the milling of coarse crystals. Response variables included the particle size parameters (D10, D50 and D90), span and milling rate. Milled particles in the size range of 5-200 μm, with D50 ranging from 15 to 60 μm, were produced. The impeller and feeder speeds were the most critical factors influencing the particle size and milling rate, respectively. Size distributions of milled particles were better described by their goodness-of-fit to a log-normal distribution (i.e. unimodality) rather than span. Milled particles with symmetrical unimodal distributions were obtained when the screen aperture size was close to the median diameter of coarse particles employed. The capacity for high throughput milling of particles to a mid-size range, which is intermediate between conventional mechanical impact mills and air jet mills, was demonstrated in the F10 mill. Prediction models from the Box-Behnken designs will aid in providing a better guide to the milling process and milled product characteristics. Copyright © 2014 Elsevier B.V. All rights reserved.

Corrosion Screening of EV31A Magnesium and Other Magnesium Alloys using Laboratory-Based Accelerated Corrosion and Electro-Chemical Methods

DTIC Science & Technology

2014-07-01

corrosion studies (16). A schematic of the SWAP process and example of the powder produced is included in figure 4. This alloy contains amounts of Al ...advanced powder -based alloy and ZAXE1711 (both from Japan) were produced using a Spinning Water Atomization Process (SWAP) to yield powder particles with...and ZAXE1711 Mg alloy powders and (b) morphology of coarse Mg alloy powder prepared by SWAP

Automatic classification techniques for type of sediment map from multibeam sonar data

NASA Astrophysics Data System (ADS)

Zakariya, R.; Abdullah, M. A.; Che Hasan, R.; Khalil, I.

2018-02-01

Sediment map can be important information for various applications such as oil drilling, environmental and pollution study. A study on sediment mapping was conducted at a natural reef (rock) in Pulau Payar using Sound Navigation and Ranging (SONAR) technology which is Multibeam Echosounder R2-Sonic. This study aims to determine sediment type by obtaining backscatter and bathymetry data from multibeam echosounder. Ground truth data were used to verify the classification produced. The method used to analyze ground truth samples consists of particle size analysis (PSA) and dry sieving methods. Different analysis being carried out due to different sizes of sediment sample obtained. The smaller size was analyzed using PSA with the brand CILAS while bigger size sediment was analyzed using sieve. For multibeam, data acquisition includes backscatter strength and bathymetry data were processed using QINSy, Qimera, and ArcGIS. This study shows the capability of multibeam data to differentiate the four types of sediments which are i) very coarse sand, ii) coarse sand, iii) very coarse silt and coarse silt. The accuracy was reported as 92.31% overall accuracy and 0.88 kappa coefficient.

A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores

PubMed Central

Yoo, Jejoong; Jackson, Meyer B.; Cui, Qiang

2013-01-01

To establish the validity of continuum mechanics models quantitatively for the analysis of membrane remodeling processes, we compare the shape and energies of the membrane fusion pore predicted by coarse-grained (MARTINI) and continuum mechanics models. The results at these distinct levels of resolution give surprisingly consistent descriptions for the shape of the fusion pore, and the deviation between the continuum and coarse-grained models becomes notable only when the radius of curvature approaches the thickness of a monolayer. Although slow relaxation beyond microseconds is observed in different perturbative simulations, the key structural features (e.g., dimension and shape of the fusion pore near the pore center) are consistent among independent simulations. These observations provide solid support for the use of coarse-grained and continuum models in the analysis of membrane remodeling. The combined coarse-grained and continuum analysis confirms the recent prediction of continuum models that the fusion pore is a metastable structure and that its optimal shape is neither toroidal nor catenoidal. Moreover, our results help reveal a new, to our knowledge, bowing feature in which the bilayers close to the pore axis separate more from one another than those at greater distances from the pore axis; bowing helps reduce the curvature and therefore stabilizes the fusion pore structure. The spread of the bilayer deformations over distances of hundreds of nanometers and the substantial reduction in energy of fusion pore formation provided by this spread indicate that membrane fusion can be enhanced by allowing a larger area of membrane to participate and be deformed. PMID:23442963

Orbitals for classical arbitrary anisotropic colloidal potentials

NASA Astrophysics Data System (ADS)

Girard, Martin; Nguyen, Trung Dac; de la Cruz, Monica Olvera

2017-11-01

Coarse-grained potentials are ubiquitous in mesoscale simulations. While various methods to compute effective interactions for spherically symmetric particles exist, anisotropic interactions are seldom used, due to their complexity. Here we describe a general formulation, based on a spatial decomposition of the density fields around the particles, akin to atomic orbitals. We show that anisotropic potentials can be efficiently computed in numerical simulations using Fourier-based methods. We validate the field formulation and characterize its computational efficiency with a system of colloids that have Gaussian surface charge distributions. We also investigate the phase behavior of charged Janus colloids immersed in screened media, with screening lengths comparable to the colloid size. The system shows rich behaviors, exhibiting vapor, liquid, gel, and crystalline morphologies, depending on temperature and screening length. The crystalline phase only appears for symmetric Janus particles. For very short screening lengths, the system undergoes a direct transition from a vapor to a crystal on cooling; while, for longer screening lengths, a vapor-liquid-crystal transition is observed. The proposed formulation can be extended to model force fields that are time or orientation dependent, such as those in systems of polymer-grafted particles and magnetic colloids.

Cyclic hardening behavior of extruded ZK60 magnesium alloy with different grain sizes

NASA Astrophysics Data System (ADS)

Zhang, Lixin; Zhang, Wencong; Chen, Wenzhen; Wang, Wenke

2018-04-01

Montonic and fully reversed strain-controlled cyclic deformation experiments were conducted on extruded ZK60 magnesium alloy with two different grain sizes in ambient air. Results revealed that the hardening rates of the ZK60 magnesium alloy rods with fine grain and coarse grain in the monotonic deformation and the fully reversed strain-controlled cyclic deformation were opposite along the extrusion direction. Electron Backscatter Diffration analysis revealed that fine grains were more easily rotated than coarse grains under the cyclic deformation. Under the twinning and detwinning process of the cyclic deformation at a large strain amplitude, the coarse grained ZK60 magnesium alloys were more prone to tension twinning {10-12}<10-11> and more residual twins were observed. Texture hardening of coarse grained magnesium alloy was more obvious in cyclic defromation than fine-grained magnesium alloy.

Diagrammatic analysis of correlations in polymer fluids: Cluster diagrams via Edwards' field theory

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

Morse, David C.

2006-10-15

Edwards' functional integral approach to the statistical mechanics of polymer liquids is amenable to a diagrammatic analysis in which free energies and correlation functions are expanded as infinite sums of Feynman diagrams. This analysis is shown to lead naturally to a perturbative cluster expansion that is closely related to the Mayer cluster expansion developed for molecular liquids by Chandler and co-workers. Expansion of the functional integral representation of the grand-canonical partition function yields a perturbation theory in which all quantities of interest are expressed as functionals of a monomer-monomer pair potential, as functionals of intramolecular correlation functions of non-interacting molecules,more » and as functions of molecular activities. In different variants of the theory, the pair potential may be either a bare or a screened potential. A series of topological reductions yields a renormalized diagrammatic expansion in which collective correlation functions are instead expressed diagrammatically as functionals of the true single-molecule correlation functions in the interacting fluid, and as functions of molecular number density. Similar renormalized expansions are also obtained for a collective Ornstein-Zernicke direct correlation function, and for intramolecular correlation functions. A concise discussion is given of the corresponding Mayer cluster expansion, and of the relationship between the Mayer and perturbative cluster expansions for liquids of flexible molecules. The application of the perturbative cluster expansion to coarse-grained models of dense multi-component polymer liquids is discussed, and a justification is given for the use of a loop expansion. As an example, the formalism is used to derive a new expression for the wave-number dependent direct correlation function and recover known expressions for the intramolecular two-point correlation function to first-order in a renormalized loop expansion for coarse-grained models of binary homopolymer blends and diblock copolymer melts.« less

Emergent space-time via a geometric renormalization method

NASA Astrophysics Data System (ADS)

Rastgoo, Saeed; Requardt, Manfred

2016-12-01

We present a purely geometric renormalization scheme for metric spaces (including uncolored graphs), which consists of a coarse graining and a rescaling operation on such spaces. The coarse graining is based on the concept of quasi-isometry, which yields a sequence of discrete coarse grained spaces each having a continuum limit under the rescaling operation. We provide criteria under which such sequences do converge within a superspace of metric spaces, or may constitute the basin of attraction of a common continuum limit, which hopefully may represent our space-time continuum. We discuss some of the properties of these coarse grained spaces as well as their continuum limits, such as scale invariance and metric similarity, and show that different layers of space-time can carry different distance functions while being homeomorphic. Important tools in this analysis are the Gromov-Hausdorff distance functional for general metric spaces and the growth degree of graphs or networks. The whole construction is in the spirit of the Wilsonian renormalization group (RG). Furthermore, we introduce a physically relevant notion of dimension on the spaces of interest in our analysis, which, e.g., for regular lattices reduces to the ordinary lattice dimension. We show that this dimension is stable under the proposed coarse graining procedure as long as the latter is sufficiently local, i.e., quasi-isometric, and discuss the conditions under which this dimension is an integer. We comment on the possibility that the limit space may turn out to be fractal in case the dimension is noninteger. At the end of the paper we briefly mention the possibility that our network carries a translocal far order that leads to the concept of wormhole spaces and a scale dependent dimension if the coarse graining procedure is no longer local.

Mapping of species richness for conservation of biological diversity: conceptual and methodological issues

Treesearch

M.J. Conroy; B.R. Noon

1996-01-01

Biodiversity mapping (e.g., the Gap Analysis Program [GAP]), in which vegetative features and categories of land use are mapped at coarse spatial scales, has been proposed as a reliable tool for land use decisions (e.g., reserve identification, selection, and design). This implicitly assumes that species richness data collected at coarse spatiotemporal scales provide a...

Quantum decimation in Hilbert space: Coarse graining without structure

NASA Astrophysics Data System (ADS)

Singh, Ashmeet; Carroll, Sean M.

2018-03-01

We present a technique to coarse grain quantum states in a finite-dimensional Hilbert space. Our method is distinguished from other approaches by not relying on structures such as a preferred factorization of Hilbert space or a preferred set of operators (local or otherwise) in an associated algebra. Rather, we use the data corresponding to a given set of states, either specified independently or constructed from a single state evolving in time. Our technique is based on principle component analysis (PCA), and the resulting coarse-grained quantum states live in a lower-dimensional Hilbert space whose basis is defined using the underlying (isometric embedding) transformation of the set of fine-grained states we wish to coarse grain. Physically, the transformation can be interpreted to be an "entanglement coarse-graining" scheme that retains most of the global, useful entanglement structure of each state, while needing fewer degrees of freedom for its reconstruction. This scheme could be useful for efficiently describing collections of states whose number is much smaller than the dimension of Hilbert space, or a single state evolving over time.

Plutonium isotopes offer an alternative approach to establishing chronological profiles in coarse sediments

NASA Astrophysics Data System (ADS)

Pondell, C.; Kuehl, S. A.; Canuel, E. A.

2016-12-01

There are several methodologies used to determine chronologies for sediments deposited within the past 100 years, including 210Pb and 137Cs radioisotopes and organic and inorganic contaminants. These techniques are quite effective in fine sediments, which generally have a high affinity for metals and organic compounds. However, the application of these chronological tools becomes limited in systems where coarse sediments accumulate. Englebright Lake is an impoundment in northern California where sediment accumulation is characterized by a combination of fine and coarse sediments. This combination of sediment grain size complicated chronological analysis using the more traditional 137Cs chronological approach. This study established a chronology of these sediments using 239+240Pu isotopes. While most of the 249+240Pu activity was measured in the fine grain size fraction (<63 microns), up to 25% of the plutonium activity was detected in the coarse size fractions of sediments from Englebright Lake. Profiles of 239+240Pu were similar to available 137Cs profiles, verifying the application of plutonium isotopes for determining sediment chronologies and expanding the established geochronology for Englebright Lake sediments. This study of sediment accumulation in Englebright Lake demonstrates the application of plutonium isotopes in establishing chronologies in coarse sediments and highlights the potential for plutonium to offer new insights into patterns of coarse sediment accumulation.

High efficiency virtual impactor

DOEpatents

Loo, Billy W.

1981-01-01

Environmental monitoring of atmospheric air is facilitated by a single stage virtual impactor (11) for separating an inlet flow (Q.sub.O) having particulate contaminants into a coarse particle flow (Q.sub.1) and a fine particle flow (Q.sub.2) to enable collection of such particles on different filters (19a, 19b) for separate analysis. An inlet particle acceleration nozzle (28) and coarse particle collection probe member (37) having a virtual impaction opening (41) are aligned along a single axis (13) and spaced apart to define a flow separation region (14) at which the fine particle flow (Q.sub.2) is drawn radially outward into a chamber (21) while the coarse particle flow (Q.sub.1) enters the virtual impaction opening (41). Symmetrical outlet means (47) for the chamber (21) provide flow symmetry at the separation region (14) to assure precise separation of particles about a cutpoint size and to minimize losses by wall impaction and gravitational settling. Impulse defocusing means (42) in the probe member (37) provides uniform coarse particle deposition on the filter (19a) to aid analysis. Particle losses of less than 1% for particles in the 0 to 20 micron range may be realized.

High efficiency virtual impactor

DOEpatents

Loo, B.W.

1980-03-27

Environmental monitoring of atmospheric air is facilitated by a single stage virtual impactor for separating an inlet flow (Q/sub 0/) having particulate contaminants into a coarse particle flow (Q/sub 1/) and a fine particle flow (Q/sub 2/) to enable collection of such particles on different filters for separate analysis. An inlet particle acceleration nozzle and coarse particle collection probe member having a virtual impaction opening are aligned along a single axis and spaced apart to define a flow separation region at which the fine particle flow (Q/sub 2/) is drawn radially outward into a chamber while the coarse particle flow (Q/sub 1/) enters the virtual impaction opening.

Absorption fluids data survey

NASA Astrophysics Data System (ADS)

Macriss, R. A.; Zawacki, T. S.

Development of improved data for the thermodynamic, transport and physical properties of absorption fluids were studied. A specific objective of this phase of the study is to compile, catalog and coarse screen the available US data of known absorption fluid systems and publish it as a first edition document to be distributed to manufacturers, researchers and others active in absorption heat pump activities. The methodology and findings of the compilation, cataloguing and coarse screening of the available US data on absorption fluid properties and presents current status and future work on this project are summarized. Both in house file and literature searches were undertaken to obtain available US publications with pertinent physical, thermodynamic and transport properties data for absorption fluids. Cross checks of literature searches were also made, using available published bibliographies and literature review articles, to eliminate secondary sources for the data and include only original sources and manuscripts. The properties of these fluids relate to the liquid and/or vapor state, as encountered in normal operation of absorption equipment employing such fluids, and to the crystallization boundary of the liquid phase, where applicable. The actual data were systematically classified according to the type of fluid and property, as well as temperature, pressure and concentration ranges over which data were available. Data were sought for 14 different properties: Vapor-Liquid Equilibria, Crystallization Temperature, Corrosion Characteristics, Heat of Mixing, Liquid-Phase-Densities, Vapor-Liquid-Phase Enthalpies, Specific Heat, Stability, Viscosity, Mass Transfer Rate, Heat Transfer Rate, Thermal Conductivity, Flammability, and Toxicity.

Adiabatic coarse-graining and simulations of stochastic biochemical networks

PubMed Central

Sinitsyn, N. A.; Hengartner, Nicolas; Nemenman, Ilya

2009-01-01

We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian fluctuations of the slow ones. Our approach is similar to the Born–Oppenheimer approximation in quantum mechanics and 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 high-accuracy, low-complexity coarse-grained numerical simulations. 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 agree, but the former is 3 orders of magnitude faster. PMID:19525397

An assessment of the impact of FIA's default assumptions on the estimates of coarse woody debris volume and biomass

Treesearch

Vicente J. Monleon

2009-01-01

Currently, Forest Inventory and Analysis estimation procedures use Smalian's formula to compute coarse woody debris (CWD) volume and assume that logs lie horizontally on the ground. In this paper, the impact of those assumptions on volume and biomass estimates is assessed using 7 years of Oregon's Phase 2 data. Estimates of log volume computed using Smalian...

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.

Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation.

PubMed

Erban, Radek; Kevrekidis, Ioannis G; Adalsteinsson, David; Elston, Timothy C

2006-02-28

We present computer-assisted methods for analyzing stochastic models of gene regulatory networks. The main idea that underlies this equation-free analysis is the design and execution of appropriately initialized short bursts of stochastic simulations; the results of these are processed to estimate coarse-grained quantities of interest, such as mesoscopic transport coefficients. In particular, using a simple model of a genetic toggle switch, we illustrate the computation of an effective free energy Phi and of a state-dependent effective diffusion coefficient D that characterize an unavailable effective Fokker-Planck equation. Additionally we illustrate the linking of equation-free techniques with continuation methods for performing a form of stochastic "bifurcation analysis"; estimation of mean switching times in the case of a bistable switch is also implemented in this equation-free context. The accuracy of our methods is tested by direct comparison with long-time stochastic simulations. This type of equation-free analysis appears to be a promising approach to computing features of the long-time, coarse-grained behavior of certain classes of complex stochastic models of gene regulatory networks, circumventing the need for long Monte Carlo simulations.

Nanoindentation testing as a powerful screening tool for assessing phase stability of nanocrystalline high-entropy alloys

DOE PAGES

Maier-Kiener, Verena; Schuh, Benjamin; George, Easo P.; ...

2016-11-19

The equiatomic high-entropy alloy (HEA), CrMnFeCoNi, has recently been shown to be microstructurally unstable, resulting in a multi-phase microstructure after intermediate-temperature annealing treatments. The decomposition occurs rapidly in the nanocrystalline (NC) state and after longer annealing times in coarse-grained states. To characterize the mechanical properties of differently annealed NC states containing multiple phases, nanoindentation was used in this paper. The results revealed besides drastic changes in hardness, also for the first time significant changes in the Young's modulus and strain rate sensitivity. Finally, nanoindentation of NC HEAs is, therefore, a useful complementary screening tool with high potential as a highmore » throughput approach to detect phase decomposition, which can also be used to qualitatively predict the long-term stability of single-phase HEAs.« less

Electrostatic beneficiation of ores on the moon surface

NASA Technical Reports Server (NTRS)

Inculet, I. I.; Criswell, D. R.

1979-01-01

The feasibility of the electrostatic beneficiation of lunar ores is studied. It is shown that the lunar environment with its sustained high vacuum, low temperature, and low acceleration of gravity, is suitable for the use of the electrostatic technique with magnetic as well as nonmagnetic ores. Only an initial coarse screening will be required prior to processing, as the lunar soil is already in fine particulate form. The low temperature and the absence of water suggest the use of tribo-electrification for the electric charging of lunar soils.

Optical characteristics of fine and coarse particulates at Grand Canyon, Arizona

NASA Astrophysics Data System (ADS)

Malm, William C.; Johnson, Christopher E.

The relationship between airborne particulate matter and atmospheric light extinction was examined using the multivariate techniques of principal component analysis and multiple linear regression on data gathered at the Grand Canyon, Arizona, from December 1979 to November 1981. Results showed that, on the average, fine sulfates were most strongly associated with light attenuation in the atmosphere. Other fine mass (nitrates, organics, soot and carbonaceous material) and coarse mass (primarily windblown dust) were much less associated with atmospheric extinction. Fine sulfate mass at the Grand Canyon was responsible for 63% of atmospheric light extinction while other fine mass and coarse mass were responsible for 17 and 20% of atmospheric extinction, respectively.

Accurate reconstruction of 3D cardiac geometry from coarsely-sliced MRI.

PubMed

Ringenberg, Jordan; Deo, Makarand; Devabhaktuni, Vijay; Berenfeld, Omer; Snyder, Brett; Boyers, Pamela; Gold, Jeffrey

2014-02-01

We present a comprehensive validation analysis to assess the geometric impact of using coarsely-sliced short-axis images to reconstruct patient-specific cardiac geometry. The methods utilize high-resolution diffusion tensor MRI (DTMRI) datasets as reference geometries from which synthesized coarsely-sliced datasets simulating in vivo MRI were produced. 3D models are reconstructed from the coarse data using variational implicit surfaces through a commonly used modeling tool, CardioViz3D. The resulting geometries were then compared to the reference DTMRI models from which they were derived to analyze how well the synthesized geometries approximate the reference anatomy. Averaged over seven hearts, 95% spatial overlap, less than 3% volume variability, and normal-to-surface distance of 0.32 mm was observed between the synthesized myocardial geometries reconstructed from 8 mm sliced images and the reference data. The results provide strong supportive evidence to validate the hypothesis that coarsely-sliced MRI may be used to accurately reconstruct geometric ventricular models. Furthermore, the use of DTMRI for validation of in vivo MRI presents a novel benchmark procedure for studies which aim to substantiate their modeling and simulation methods using coarsely-sliced cardiac data. In addition, the paper outlines a suggested original procedure for deriving image-based ventricular models using the CardioViz3D software. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Multidisciplinary Optimization Methods for Aircraft Preliminary Design

NASA Technical Reports Server (NTRS)

Kroo, Ilan; Altus, Steve; Braun, Robert; Gage, Peter; Sobieski, Ian

1994-01-01

This paper describes a research program aimed at improved methods for multidisciplinary design and optimization of large-scale aeronautical systems. The research involves new approaches to system decomposition, interdisciplinary communication, and methods of exploiting coarse-grained parallelism for analysis and optimization. A new architecture, that involves a tight coupling between optimization and analysis, is intended to improve efficiency while simplifying the structure of multidisciplinary, computation-intensive design problems involving many analysis disciplines and perhaps hundreds of design variables. Work in two areas is described here: system decomposition using compatibility constraints to simplify the analysis structure and take advantage of coarse-grained parallelism; and collaborative optimization, a decomposition of the optimization process to permit parallel design and to simplify interdisciplinary communication requirements.

Mechanical behavior of a Y-TZP ceramic for monolithic restorations: effect of grinding and low-temperature aging.

PubMed

Pereira, G K R; Silvestri, T; Camargo, R; Rippe, M P; Amaral, M; Kleverlaan, C J; Valandro, L F

2016-06-01

This study aimed to investigate the effects of grinding with diamond burs and low-temperature aging on the mechanical behavior (biaxial flexural strength and structural reliability), surface topography, and phase transformation of a Y-TZP ceramic for monolithic dental restorations. Disc-shaped specimens (Zirlux FC, Ivoclar Vivadent) were manufactured according to ISO 6872 (2008) and divided in accordance with two factors: "grinding - 3 levels" and "LTD - 2 levels". Grinding was performed using a contra-angle handpiece under constant water-cooling with different grit-sizes (extra-fine and coarse diamond burs). LTD was simulated in an autoclave at 134°C, under a pressure of 2 bar, over a period of 20h. Surface topography analysis showed an increase in roughness based on surface treatment grit-size (Coarse>Xfine>Ctrl), LTD did not influence roughness values. Both grinding and LTD promoted an increase in the amount of m-phase, although different susceptibilities to degradation were observed. According to existing literature the increase of m-phase content is a direct indicative of Y-TZP degradation. Weibull analysis showed an increase in characteristic strength after grinding (Coarse=Xfine>Ctrl), while for LTD, distinct effects were observed (Ctrl

Mapping Forest Fuels through Vegetation Phenology: The Role of Coarse-Resolution Satellite Time-Series

PubMed Central

Bajocco, Sofia; Dragoz, Eleni; Gitas, Ioannis; Smiraglia, Daniela; Salvati, Luca; Ricotta, Carlo

2015-01-01

Traditionally fuel maps are built in terms of ‘fuel types’, thus considering the structural characteristics of vegetation only. The aim of this work is to derive a phenological fuel map based on the functional attributes of coarse-scale vegetation phenology, such as seasonality and productivity. MODIS NDVI 250m images of Sardinia (Italy), a large Mediterranean island with high frequency of fire incidence, were acquired for the period 2000–2012 to construct a mean annual NDVI profile of the vegetation at the pixel-level. Next, the following procedure was used to develop the phenological fuel map: (i) image segmentation on the Fourier components of the NDVI profiles to identify phenologically homogeneous landscape units, (ii) cluster analysis of the phenological units and post-hoc analysis of the fire-proneness of the phenological fuel classes (PFCs) obtained, (iii) environmental characterization (in terms of land cover and climate) of the PFCs. Our results showed the ability of coarse-resolution satellite time-series to characterize the fire-proneness of Sardinia with an adequate level of accuracy. The remotely sensed phenological framework presented may represent a suitable basis for the development of fire distribution prediction models, coarse-scale fuel maps and for various biogeographic studies. PMID:25822505

Effect of aggregate graining compositions on skid resistance of Exposed Aggregate Concrete pavement

NASA Astrophysics Data System (ADS)

Wasilewska, Marta; Gardziejczyk, Wladysław; Gierasimiuk, Pawel

2018-05-01

The paper presents the evaluation of skid resistance of EAC (Exposed Aggregate Concrete) pavements which differ in aggregate graining compositions. The tests were carried out on concrete mixes with a maximum aggregate size of 8 mm. Three types of coarse aggregates were selected depending on their resistance to polishing which was determined on the basis of the PSV (Polished Stone Value). Basalt (PSV 48), gabbro (PSV 50) and trachybasalt (PSV 52) aggregates were chosen. For each type of aggregate three graining compositions were designed, which differed in the content of coarse aggregate > 4mm. Their content for each series was as follows: A - 38%, B - 50% and C - 68%. Evaluation of the skid resistance has been performed using the FAP (Friction After Polishing) test equipment also known as the Wehner/Schulze machine. Laboratory method enables to compare the skid resistance of different types of wearing course under specified conditions simulating polishing processes. In addition, macrotexture measurements were made on the surface of each specimen using the Elatexure laser profile. Analysis of variance showed that at significance level α = 0.05, aggregate graining compositions as well as the PSV have a significant influence on the obtained values of the friction coefficient μm of the tested EAC pavements. The highest values of the μm have been obtained for EAC with the lowest amount of coarse aggregates (compositions A). In these cases the resistance to polishing of the aggregate does not significantly affect the friction coefficients. This is related to the large areas of cement mortar between the exposed coarse grains. Based on the analysis of microscope images, it was observed that the coarse aggregates were not sufficiently exposed. It has been proved that PSV significantly affected the coefficient of friction in the case of compositions B and C. This is caused by large areas of exposed coarse aggregate. The best parameters were achieved for the EAC pavements with graining composition B and C and trachybasalt aggregate.

Optical techniques: using coarse and detailed scans for the preventive acquisition of fingerprints with chromatic white-light sensors

NASA Astrophysics Data System (ADS)

Hildebrandt, Mario; Dittmann, Jana; Vielhauer, Claus; Leich, Marcus

2011-11-01

The preventive application of automated latent fingerprint acquisition devices can enhance the Homeland Defence, e.g. by improving the border security. Here, contact-less optical acquisition techniques for the capture of traces are subject to research; chromatic white light sensors allow for multi-mode operation using coarse or detailed scans. The presence of potential fingerprints could be detected using fast coarse scans. Those Regions-of- Interest can be acquired afterwards with high-resolution detailed scans to allow for a verification or identification of individuals. An acquisition and analysis of fingerprint traces on different objects that are imported or pass borders might be a great enhancement for security. Additionally, if suspicious objects require a further investigation, an initial securing of potential fingerprints could be very useful. In this paper we show current research results for the coarse detection of fingerprints to prepare the detailed acquisition from various surface materials that are relevant for preventive applications.

Effects of microstructural variation on Charpy impact properties in heavy-section Mn-Mo-Ni low alloy steel for reactor pressure vessel

NASA Astrophysics Data System (ADS)

Hong, Seokmin; Song, Jaemin; Kim, Min-Chul; Choi, Kwon-Jae; Lee, Bong-Sang

2016-03-01

The effects of microstructural changes in heavy-section Mn-Mo-Ni low alloy steel on Charpy impact properties were investigated using a 210 mm thick reactor pressure vessel. Specimens were sampled from 5 different positions at intervals of 1/4 thickness from the inner surface to the outer surface. A detailed microstructural analysis of impact-fractured specimens showed that coarse carbides along the lath boundaries acted as fracture initiation sites, and cleavage cracks deviated at prior-austenite grain boundaries and bainite lath boundaries. Upper shelf energy was higher and energy transition temperature was lower at the surface positon, where fine bainitic microstructure with homogeneously distributed fine carbides were present. Toward the center, coarse upper bainite and precipitation of coarse inter-lath carbides were observed, which deteriorated impact properties. At the 1/4T position, the Charpy impact properties were worse than those at other positions owing to the combination of elongated-coarse inter-lath carbides and large effective grain size.

A unified data representation theory for network visualization, ordering and coarse-graining

PubMed Central

Kovács, István A.; Mizsei, Réka; Csermely, Péter

2015-01-01

Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of extensive data sets, by revealing the large-scale structure of complex networks in a comprehensible form. PMID:26348923

A Factorial Design Approach to Analyse the Effect of Coarse Recycled Concrete Aggregates on the Properties of Hot Mix Asphalt

NASA Astrophysics Data System (ADS)

Tanty, Kiranbala; Mukharjee, Bibhuti Bhusan; Das, Sudhanshu Shekhar

2018-06-01

The present study investigates the effect of replacement of coarse fraction of natural aggregates by recycled concrete aggregates on the properties of hot mix asphalt (HMA) using general factorial design approach. For this two factors i.e. recycled coarse aggregates percentage [RCA (%)] and bitumen content percentage [BC (%)] are considered. Tests have been carried out on the HMA type bituminous concrete, prepared with varying RCA (%) and BC (%). Analysis of variance has been performed on the experimental data to determine the effect of the chosen factors on various parameters such as stability, flow, air void, void mineral aggregate, void filled with bitumen and bulk density. The study depicts that RCA (%) and BC (%) have significant effect on the selected responses as p value is less than the chosen significance level. In addition to above, the outcomes of the statistical analysis indicate that interaction between factors have significant effects on void mineral aggregate and bulk density of bituminous concrete.

A Factorial Design Approach to Analyse the Effect of Coarse Recycled Concrete Aggregates on the Properties of Hot Mix Asphalt

NASA Astrophysics Data System (ADS)

Tanty, Kiranbala; Mukharjee, Bibhuti Bhusan; Das, Sudhanshu Shekhar

2018-02-01

The present study investigates the effect of replacement of coarse fraction of natural aggregates by recycled concrete aggregates on the properties of hot mix asphalt (HMA) using general factorial design approach. For this two factors i.e. recycled coarse aggregates percentage [RCA (%)] and bitumen content percentage [BC (%)] are considered. Tests have been carried out on the HMA type bituminous concrete, prepared with varying RCA (%) and BC (%). Analysis of variance has been performed on the experimental data to determine the effect of the chosen factors on various parameters such as stability, flow, air void, void mineral aggregate, void filled with bitumen and bulk density. The study depicts that RCA (%) and BC (%) have significant effect on the selected responses as p value is less than the chosen significance level. In addition to above, the outcomes of the statistical analysis indicate that interaction between factors have significant effects on void mineral aggregate and bulk density of bituminous concrete.

Relationship between the Decomposition Process of Coarse Woody Debris and Fungal Community Structure as Detected by High-Throughput Sequencing in a Deciduous Broad-Leaved Forest in Japan

PubMed Central

Yamashita, Satoshi; Masuya, Hayato; Abe, Shin; Masaki, Takashi; Okabe, Kimiko

2015-01-01

We examined the relationship between the community structure of wood-decaying fungi, detected by high-throughput sequencing, and the decomposition rate using 13 years of data from a forest dynamics plot. For molecular analysis and wood density measurements, drill dust samples were collected from logs and stumps of Fagus and Quercus in the plot. Regression using a negative exponential model between wood density and time since death revealed that the decomposition rate of Fagus was greater than that of Quercus. The residual between the expected value obtained from the regression curve and the observed wood density was used as a decomposition rate index. Principal component analysis showed that the fungal community compositions of both Fagus and Quercus changed with time since death. Principal component analysis axis scores were used as an index of fungal community composition. A structural equation model for each wood genus was used to assess the effect of fungal community structure traits on the decomposition rate and how the fungal community structure was determined by the traits of coarse woody debris. Results of the structural equation model suggested that the decomposition rate of Fagus was affected by two fungal community composition components: one that was affected by time since death and another that was not affected by the traits of coarse woody debris. In contrast, the decomposition rate of Quercus was not affected by coarse woody debris traits or fungal community structure. These findings suggest that, in the case of Fagus coarse woody debris, the fungal community structure is related to the decomposition process of its host substrate. Because fungal community structure is affected partly by the decay stage and wood density of its substrate, these factors influence each other. Further research on interactive effects is needed to improve our understanding of the relationship between fungal community structure and the woody debris decomposition process. PMID:26110605

A matter of scale: apparent niche differentiation of diploid and tetraploid plants may depend on extent and grain of analysis.

PubMed

Kirchheimer, Bernhard; Schinkel, Christoph C F; Dellinger, Agnes S; Klatt, Simone; Moser, Dietmar; Winkler, Manuela; Lenoir, Jonathan; Caccianiga, Marco; Guisan, Antoine; Nieto-Lugilde, Diego; Svenning, Jens-Christian; Thuiller, Wilfried; Vittoz, Pascal; Willner, Wolfgang; Zimmermann, Niklaus E; Hörandl, Elvira; Dullinger, Stefan

2016-03-22

Emerging polyploids may depend on environmental niche shifts for successful establishment. Using the alpine plant Ranunculus kuepferi as a model system, we explore the niche shift hypothesis at different spatial resolutions and in contrasting parts of the species range. European Alps. We sampled 12 individuals from each of 102 populations of R. kuepferi across the Alps, determined their ploidy levels, derived coarse-grain (100 × 100 m) environmental descriptors for all sampling sites by downscaling WorldClim maps, and calculated fine-scale environmental descriptors (2 × 2 m) from indicator values of the vegetation accompanying the sampled individuals. Both coarse and fine-scale variables were further computed for 8239 vegetation plots from across the Alps. Subsequently, we compared niche optima and breadths of diploid and tetraploid cytotypes by combining principal components analysis and kernel smoothing procedures. Comparisons were done separately for coarse and fine-grain data sets and for sympatric, allopatric and the total set of populations. All comparisons indicate that the niches of the two cytotypes differ in optima and/or breadths, but results vary in important details. The whole-range analysis suggests differentiation along the temperature gradient to be most important. However, sympatric comparisons indicate that this climatic shift was not a direct response to competition with diploid ancestors. Moreover, fine-grained analyses demonstrate niche contraction of tetraploids, especially in the sympatric range, that goes undetected with coarse-grained data. Although the niche optima of the two cytotypes differ, separation along ecological gradients was probably less decisive for polyploid establishment than a shift towards facultative apomixis, a particularly effective strategy to avoid minority cytotype exclusion. In addition, our results suggest that coarse-grained analyses overestimate niche breadths of widely distributed taxa. Niche comparison analyses should hence be conducted at environmental data resolutions appropriate for the organism and question under study.

Recovery of macroinvertebrates by screening in the field: a comparison between coarse (1.18 mm) and fine (0.60 mm) mesh sieves

USGS Publications Warehouse

Dukerschein, J.T.; Gent, R.; Sauer, J.

1996-01-01

We evaluated the potential loss of target benthic macroinvertebrates from coarse-mesh field wash down of samples through a 1.18-mm mesh sieve nested on a 0.60-mm mesh sieve. Visible target organisms (midges, mayflies, and fingernail clams) in the 1.18-mm mesh sieve were removed from the sample and enumerated in the field. The entire contents of both sieves were preserved for subsequent laboratory enumeration under 4X magnification. Percent recoveries from each treatment were based on total intact organisms found in all sieves. Percent recovery for fingernail clams found in the field (31%) was lower than for mayflies (79%) and midges (88%). Laboratory enumeration of organisms retained by the 1.18-mm sieve yielded additional fingernail clams (to total 74% recovered in the field and lab), mayflies (to total 89%), and midges (to total 91%). If the 1.18-mm sieve is used alone in the field, it is adequate to monitor mayflies, midges >1 cm, and adult fingernail clams greater than or equal to 5.0 mm shell length.

Accurate registration of temporal CT images for pulmonary nodules detection

NASA Astrophysics Data System (ADS)

Yan, Jichao; Jiang, Luan; Li, Qiang

2017-02-01

Interpretation of temporal CT images could help the radiologists to detect some subtle interval changes in the sequential examinations. The purpose of this study was to develop a fully automated scheme for accurate registration of temporal CT images for pulmonary nodule detection. Our method consisted of three major registration steps. Firstly, affine transformation was applied in the segmented lung region to obtain global coarse registration images. Secondly, B-splines based free-form deformation (FFD) was used to refine the coarse registration images. Thirdly, Demons algorithm was performed to align the feature points extracted from the registered images in the second step and the reference images. Our database consisted of 91 temporal CT cases obtained from Beijing 301 Hospital and Shanghai Changzheng Hospital. The preliminary results showed that approximately 96.7% cases could obtain accurate registration based on subjective observation. The subtraction images of the reference images and the rigid and non-rigid registered images could effectively remove the normal structures (i.e. blood vessels) and retain the abnormalities (i.e. pulmonary nodules). This would be useful for the screening of lung cancer in our future study.

Effect of grinding intensity and pelleting of the diet on indoor particulate matter concentrations and growth performance of weanling pigs.

PubMed

Ulens, T; Demeyer, P; Ampe, B; Van Langenhove, H; Millet, S

2015-02-01

This study evaluated the effect of feed form and grinding intensity of the pig diet and the interaction between both on the particulate matter (PM) concentrations inside a pig nursery and the growth performances of weanling pigs. Four diets were compared: finely ground meal, coarsely ground meal, finely ground pellets, and coarsely ground pellets. Four weaning rounds with 144 pigs per weaning round, divided over 4 identical compartments, were monitored. Within each weaning round, each compartment was randomly assigned to 1 of 4 treatments. A hammer mill with a screen of 1.5 or 6 mm was used to grind the ingredients of the finely ground and coarsely ground feeds, respectively. Indoor concentrations of the following PM fractions were measured: PM that passes through a size-selective inlet with a 50 % efficiency cutoff at 10 (PM10) , 2.5 (PM2.5), or 1 (PM1) μm aerodynamic diameter, respectively (USEPA, 2004). Feeding pelleted diets instead of meal diets gave rise to higher PM10 (P < 0.001), PM2.5 (P < 0.001), and PM1 (P < 0.001) concentrations. Grinding intensity had an effect only on PM10 (P < 0.05) concentrations. No interaction between feed form and grinding intensity was found for any of the PM fractions. Interactions (P < 0.05) between feed form and grinding intensity on ADFI and ADG were found. Grinding intensity had an effect only on the meal diets with higher ADFI for the coarsely ground meal. Pigs fed the finely ground meal had a lower (P < 0.001) ADG than the other 3 diets. Feed efficiency was influenced only by the feed form (P < 0.001) and not by the grinding intensity. Pelleting the feed gave rise to a higher G:F. In conclusion, a contradiction between environmental concerns and performance results was found. Feeding pelleted diets to the piglets improved growth performance but also increased indoor PM concentrations.

Characterization of coarse particulate matter in school gyms

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

Branis, Martin, E-mail: branis@natur.cuni.cz; 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} andmore » 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 gyms were found to be indoor microenvironments with high concentrations of coarse particulate matter, which can contribute to increased short-term inhalation exposure of exercising children. - Highlights: {yields} We studied concentration, composition and morphology of coarse particles in gyms. {yields} Indoor concentration of coarse particles was high during days with pupils activity. {yields} Effect of outdoor coarse dust on indoor levels was weak and inconsistent. {yields} Six main groups of minerals contributing to indoor resuspended dust were determined. {yields} The most abundant coarse particles were human skin scales.« less

School Locations and Traffic Emissions — Environmental (In)Justice Findings Using a New Screening Method

PubMed Central

Gaffron, Philine; Niemeier, Deb

2015-01-01

It has been shown that the location of schools near heavily trafficked roads can have detrimental effects on the health of children attending those schools. It is therefore desirable to screen both existing school locations and potential new school sites to assess either the need for remedial measures or suitability for the intended use. Current screening tools and public guidance on school siting are either too coarse in their spatial resolution for assessing individual sites or are highly resource intensive in their execution (e.g., through dispersion modeling). We propose a new method to help bridge the gap between these two approaches. Using this method, we also examine the public K-12 schools in the Sacramento Area Council of Governments Region, California (USA) from an environmental justice perspective. We find that PM2.5 emissions from road traffic affecting a school site are significantly positively correlated with the following metrics: percent share of Black, Hispanic and multi-ethnic students, percent share of students eligible for subsidized meals. The emissions metric correlates negatively with the schools’ Academic Performance Index, the share of White students and average parental education levels. Our PM2.5 metric also correlates with the traffic related, census tract level screening indicators from the California Communities Environmental Health Screening Tool and the tool’s tract level rate of asthma related emergency department visits. PMID:25679341

Cytopathological image analysis using deep-learning networks in microfluidic microscopy.

PubMed

Gopakumar, G; Hari Babu, K; Mishra, Deepak; Gorthi, Sai Siva; Sai Subrahmanyam, Gorthi R K

2017-01-01

Cytopathologic testing is one of the most critical steps in the diagnosis of diseases, including cancer. However, the task is laborious and demands skill. Associated high cost and low throughput drew considerable interest in automating the testing process. Several neural network architectures were designed to provide human expertise to machines. In this paper, we explore and propose the feasibility of using deep-learning networks for cytopathologic analysis by performing the classification of three important unlabeled, unstained leukemia cell lines (K562, MOLT, and HL60). The cell images used in the classification are captured using a low-cost, high-throughput cell imaging technique: microfluidics-based imaging flow cytometry. We demonstrate that without any conventional fine segmentation followed by explicit feature extraction, the proposed deep-learning algorithms effectively classify the coarsely localized cell lines. We show that the designed deep belief network as well as the deeply pretrained convolutional neural network outperform the conventionally used decision systems and are important in the medical domain, where the availability of labeled data is limited for training. We hope that our work enables the development of a clinically significant high-throughput microfluidic microscopy-based tool for disease screening/triaging, especially in resource-limited settings.

Sedimentary and petrofacies analyses of the Amasiri Sandstone, southern Benue Trough, Nigeria: Implications for depositional environment and tectonic provenance

NASA Astrophysics Data System (ADS)

Okoro, A. U.; Igwe, E. O.; Nwajide, C. S.

2016-11-01

This study was undertaken to determine the depositional environment, provenance and tectonic setting for the Turonian Amasiri Sandstone, southern Benue Trough, Nigeria, using lithofacies analysis and re-appraisal of petrography of the sandstones. Local stratigraphy and field relationships show a thick succession of shales alternating with elongate/parallel sandstone ridges extending eastwards from Akpoha to Amasiri through Itigidi and Ugep to Apiapum areas. Lithofacies analysis reveals 9 lithofacies suggestive of storm (mass flow) and tidal shelf processes. These include dark grey to black laminated shale/silty mudstones, bioturbated mudstones, coquinoid limestones, very fine-grained bioturbated sandstones with shell hash/debris in places and limestone rip-up clasts, massive and chaotic sandy conglomerate with rip - up clasts, fine to medium-grained, parallel laminated sandstone, hummocky cross-stratified, massive, medium to coarse-grained sandstones, medium to very coarse-grained, planar cross-bedded sandstone, with clay-draped foresets and Ophiomorpha burrows, and coarse-grained trough cross-bedded sandstone. Petrofacies analysis identifies the sandstones as feldspathic and arkosic arenites. Ternary plot of framework mineralogy indicates derivation from an uplifted continental block related to the nearby Oban Massif and Cameroon Basement Complex.

GPU-based simulation of optical propagation through turbulence for active and passive imaging

NASA Astrophysics Data System (ADS)

Monnier, Goulven; Duval, François-Régis; Amram, Solène

2014-10-01

IMOTEP is a GPU-based (Graphical Processing Units) software relying on a fast parallel implementation of Fresnel diffraction through successive phase screens. Its applications include active imaging, laser telemetry and passive imaging through turbulence with anisoplanatic spatial and temporal fluctuations. Thanks to parallel implementation on GPU, speedups ranging from 40X to 70X are achieved. The present paper gives a brief overview of IMOTEP models, algorithms, implementation and user interface. It then focuses on major improvements recently brought to the anisoplanatic imaging simulation method. Previously, we took advantage of the computational power offered by the GPU to develop a simulation method based on large series of deterministic realisations of the PSF distorted by turbulence. The phase screen propagation algorithm, by reproducing higher moments of the incident wavefront distortion, provides realistic PSFs. However, we first used a coarse gaussian model to fit the numerical PSFs and characterise there spatial statistics through only 3 parameters (two-dimensional displacements of centroid and width). Meanwhile, this approach was unable to reproduce the effects related to the details of the PSF structure, especially the "speckles" leading to prominent high-frequency content in short-exposure images. To overcome this limitation, we recently implemented a new empirical model of the PSF, based on Principal Components Analysis (PCA), ought to catch most of the PSF complexity. The GPU implementation allows estimating and handling efficiently the numerous (up to several hundreds) principal components typically required under the strong turbulence regime. A first demanding computational step involves PCA, phase screen propagation and covariance estimates. In a second step, realistic instantaneous images, fully accounting for anisoplanatic effects, are quickly generated. Preliminary results are presented.

The optical properties, physical properties and direct radiative forcing of urban columnar aerosols in the Yangtze River Delta, China

NASA Astrophysics Data System (ADS)

Zhuang, Bingliang; Wang, Tijian; Liu, Jane; Che, Huizheng; Han, Yong; Fu, Yu; Li, Shu; Xie, Min; Li, Mengmeng; Chen, Pulong; Chen, Huimin; Yang, Xiu-qun; Sun, Jianning

2018-02-01

The optical and physical properties as well as the direct radiative forcings (DRFs) of fractionated aerosols in the urban area of the western Yangtze River Delta (YRD) are investigated with measurements from a Cimel sun photometer combined with a radiation transfer model. Ground-based observations of aerosols have much higher temporal resolutions than satellite retrievals. An initial analysis reveals the characteristics of the optical properties of different types of fractionated aerosols in the western YRD. The total aerosols, mostly composed of scattering components (93.8 %), have mean optical depths of 0.65 at 550 nm and refractive index of 1.44 + 0.0084i at 440 nm. The fine aerosols are approximately four times more abundant and have very different compositions from coarse aerosols. The absorbing components account for only ˜ 4.6 % of fine aerosols and 15.5 % of coarse aerosols and have smaller sizes than the scattering aerosols within the same mode. Therefore, fine particles have stronger scattering than coarse ones, simultaneously reflecting the different size distributions between the absorbing and scattering aerosols. The relationships among the optical properties quantify the aerosol mixing and imply that approximately 15 and 27.5 % of the total occurrences result in dust- and black-carbon-dominating mixing aerosols, respectively, in the western YRD. Unlike the optical properties, the size distributions of aerosols in the western YRD are similar to those found at other sites over eastern China on a climatological scale, peaking at radii of 0.148 and 2.94 µm. However, further analysis reveals that the coarse-dominated particles can also lead to severe haze pollution over the YRD. Observation-based estimations indicate that both fine and coarse aerosols in the western YRD exert negative DRFs, and this is especially true for fine aerosols (-11.17 W m-2 at the top of atmosphere, TOA). A higher absorption fraction leads directly to the negative DRF being further offset for coarse aerosols (-0.33 W m-2) at the TOA. Similarly, the coarse-mode DRF contributes to only 13.3 % of the total scattering aerosols but > 33.7 % to the total absorbing aerosols. A sensitivity analysis states that aerosol DRFs are not highly sensitive to their profiles in clear-sky conditions. Most of the aerosol properties and DRFs have substantial seasonality in the western YRD. The results further reveal the contributions of each component of the different size particles to the total aerosol optical depths (AODs) and DRFs. Additionally, these results can be used to improve aerosol modelling performance and the modelling of aerosol effects in the eastern regions of China.

The anterior hippocampus supports a coarse, global environmental representation and the posterior hippocampus supports fine-grained, local environmental representations.

PubMed

Evensmoen, Hallvard Røe; Lehn, Hanne; Xu, Jian; Witter, Menno P; Nadel, Lynn; Håberg, Asta K

2013-11-01

Representing an environment globally, in a coarse way, and locally, in a fine-grained way, are two fundamental aspects of how our brain interprets the world that surrounds us. The neural correlates of these representations have not been explicated in humans. In this study we used fMRI to investigate these correlates and to explore a possible functional segregation in the hippocampus and parietal cortex. We hypothesized that processing a coarse, global environmental representation engages anterior parts of these regions, whereas processing fine-grained, local environmental information engages posterior parts. Participants learned a virtual environment and then had to find their way during fMRI. After scanning, we assessed strategies used and representations stored. Activation in the hippocampal head (anterior) was related to the multiple distance and global direction judgments and to the use of a coarse, global environmental representation during navigation. Activation in the hippocampal tail (posterior) was related to both local and global direction judgments and to using strategies like number of turns. A structural shape analysis showed that the use of a coarse, global environmental representation was related to larger right hippocampal head volume and smaller right hippocampal tail volume. In the inferior parietal cortex, a similar functional segregation was observed, with global routes represented anteriorly and fine-grained route information such as number of turns represented posteriorly. In conclusion, moving from the anterior to the posterior hippocampus and inferior parietal cortex reflects a shift from processing coarse global environmental representations to processing fine-grained, local environmental representations.

Bayesian calibration of coarse-grained forces: Efficiently addressing transferability

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Hierarchical coarse-graining model for photosystem II including electron and excitation-energy transfer processes.

PubMed

Matsuoka, Takeshi; Tanaka, Shigenori; Ebina, Kuniyoshi

2014-03-01

We propose a hierarchical reduction scheme to cope with coupled rate equations that describe the dynamics of multi-time-scale photosynthetic reactions. To numerically solve nonlinear dynamical equations containing a wide temporal range of rate constants, we first study a prototypical three-variable model. Using a separation of the time scale of rate constants combined with identified slow variables as (quasi-)conserved quantities in the fast process, we achieve a coarse-graining of the dynamical equations reduced to those at a slower time scale. By iteratively employing this reduction method, the coarse-graining of broadly multi-scale dynamical equations can be performed in a hierarchical manner. We then apply this scheme to the reaction dynamics analysis of a simplified model for an illuminated photosystem II, which involves many processes of electron and excitation-energy transfers with a wide range of rate constants. We thus confirm a good agreement between the coarse-grained and fully (finely) integrated results for the population dynamics. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Reducing numerical costs for core wide nuclear reactor CFD simulations by the Coarse-Grid-CFD

NASA Astrophysics Data System (ADS)

Viellieber, Mathias; Class, Andreas G.

2013-11-01

Traditionally complete nuclear reactor core simulations are performed with subchannel analysis codes, that rely on experimental and empirical input. The Coarse-Grid-CFD (CGCFD) intends to replace the experimental or empirical input with CFD data. The reactor core consists of repetitive flow patterns, allowing the general approach of creating a parametrized model for one segment and composing many of those to obtain the entire reactor simulation. The method is based on a detailed and well-resolved CFD simulation of one representative segment. From this simulation we extract so-called parametrized volumetric forces which close, an otherwise strongly under resolved, coarsely-meshed model of a complete reactor setup. While the formulation so far accounts for forces created internally in the fluid others e.g. obstruction and flow deviation through spacers and wire wraps, still need to be accounted for if the geometric details are not represented in the coarse mesh. These are modelled with an Anisotropic Porosity Formulation (APF). This work focuses on the application of the CGCFD to a complete reactor core setup and the accomplishment of the parametrization of the volumetric forces.

Multilevel Methods for Elliptic Problems with Highly Varying Coefficients on Nonaligned Coarse Grids

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

Scheichl, Robert; Vassilevski, Panayot S.; Zikatanov, Ludmil T.

2012-06-21

We generalize the analysis of classical multigrid and two-level overlapping Schwarz methods for 2nd order elliptic boundary value problems to problems with large discontinuities in the coefficients that are not resolved by the coarse grids or the subdomain partition. The theoretical results provide a recipe for designing hierarchies of standard piecewise linear coarse spaces such that the multigrid convergence rate and the condition number of the Schwarz preconditioned system do not depend on the coefficient variation or on any mesh parameters. One assumption we have to make is that the coarse grids are sufficiently fine in the vicinity of crossmore » points or where regions with large diffusion coefficients are separated by a narrow region where the coefficient is small. We do not need to align them with possible discontinuities in the coefficients. The proofs make use of novel stable splittings based on weighted quasi-interpolants and weighted Poincaré-type inequalities. Finally, numerical experiments are included that illustrate the sharpness of the theoretical bounds and the necessity of the technical assumptions.« less

Quantitative comparison of alternative methods for coarse-graining biological networks

PubMed Central

Bowman, Gregory R.; Meng, Luming; Huang, Xuhui

2013-01-01

Markov models and master equations are a powerful means of modeling dynamic processes like protein conformational changes. However, these models are often difficult to understand because of the enormous number of components and connections between them. Therefore, a variety of methods have been developed to facilitate understanding by coarse-graining these complex models. Here, we employ Bayesian model comparison to determine which of these coarse-graining methods provides the models that are most faithful to the original set of states. We find that the Bayesian agglomerative clustering engine and the hierarchical Nyström expansion graph (HNEG) typically provide the best performance. Surprisingly, the original Perron cluster cluster analysis (PCCA) method often provides the next best results, outperforming the newer PCCA+ method and the most probable paths algorithm. We also show that the differences between the models are qualitatively significant, rather than being minor shifts in the boundaries between states. The performance of the methods correlates well with the entropy of the resulting coarse-grainings, suggesting that finding states with more similar populations (i.e., avoiding low population states that may just be noise) gives better results. PMID:24089717

Seasonal dynamics of coarse atmospheric particulate matter between 2.5 μm and 80 μm in Beijing and the impact of 2008 Olympic Games

NASA Astrophysics Data System (ADS)

Norra, Stefan; Yu, Yang; Dietze, Volker; Schleicher, Nina; Fricker, Mathieu; Kaminski, Uwe; Chen, Yuan; Stüben, Doris; Cen, Kuang

2016-01-01

Beijing is well known as a megacity facing severe atmospheric pollution problems. One very important kind of pollution is the high amount of particles in Beijing's atmosphere. Numerous studies investigated the dynamics of fine particles smaller 10 μm. Less information is available on the coarse particle fraction larger 10 μm, although geogenic dusts, which often are composed by those coarser particles, frequently affect the air quality in Beijing. Therefore, systematic sampling and analysis of size fractionated particulate matter between 2.5 and 80 μm was performed in Beijing from April 2005 till October 2009. Atmospheric particles were collected in the North-West of Beijing using a cost-effective passive sampling method called Sigma-2. Altogether, 200 weeks could be analysed and assessed. Concentrations and size distribution of atmospheric coarse particles were determined by automated microscopic single particle analysis. Seasonal variability of the total mass of different size fractions was identified as follows: spring > winter > autumn > summer. High concentrations of transparent mineral particles indicate the activity of geogenic sources in spring and winter time, due to asian dust events and resuspension of soil from local bare land during dry and windy periods. The percentage of opaque particle components differs seasonally with relatively high values in winter, confirming combustion of fossil fuels for heating purposes as a predominant pollution source in this season. The influence of meteorological conditions on concentrations and size distribution of atmospheric particulate matter between 2.5 and 80 μm is demonstrated for the whole sampling period. Lowest pollution by coarse aerosols occurred during the period of the 2008 Olympic Summer Games. A general trend of decreasing total coarse particle mass concentrations was observed. Due to frequently observed high total coarse particle mass concentrations of several 100 μg·m-³ it is strongly recommended to enhance research and observation regarding these air pollutants to gain a better understanding of their dynamics, health effects, well being impacts on Beijing inhabitants and the effectiveness of mitigation measures.

Experimental Investigation on Damping Property of Coarse Aggregate Replaced Rubber Concrete

NASA Astrophysics Data System (ADS)

Sugapriya, P.; Ramkrishnan, R.; Keerthana, G.; Saravanamurugan, S.

2018-02-01

Rubber has good damping and vibrational characteristics and can reduce cracking significantly due to its elastic nature. This property of rubber can be incorporated in concrete to control vibrations and create better pavements. Crumb Rubber on being dumped in landfills has serious repercussions and causes soil and land pollution. An innovative use of waste tires is shredding them into small pieces and using them as a replacement for coarse aggregate. Crumb rubber is obtained by chopping scrap tires, and in this study it was added in two different sets named SET 1 - Treated Crumb Rubber and concrete, and SET 2 - Treated Crumb rubber with Ultra Fine GGBS as admixture in concrete. Coarse aggregate replaces Rubber in each of the 2 SET’s in proportions of 5, 10, 15 and 20%. Properties like Compressive Strength, Young’s Modulus, Direct and Semi direct Ultrasonic Pulse Velocity, Sorptivity, Damping ratio and Frequency were found out. Deformation and mode shape were studied with modal analysis and static analysis by applying a uniform pressure corresponding to the highest compressive strength of the slab, using ANSYS.

Method and system for pattern analysis using a coarse-coded neural network

NASA Technical Reports Server (NTRS)

Spirkovska, Liljana (Inventor); Reid, Max B. (Inventor)

1994-01-01

A method and system for performing pattern analysis with a neural network coarse-coding a pattern to be analyzed so as to form a plurality of sub-patterns collectively defined by data. Each of the sub-patterns comprises sets of pattern data. The neural network includes a plurality fields, each field being associated with one of the sub-patterns so as to receive the sub-pattern data therefrom. Training and testing by the neural network then proceeds in the usual way, with one modification: the transfer function thresholds the value obtained from summing the weighted products of each field over all sub-patterns associated with each pattern being analyzed by the system.

Voxel-Based Lesion Symptom Mapping of Coarse Coding and Suppression Deficits in Patients With Right Hemisphere Damage

PubMed Central

Tompkins, Connie A.; Meigh, Kimberly M.; Prat, Chantel S.

2015-01-01

Purpose This study examined right hemisphere (RH) neuroanatomical correlates of lexical–semantic deficits that predict narrative comprehension in adults with RH brain damage. Coarse semantic coding and suppression deficits were related to lesions by voxel-based lesion symptom mapping. Method Participants were 20 adults with RH cerebrovascular accidents. Measures of coarse coding and suppression deficits were computed from lexical decision reaction times at short (175 ms) and long (1000 ms) prime-target intervals. Lesions were drawn on magnetic resonance imaging images and through normalization were registered on an age-matched brain template. Voxel-based lesion symptom mapping analysis was applied to build a general linear model at each voxel. Z score maps were generated for each deficit, and results were interpreted using automated anatomical labeling procedures. Results A deficit in coarse semantic activation was associated with lesions to the RH posterior middle temporal gyrus, dorsolateral prefrontal cortex, and lenticular nuclei. A maintenance deficit for coarsely coded representations involved the RH temporal pole and dorsolateral prefrontal cortex more medially. Ineffective suppression implicated lesions to the RH inferior frontal gyrus and subcortical regions, as hypothesized, along with the rostral temporal pole. Conclusion Beyond their scientific implications, these lesion–deficit correspondences may help inform the clinical diagnosis and enhance decisions about candidacy for deficit-focused treatment to improve narrative comprehension in individuals with RH damage. PMID:26425785

Voxel-Based Lesion Symptom Mapping of Coarse Coding and Suppression Deficits in Patients With Right Hemisphere Damage.

PubMed

Yang, Ying; Tompkins, Connie A; Meigh, Kimberly M; Prat, Chantel S

2015-11-01

This study examined right hemisphere (RH) neuroanatomical correlates of lexical-semantic deficits that predict narrative comprehension in adults with RH brain damage. Coarse semantic coding and suppression deficits were related to lesions by voxel-based lesion symptom mapping. Participants were 20 adults with RH cerebrovascular accidents. Measures of coarse coding and suppression deficits were computed from lexical decision reaction times at short (175 ms) and long (1000 ms) prime-target intervals. Lesions were drawn on magnetic resonance imaging images and through normalization were registered on an age-matched brain template. Voxel-based lesion symptom mapping analysis was applied to build a general linear model at each voxel. Z score maps were generated for each deficit, and results were interpreted using automated anatomical labeling procedures. A deficit in coarse semantic activation was associated with lesions to the RH posterior middle temporal gyrus, dorsolateral prefrontal cortex, and lenticular nuclei. A maintenance deficit for coarsely coded representations involved the RH temporal pole and dorsolateral prefrontal cortex more medially. Ineffective suppression implicated lesions to the RH inferior frontal gyrus and subcortical regions, as hypothesized, along with the rostral temporal pole. Beyond their scientific implications, these lesion-deficit correspondences may help inform the clinical diagnosis and enhance decisions about candidacy for deficit-focused treatment to improve narrative comprehension in individuals with RH damage.

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

Sehgal, Ray M.; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu, E-mail: ford@ecs.umass.edu; Ford, David M., E-mail: maroudas@ecs.umass.edu, E-mail: ford@ecs.umass.edu

We have developed a coarse-grained description of the phase behavior of the isolated 38-atom Lennard-Jones cluster (LJ{sub 38}). The model captures both the solid-solid polymorphic transitions at low temperatures and the complex cluster breakup and melting transitions at higher temperatures. For this coarse model development, we employ the manifold learning technique of diffusion mapping. The outcome of the diffusion mapping analysis over a broad temperature range indicates that two order parameters are sufficient to describe the cluster's phase behavior; we have chosen two such appropriate order parameters that are metrics of condensation and overall crystallinity. In this well-justified coarse-variable space,more » we calculate the cluster's free energy landscape (FEL) as a function of temperature, employing Monte Carlo umbrella sampling. These FELs are used to quantify the phase behavior and onsets of phase transitions of the LJ{sub 38} cluster.« less

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

Optimization of droplets for UV-NIL using coarse-grain simulation of resist flow

NASA Astrophysics Data System (ADS)

Sirotkin, Vadim; Svintsov, Alexander; Zaitsev, Sergey

2009-03-01

A mathematical model and numerical method are described, which make it possible to simulate ultraviolet ("step and flash") nanoimprint lithography (UV-NIL) process adequately even using standard Personal Computers. The model is derived from 3D Navier-Stokes equations with the understanding that the resist motion is largely directed along the substrate surface and characterized by ultra-low values of the Reynolds number. By the numerical approximation of the model, a special finite difference method is applied (a coarse-grain method). A coarse-grain modeling tool for detailed analysis of resist spreading in UV-NIL at the structure-scale level is tested. The obtained results demonstrate the high ability of the tool to calculate optimal dispensing for given stamp design and process parameters. This dispensing provides uniform filled areas and a homogeneous residual layer thickness in UV-NIL.

Winter-time size distribution and source apportionment of total suspended particulate matter and associated metals in Delhi

NASA Astrophysics Data System (ADS)

Srivastava, Arun; Gupta, Sandeep; Jain, V. K.

2009-03-01

A study of the winter time size distribution and source apportionment of total suspended particulate matter (TSPM) and associated heavy metal concentrations have been carried out for the city of Delhi. This study is important from the point of view of implementation of compressed natural gas (CNG) as alternate of diesel fuel in the public transport system in 2001 to reduce the pollution level. TSPM were collected using a five-stage cascade impactor at six sites in the winters of 2005-06. The results of size distribution indicate that a major portion (~ 40%) of TSPM concentration is in the form of PM0.7 (< 0.7 μm). Similar trends were observed with most of the heavy metals associated with various size fractions of TSPM. A very good correlation between coarse and fine size fraction of TSPM was observed. It was also observed that the metals associated with coarse particles have more chances of correlation with other metals; rather they are associated with fine particles. Source apportionment was carried out separately in coarse and fine size modes of TSPM by Chemical Mass Balance Receptor Model (CMB8) as well as by Principle Component Analysis (PCA) of SPSS. Source apportionment by PCA reveals that there are two major sources (possibly vehicular and crustal re-suspension) in both coarse and fine size fractions. Results obtained by CMB8 show the dominance of vehicular pollutants and crustal dust in fine and coarse size mode respectively. Noticeably the dominance of vehicular pollutants are now confined to fine size only whilst during pre CNG era it dominated both coarse and fine size mode. An increase of 42.5, 44.4, 48.2, 38.6 and 38.9% in the concentrations of TSPM, PM10.9, coarse particles, fine particles and lead respectively was observed during pre (2001) to post CNG (2005-06) period.

Generation, Validation, and Application of Abundance Map Reference Data for Spectral Unmixing

NASA Astrophysics Data System (ADS)

Williams, McKay D.

Reference data ("ground truth") maps traditionally have been used to assess the accuracy of imaging spectrometer classification algorithms. However, these reference data can be prohibitively expensive to produce, often do not include sub-pixel abundance estimates necessary to assess spectral unmixing algorithms, and lack published validation reports. Our research proposes methodologies to efficiently generate, validate, and apply abundance map reference data (AMRD) to airborne remote sensing scenes. We generated scene-wide AMRD for three different remote sensing scenes using our remotely sensed reference data (RSRD) technique, which spatially aggregates unmixing results from fine scale imagery (e.g., 1-m Ground Sample Distance (GSD)) to co-located coarse scale imagery (e.g., 10-m GSD or larger). We validated the accuracy of this methodology by estimating AMRD in 51 randomly-selected 10 m x 10 m plots, using seven independent methods and observers, including field surveys by two observers, imagery analysis by two observers, and RSRD using three algorithms. Results indicated statistically-significant differences between all versions of AMRD, suggesting that all forms of reference data need to be validated. Given these significant differences between the independent versions of AMRD, we proposed that the mean of all (MOA) versions of reference data for each plot and class were most likely to represent true abundances. We then compared each version of AMRD to MOA. Best case accuracy was achieved by a version of imagery analysis, which had a mean coverage area error of 2.0%, with a standard deviation of 5.6%. One of the RSRD algorithms was nearly as accurate, achieving a mean error of 3.0%, with a standard deviation of 6.3%, showing the potential of RSRD-based AMRD generation. Application of validated AMRD to specific coarse scale imagery involved three main parts: 1) spatial alignment of coarse and fine scale imagery, 2) aggregation of fine scale abundances to produce coarse scale imagery-specific AMRD, and 3) demonstration of comparisons between coarse scale unmixing abundances and AMRD. Spatial alignment was performed using our scene-wide spectral comparison (SWSC) algorithm, which aligned imagery with accuracy approaching the distance of a single fine scale pixel. We compared simple rectangular aggregation to coarse sensor point spread function (PSF) aggregation, and found that the PSF approach returned lower error, but that rectangular aggregation more accurately estimated true abundances at ground level. We demonstrated various metrics for comparing unmixing results to AMRD, including mean absolute error (MAE) and linear regression (LR). We additionally introduced reference data mean adjusted MAE (MA-MAE), and reference data confidence interval adjusted MAE (CIA-MAE), which account for known error in the reference data itself. MA-MAE analysis indicated that fully constrained linear unmixing of coarse scale imagery across all three scenes returned an error of 10.83% per class and pixel, with regression analysis yielding a slope = 0.85, intercept = 0.04, and R2 = 0.81. Our reference data research has demonstrated a viable methodology to efficiently generate, validate, and apply AMRD to specific examples of airborne remote sensing imagery, thereby enabling direct quantitative assessment of spectral unmixing performance.

Sedimentary structures and textures of Rio Orinoco channel sands, Venezuela and Colombia

USGS Publications Warehouse

McKee, Edwin Dinwiddie

1989-01-01

Most sedimentary structures represented in sand bodies of the Rio Orinoco are tabular-planar cross-strata which, together with some wedge-planar cross-strata, are the products of sand-wave deposition. Locally, in areas of river meander where point bars characteristically form, trough structures forming festoon patterns are numerous. At a few localities, sets of nearly horizontal strata occur between tabular-planar sets and are interpreted to be the deposits of very fast currents of the upper flow regime; elsewhere, uncommon lenses and beds of silt, clay, or organic matter consisting of leaves and twigs, seem to be the result of quiet-water settling through gravity. By far the most common grain size represented in the tabular-planar and wedge-planar cross-strata of the sandwave deposits is medium sand (? - ? millimeter) as determined by screen analyses. Many samples, however, also contain moderate quantities of coarse or very coarse sand. Eolian dunes on top of the sand-wave deposits are dominantly fine grained. The river channel sands were determined to be largely moderately well sorted, although in some places they were mostly well sorted, and in others, mostly moderately sorted.

Dynamic screening in a two-species asymmetric exclusion process

NASA Astrophysics Data System (ADS)

Kim, Kyung Hyuk; den Nijs, Marcel

2007-08-01

The dynamic scaling properties of the one-dimensional Burgers equation are expected to change with the inclusion of additional conserved degrees of freedom. We study this by means of one-dimensional (1D) driven lattice gas models that conserve both mass and momentum. The most elementary version of this is the Arndt-Heinzel-Rittenberg (AHR) process, which is usually presented as a two-species diffusion process, with particles of opposite charge hopping in opposite directions and with a variable passing probability. From the hydrodynamics perspective this can be viewed as two coupled Burgers equations, with the number of positive and negative momentum quanta individually conserved. We determine the dynamic scaling dimension of the AHR process from the time evolution of the two-point correlation functions, and find numerically that the dynamic critical exponent is consistent with simple Kardar-Parisi-Zhang- (KPZ) type scaling. We establish that this is the result of perfect screening of fluctuations in the stationary state. The two-point correlations decay exponentially in our simulations and in such a manner that in terms of quasiparticles, fluctuations fully screen each other at coarse grained length scales. We prove this screening rigorously using the analytic matrix product structure of the stationary state. The proof suggests the existence of a topological invariant. The process remains in the KPZ universality class but only in the sense of a factorization, as (KPZ)2 . The two Burgers equations decouple at large length scales due to the perfect screening.

Peculiar Traits of Coarse AP (Briefing Charts)

DTIC Science & Technology

2014-12-01

coarse AP Bircumshaw, Newman Active centers are sources of AP decomposition gases AP low temperature decomposition (LTD) Most unstable AP particles ...delay before coarse AP ejection *Coarse AP particle flame retardancy 19 Air Force Research Laboratory Distribution A: Approved for public release...distribution unlimited. PA clearance #. Combustion bomb trials 2 AP phase change may enable coarse particle breakage Fractured coarse AP ejection agrees

Effects of dietary coarsely ground corn and 3 bedding floor types on broiler live performance, litter characteristics, gizzard and proventriculus weight, and nutrient digestibility.

PubMed

Xu, Y; Lin, Y M; Stark, C R; Ferket, P R; Williams, C M; Brake, J

2017-07-01

The effects of zero or 50% dietary coarsely ground corn (CC) in pelleted and screened grower and finisher diets on broilers reared on 3 bedding floor types (plastic net [NET], new pine wood shavings litter [NEW], or old pine wood shavings litter [OLD]) on broiler live performance, litter characteristics, gizzard and proventriculus weight, and apparent ileal digestibility (AID) were studied in a 2 × 3 factorial arrangement of treatments. Fine corn was produced with a hammermill (271 μm) and CC with a roller mill (1145 μm). Utilization of CC reduced milling cost by 9.47 cents per MT with similar nutrient content of screened pellets. The 50% CC treatment exhibited improved (P ≤ 0.05) feed intake at 42 d (2.5%) and 49 d (3.0%), and BW (5.4%) and FCR from 28 d (1.4%). Birds on NEW litter exhibited improved (P < 0.05) BW at 28 and 35 d and 42 d FCR as compared to NET and 49 d FCR compared to NET and OLD. The 50% CC treatment exhibited increased (P < 0.05) gizzard weight but decreased proventriculus weight at 49 d. NEW litter birds exhibited increased (P ≤ 0.05) gizzard weight at 28 d and 49 d and decreased proventriculus weight as compared to NET at 49 days. The 50% CC treatment exhibited decreased (P ≤ 0.05) litter moisture at 35 and 42 d, litter N at 35 and 49 d, and litter pH at 49 days. OLD litter birds exhibited greater (P < 0.05) litter N at 14, 35, and 49 d, as well as litter moisture, pH, and ammonia concentration at 49 days. The 50% CC group also exhibited improved AID of nitrogen (P < 0.05). Broilers fed pelleted and screened diets containing 50% CC exhibited improved live performance and reduced litter moisture while use of NEW litter resulted in a somewhat similar effect, which indicated that consumption of NEW litter also facilitated gastric development and function. © 2017 Poultry Science Association Inc.

An in situ approach to detect tree root ecology: linking ground-penetrating radar imaging to isotope-derived water acquisition zones

PubMed Central

Isaac, Marney E; Anglaaere, Luke C N

2013-01-01

Tree root distribution and activity are determinants of belowground competition. However, studying root response to environmental and management conditions remains logistically challenging. Methodologically, nondestructive in situ tree root ecology analysis has lagged. In this study, we tested a nondestructive approach to determine tree coarse root architecture and function of a perennial tree crop, Theobroma cacao L., at two edaphically contrasting sites (sandstone and phyllite–granite derived soils) in Ghana, West Africa. We detected coarse root vertical distribution using ground-penetrating radar and root activity via soil water acquisition using isotopic matching of δ18O plant and soil signatures. Coarse roots were detected to a depth of 50 cm, however, intraspecifc coarse root vertical distribution was modified by edaphic conditions. Soil δ18O isotopic signature declined with depth, providing conditions for plant–soil δ18O isotopic matching. This pattern held only under sandstone conditions where water acquisition zones were identifiably narrow in the 10–20 cm depth but broader under phyllite–granite conditions, presumably due to resource patchiness. Detected coarse root count by depth and measured fine root density were strongly correlated as were detected coarse root count and identified water acquisition zones, thus validating root detection capability of ground-penetrating radar, but exclusively on sandstone soils. This approach was able to characterize trends between intraspecific root architecture and edaphic-dependent resource availability, however, limited by site conditions. This study successfully demonstrates a new approach for in situ root studies that moves beyond invasive point sampling to nondestructive detection of root architecture and function. We discuss the transfer of such an approach to answer root ecology questions in various tree-based landscapes. PMID:23762519

On the removal of hexavalent chromium from a Class F fly ash.

PubMed

Huggins, F E; Rezaee, M; Honaker, R Q; Hower, J C

2016-05-01

Coarse and fine samples of a Class F fly ash obtained from commercial combustion of Illinois bituminous coal have been exposed to two long-term leaching tests designed to simulate conditions in waste impoundments. ICP-AES analysis indicated that the coarse and fine fly ash samples contained 135 and 171mg/kg Cr, respectively. Measurements by XAFS spectroscopy showed that the ash samples originally contained 5 and 8% of the chromium, respectively, in the hexavalent oxidation state, Cr(VI). After exposure to water for more than four months, the percentage of chromium as Cr(VI) in the fly-ash decreased significantly for the coarse and fine fly-ash in both tests. Combining the XAFS data with ICP-AES data on the concentration of chromium in the leachates indicated that, after the nineteen-week-long, more aggressive, kinetic test on the coarse fly ash, approximately 60% of the Cr(VI) had been leached, 20% had been reduced to Cr(III) and retained in the ash, and 20% remained as Cr(VI) in the ash. In contrast, during the six-month-long baseline test, very little Cr was actually leached from either the coarse or the fine fly-ash (<0.1mg/kg); rather, about 66% and 20%, respectively, of the original Cr(VI) in the coarse and fine fly-ash was retained in the ash in that form, while the remainder, 34% and 80%, respectively, was reduced and retained in the ash as Cr(III). The results are interpreted as indicating that Cr(VI) present in Class F fly-ash can be reduced to Cr(III) when in contact with water and that such chemical reduction can compete with physical removal of Cr(VI) from the ash by aqueous leaching. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach.

PubMed

Gan, Hin Hark; Schlick, Tamar

2010-10-20

Characterizing the ionic distribution around chromatin is important for understanding the electrostatic forces governing chromatin structure and function. Here we develop an electrostatic model to handle multivalent ions and compute the ionic distribution around a mesoscale chromatin model as a function of conformation, number of nucleosome cores, and ionic strength and species using Poisson-Boltzmann theory. This approach enables us to visualize and measure the complex patterns of counterion condensation around chromatin by examining ionic densities, free energies, shielding charges, and correlations of shielding charges around the nucleosome core and various oligonucleosome conformations. We show that: counterions, especially divalent cations, predominantly condense around the nucleosomal and linker DNA, unburied regions of histone tails, and exposed chromatin surfaces; ionic screening is sensitively influenced by local and global conformations, with a wide ranging net nucleosome core screening charge (56-100e); and screening charge correlations reveal conformational flexibility and interactions among chromatin subunits, especially between the histone tails and parental nucleosome cores. These results provide complementary and detailed views of ionic effects on chromatin structure for modest computational resources. The electrostatic model developed here is applicable to other coarse-grained macromolecular complexes. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Musical structure analysis using similarity matrix and dynamic programming

NASA Astrophysics Data System (ADS)

Shiu, Yu; Jeong, Hong; Kuo, C.-C. Jay

2005-10-01

Automatic music segmentation and structure analysis from audio waveforms based on a three-level hierarchy is examined in this research, where the three-level hierarchy includes notes, measures and parts. The pitch class profile (PCP) feature is first extracted at the note level. Then, a similarity matrix is constructed at the measure level, where a dynamic time warping (DTW) technique is used to enhance the similarity computation by taking the temporal distortion of similar audio segments into account. By processing the similarity matrix, we can obtain a coarse-grain music segmentation result. Finally, dynamic programming is applied to the coarse-grain segments so that a song can be decomposed into several major parts such as intro, verse, chorus, bridge and outro. The performance of the proposed music structure analysis system is demonstrated for pop and rock music.

APPARATUS FOR CATALYTICALLY COMBINING GASES

DOEpatents

Busey, H.M.

1958-08-12

A convection type recombiner is described for catalytically recombining hydrogen and oxygen which have been radiolytically decomposed in an aqueous homogeneous nuclear reactor. The device is so designed that the energy of recombination is used to circulate the gas mixture over the catalyst. The device consists of a vertical cylinder having baffles at its lower enda above these coarse screens having platinum and alumina pellets cemented thereon, and an annular passage for the return of recombined, condensed water to the reactor moderator system. This devicea having no moving parts, provides a simple and efficient means of removing the danger of accumulated hot radioactive, explosive gases, and restoring them to the moderator system for reuse.

Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration

PubMed Central

Miller, Thomas F.

2017-01-01

We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency. PMID:28328943

Coarse-grained forms for equations describing the microscopic motion of particles in a fluid.

PubMed

Das, Shankar P; Yoshimori, Akira

2013-10-01

Exact equations of motion for the microscopically defined collective density ρ(x,t) and the momentum density ĝ(x,t) of a fluid have been obtained in the past starting from the corresponding Langevin equations representing the dynamics of the fluid particles. In the present work we average these exact equations of microscopic dynamics over the local equilibrium distribution to obtain stochastic partial differential equations for the coarse-grained densities with smooth spatial and temporal dependence. In particular, we consider Dean's exact balance equation for the microscopic density of a system of interacting Brownian particles to obtain the basic equation of the dynamic density functional theory with noise. Our analysis demonstrates that on thermal averaging the dependence of the exact equations on the bare interaction potential is converted to dependence on the corresponding thermodynamic direct correlation functions in the coarse-grained equations.

Parallel program debugging with flowback analysis

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

Choi, Jongdeok.

1989-01-01

This thesis describes the design and implementation of an integrated debugging system for parallel programs running on shared memory multi-processors. The goal of the debugging system is to present to the programmer a graphical view of the dynamic program dependences while keeping the execution-time overhead low. The author first describes the use of flowback analysis to provide information on causal relationship between events in a programs' execution without re-executing the program for debugging. Execution time overhead is kept low by recording only a small amount of trace during a program's execution. He uses semantic analysis and a technique called incrementalmore » tracing to keep the time and space overhead low. As part of the semantic analysis, he uses a static program dependence graph structure that reduces the amount of work done at compile time and takes advantage of the dynamic information produced during execution time. The cornerstone of the incremental tracing concept is to generate a coarse trace during execution and fill incrementally, during the interactive portion of the debugging session, the gap between the information gathered in the coarse trace and the information needed to do the flowback analysis using the coarse trace. Then, he describes how to extend the flowback analysis to parallel programs. The flowback analysis can span process boundaries; i.e., the most recent modification to a shared variable might be traced to a different process than the one that contains the current reference. The static and dynamic program dependence graphs of the individual processes are tied together with synchronization and data dependence information to form complete graphs that represent the entire program.« less

Dust episodes in Beirut and their effect on the chemical composition of coarse and fine particulate matter.

PubMed

Jaafar, Malek; Baalbaki, Rima; Mrad, Raya; Daher, Nancy; Shihadeh, Alan; Sioutas, Constantinos; Saliba, Najat A

2014-10-15

Particles captured during dust episodes in Beirut originated from both the African and Arabian deserts. This particular air mixture showed an increase, over non-dust episodes, in particle volume distribution which was mostly noticed for particles ranging in sizes between 2.25 and 5 μm. It also resulted in an increase in average mass concentration by 48.5% and 14.6%, for the coarse and fine fractions, respectively. Chemical analysis of major aerosol components accounted for 93% of fine PM and 71% of coarse PM. Crustal material (CM) dominated the coarse PM fraction, contributing to 39 ± 15% of the total mass. Sea salt (SS) (11 ± 10%) and secondary ions (SI) (11 ± 7%) were the second most abundant elements. In the fine fraction, SI (36 ± 14%) were the most abundant PM constituent, followed by organic matter (OM) (33 ± 7%) and CM (13 ± 2%). Enrichment factors (EF) and correlation coefficients show that biogenic and anthropogenic sources contribute to the elemental composition of particles during dust episodes. This study emphasizes on the role played by the long-range transport of aerosols in changing the chemical composition of the organic and inorganic constituents of urban coarse and fine PM. The chemical reactions between aged urban and dust aerosols are enhanced during transport, leading to the formation of organo-nitrogenated and -sulfonated compounds. Their oligomeric morphologies are further confirmed by SEM-EDX measurements. Copyright © 2014 Elsevier B.V. All rights reserved.

Trace metal content in inhalable particulate matter (PM2.5-10 and PM2.5) collected from historical mine waste deposits using a laboratory-based approach.

PubMed

Martin, Rachael; Dowling, Kim; Pearce, Dora C; Florentine, Singarayer; McKnight, Stafford; Stelcer, Eduard; Cohen, David D; Stopic, Attila; Bennett, John W

2017-06-01

Mine wastes and tailings are considered hazardous to human health because of their potential to generate large quantities of highly toxic emissions of particulate matter (PM). Human exposure to As and other trace metals in PM may occur via inhalation of airborne particulates or through ingestion of contaminated dust. This study describes a laboratory-based method for extracting PM 2.5-10 (coarse) and PM 2.5 (fine) particles from As-rich mine waste samples collected from an historical gold mining region in regional, Victoria, Australia. We also report on the trace metal and metalloid content of the coarse and fine fraction, with an emphasis on As as an element of potential concern. Laser diffraction analysis showed that the proportions of coarse and fine particles in the bulk samples ranged between 3.4-26.6 and 0.6-7.6 %, respectively. Arsenic concentrations were greater in the fine fraction (1680-26,100 mg kg -1 ) compared with the coarse fraction (1210-22,000 mg kg -1 ), and Co, Fe, Mn, Ni, Sb and Zn were found to be present in the fine fraction at levels around twice those occurring in the coarse. These results are of particular concern given that fine particles can accumulate in the human respiratory system. Our study demonstrates that mine wastes may be an important source of metal-enriched PM for mining communities.

Prediction of unsaturated flow and water backfill during infiltration in layered soils

NASA Astrophysics Data System (ADS)

Cui, Guotao; Zhu, Jianting

2018-02-01

We develop a new analytical infiltration model to determine water flow dynamics around layer interfaces during infiltration process in layered soils. The model mainly involves the analytical solutions to quadratic equations to determine the flux rates around the interfaces. Active water content profile behind the wetting front is developed based on the solution of steady state flow to dynamically update active parameters in sharp wetting front infiltration equations and to predict unsaturated flow in coarse layers before the front reaches an impeding fine layer. The effect of water backfill to saturate the coarse layers after the wetting front encounters the impeding fine layer is analytically expressed based on the active water content profiles. Comparison to the numerical solutions of the Richards equation shows that the new model can well capture water dynamics in relation to the arrangement of soil layers. The steady state active water content profile can be used to predict the saturation state of all layers when the wetting front first passes through these layers during the unsteady infiltration process. Water backfill effect may occur when the unsaturated wetting front encounters a fine layer underlying a coarse layer. Sensitivity analysis shows that saturated hydraulic conductivity is the parameter dictating the occurrence of unsaturated flow and water backfill and can be used to represent the coarseness of soil layers. Water backfill effect occurs in coarse layers between upper and lower fine layers when the lower layer is not significantly coarser than the upper layer.

Physics-based statistical learning approach to mesoscopic model selection.

PubMed

Taverniers, Søren; Haut, Terry S; Barros, Kipton; Alexander, Francis J; Lookman, Turab

2015-11-01

In materials science and many other research areas, models are frequently inferred without considering their generalization to unseen data. We apply statistical learning using cross-validation to obtain an optimally predictive coarse-grained description of a two-dimensional kinetic nearest-neighbor Ising model with Glauber dynamics (GD) based on the stochastic Ginzburg-Landau equation (sGLE). The latter is learned from GD "training" data using a log-likelihood analysis, and its predictive ability for various complexities of the model is tested on GD "test" data independent of the data used to train the model on. Using two different error metrics, we perform a detailed analysis of the error between magnetization time trajectories simulated using the learned sGLE coarse-grained description and those obtained using the GD model. We show that both for equilibrium and out-of-equilibrium GD training trajectories, the standard phenomenological description using a quartic free energy does not always yield the most predictive coarse-grained model. Moreover, increasing the amount of training data can shift the optimal model complexity to higher values. Our results are promising in that they pave the way for the use of statistical learning as a general tool for materials modeling and discovery.

Influence of wheat kernel physical properties on the pulverizing process.

PubMed

Dziki, Dariusz; Cacak-Pietrzak, Grażyna; Miś, Antoni; Jończyk, Krzysztof; Gawlik-Dziki, Urszula

2014-10-01

The physical properties of wheat kernel were determined and related to pulverizing performance by correlation analysis. Nineteen samples of wheat cultivars about similar level of protein content (11.2-12.8 % w.b.) and obtained from organic farming system were used for analysis. The kernel (moisture content 10 % w.b.) was pulverized by using the laboratory hammer mill equipped with round holes 1.0 mm screen. The specific grinding energy ranged from 120 kJkg(-1) to 159 kJkg(-1). On the basis of data obtained many of significant correlations (p < 0.05) were found between wheat kernel physical properties and pulverizing process of wheat kernel, especially wheat kernel hardness index (obtained on the basis of Single Kernel Characterization System) and vitreousness significantly and positively correlated with the grinding energy indices and the mass fraction of coarse particles (> 0.5 mm). Among the kernel mechanical properties determined on the basis of uniaxial compression test only the rapture force was correlated with the impact grinding results. The results showed also positive and significant relationships between kernel ash content and grinding energy requirements. On the basis of wheat physical properties the multiple linear regression was proposed for predicting the average particle size of pulverized kernel.

A procedure for partitioning bulk sediments into distinct grain-size fractions for geochemical analysis

USGS Publications Warehouse

Barbanti, A.; Bothner, Michael H.

1993-01-01

A method to separate sediments into discrete size fractions for geochemical analysis has been tested. The procedures were chosen to minimize the destruction or formation of aggregates and involved gentle sieving and settling of wet samples. Freeze-drying and sonication pretreatments, known to influence aggregates, were used for comparison. Freeze-drying was found to increase the silt/clay ratio by an average of 180 percent compared to analysis of a wet sample that had been wet sieved only. Sonication of a wet sample decreased the silt/clay ratio by 51 percent. The concentrations of metals and organic carbon in the separated fractions changed depending on the pretreatment procedures in a manner consistent with the hypothesis that aggregates consist of fine-grained organic- and metal-rich particles. The coarse silt fraction of a freeze-dried sample contained 20–44 percent higher concentrations of Zn, Cu, and organic carbon than the coarse silt fraction of the wet sample. Sonication resulted in concentrations of these analytes that were 18–33 percent lower in the coarse silt fraction than found in the wet sample. Sonication increased the concentration of lead in the clay fraction by an average of 40 percent compared to an unsonicated sample. Understanding the magnitude of change caused by different analysis protocols is an aid in designing future studies that seek to interpret the spatial distribution of contaminated sediments and their transport mechanisms.

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 concentrations of coarse particulate matter, which can contribute to increased short-term inhalation exposure of exercising children. Copyright © 2011 Elsevier Inc. All rights reserved.

Comprehensive characterisation of atmospheric aerosols in Budapest, Hungary: physicochemical properties of inorganic species

NASA Astrophysics Data System (ADS)

Salma, Imre; Maenhaut, Willy; Zemplén-Papp, Éva; Záray, Gyula

As part of an air pollution project in Budapest, aerosol samples were collected by stacked filter units and cascade impactors at an urban background site, two downtown sites, and within a road tunnel in field campaigns conducted in 1996, 1998 and 1999. Some criteria pollutants were also measured at one of the downtown sites. The aerosol samples were analysed by one or more of the following methods: instrumental neutron activation analysis, particle-induced X-ray emission analysis, a light reflection technique, gravimetry, thermal profiling carbon analysis and capillary electrophoresis. The quantities measured or derived include atmospheric concentrations of elements (from Na to U), of particulate matter, of black and elemental carbon, and total carbonaceous fraction, of some ionic species (e.g., nitrate and sulphate) in the fine ( <2 μm equivalent aerodynamic diameter, EAD) or in both coarse (10- 2 μm EAD) and fine size fractions, atmospheric concentrations of NO, NO 2, SO 2, CO and total suspended particulate matter, and meteorological parameters. The analytical results were used for characterisation of the concentration levels, elemental composition, time trends, enrichment of and relationships among the aerosol species in coarse and fine size fractions, for studying their fine-to-coarse concentration ratios, spatial and temporal variability, for determining detailed elemental mass size distributions, and for examining the extent of chemical mass closure.

Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

NASA Astrophysics Data System (ADS)

Asafi, M. S.; Yildirim, A.; Tekpinar, M.

2016-04-01

Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

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...

Experiments in monthly mean simulation of the atmosphere with a coarse-mesh general circulation model

NASA Technical Reports Server (NTRS)

Lutz, R. J.; Spar, J.

1978-01-01

The Hansen atmospheric model was used to compute five monthly forecasts (October 1976 through February 1977). The comparison is based on an energetics analysis, meridional and vertical profiles, error statistics, and prognostic and observed mean maps. The monthly mean model simulations suffer from several defects. There is, in general, no skill in the simulation of the monthly mean sea-level pressure field, and only marginal skill is indicated for the 850 mb temperatures and 500 mb heights. The coarse-mesh model appears to generate a less satisfactory monthly mean simulation than the finer mesh GISS model.

Systematic and simulation-free coarse graining of homopolymer melts: a relative-entropy-based study.

PubMed

Yang, Delian; Wang, Qiang

2015-09-28

We applied the systematic and simulation-free strategy proposed in our previous work (D. Yang and Q. Wang, J. Chem. Phys., 2015, 142, 054905) to the relative-entropy-based (RE-based) coarse graining of homopolymer melts. RE-based coarse graining provides a quantitative measure of the coarse-graining performance and can be used to select the appropriate analytic functional forms of the pair potentials between coarse-grained (CG) segments, which are more convenient to use than the tabulated (numerical) CG potentials obtained from structure-based coarse graining. In our general coarse-graining strategy for homopolymer melts using the RE framework proposed here, the bonding and non-bonded CG potentials are coupled and need to be solved simultaneously. Taking the hard-core Gaussian thread model (K. S. Schweizer and J. G. Curro, Chem. Phys., 1990, 149, 105) as the original system, we performed RE-based coarse graining using the polymer reference interaction site model theory under the assumption that the intrachain segment pair correlation functions of CG systems are the same as those in the original system, which de-couples the bonding and non-bonded CG potentials and simplifies our calculations (that is, we only calculated the latter). We compared the performance of various analytic functional forms of non-bonded CG pair potential and closures for CG systems in RE-based coarse graining, as well as the structural and thermodynamic properties of original and CG systems at various coarse-graining levels. Our results obtained from RE-based coarse graining are also compared with those from structure-based coarse graining.

Predicting Vulnerability of the Integrity and Connectivity Associated with Culverts in Low Order Streams of Northern Michigan

NASA Astrophysics Data System (ADS)

King, C. H.; Wagenbrenner, J.; Fedora, M.; Watkins, D.; Watkins, M. K.; Huckins, C.

2017-12-01

The Great Lakes Region of North America has experienced more frequent extreme precipitation events in recent decades, resulting in a large number of stream crossing failures. While there are accepted methods for designing stream crossings to accommodate peak storm discharges, less attention has been paid to assessing the risk of failure. To evaluate failure risk and potential impacts, coarse-resolution stream crossing surveys were completed on 51 stream crossings and dams in the North Branch Paint River watershed in Michigan's Upper Peninsula. These inventories determined stream crossing dimensions along with stream and watershed characteristics. Eleven culverts were selected from the coarse surveys for high resolution hydraulic analysis to estimate discharge conditions expected at crossing failure. Watershed attributes upstream of the crossing, including area, slope, and storage, were acquired. Sediment discharge and the economic impact associated with a failure event were also estimated for each stream crossing. Impacts to stream connectivity and fish passability were assessed from the coarse-level surveys. Using information from both the coarse and high-resolution surveys, we also developed indicators to predict failure risk without the need for complex hydraulic modeling. These passability scores and failure risk indicators will help to prioritize infrastructure replacement and improve the overall connectivity of river systems throughout the upper Great Lakes Region.

Thermal and Mechanical Property Characterization of the Advanced Disk Alloy LSHR

NASA Technical Reports Server (NTRS)

Gabb, Timothy P.; Gayda, John; Telesman, Jack; Kantzos, Peter T.

2005-01-01

A low solvus, high refractory (LSHR) powder metallurgy disk alloy was recently designed using experimental screening and statistical modeling of composition and processing variables on sub-scale disks to have versatile processing-property capabilities for advanced disk applications. The objective of the present study was to produce a scaled-up disk and apply varied heat treat processes to enable full-scale demonstration of LSHR properties. Scaled-up disks were produced, heat treated, sectioned, and then machined into specimens for mechanical testing. Results indicate the LSHR alloy can be processed to produce fine and coarse grain microstructures with differing combinations of strength and time-dependent mechanical properties, for application at temperatures exceeding 1300 F.

Pseudo-shading technique in the two-dimensional domain: a post-processing algorithm for enhancing the Z-buffer of a three-dimensional binary image.

PubMed

Tan, A C; Richards, R

1989-01-01

Three-dimensional (3D) medical graphics is becoming popular in clinical use on tomographic scanners. Research work in 3D reconstructive display of computerized tomography (CT) and magnetic resonance imaging (MRI) scans on conventional computers has produced many so-called pseudo-3D images. The quality of these images depends on the rendering algorithm, the coarseness of the digitized object, the number of grey levels and the image screen resolution. CT and MRI data are fundamentally voxel based and they produce images that are coarse because of the resolution of the data acquisition system. 3D images produced by the Z-buffer depth shading technique suffer loss of detail when complex objects with fine textural detail need to be displayed. Attempts have been made to improve the display of voxel objects, and existing techniques have shown the improvement possible using these post-processing algorithms. The improved rendering technique works on the Z-buffer image to generate a shaded image using a single light source in any direction. The effectiveness of the technique in generating a shaded image has been shown to be a useful means of presenting 3D information for clinical use.

Marginally trapped surfaces and AdS/CFT

NASA Astrophysics Data System (ADS)

Grado-White, Brianna; Marolf, Donald

2018-02-01

It has been proposed that the areas of marginally trapped or anti-trapped surfaces (also known as leaves of holographic screens) may encode some notion of entropy. To connect this to AdS/CFT, we study the case of marginally trapped surfaces anchored to an AdS boundary. We establish that such boundary-anchored leaves lie between the causal and extremal surfaces defined by the anchor and that they have area bounded below by that of the minimal extremal surface. This suggests that the area of any leaf represents a coarse-grained von Neumann entropy for the associated region of the dual CFT. We further demonstrate that the leading area-divergence of a boundary-anchored marginally trapped surface agrees with that for the associated extremal surface, though subleading divergences generally differ. Finally, we generalize an argument of Bousso and Engelhardt to show that holographic screens with all leaves anchored to the same boundary set have leaf-areas that increase monotonically along the screen, and we describe a construction through which this monotonicity can take the more standard form of requiring entropy to increase with boundary time. This construction is related to what one might call future causal holographic information, which in such cases also provides an upper bound on the area of the associated leaves.

Texture coarseness responsive neurons and their mapping in layer 2–3 of the rat barrel cortex in vivo

PubMed Central

Garion, Liora; Dubin, Uri; Rubin, Yoav; Khateb, Mohamed; Schiller, Yitzhak; Azouz, Rony; Schiller, Jackie

2014-01-01

Texture discrimination is a fundamental function of somatosensory systems, yet the manner by which texture is coded and spatially represented in the barrel cortex are largely unknown. Using in vivo two-photon calcium imaging in the rat barrel cortex during artificial whisking against different surface coarseness or controlled passive whisker vibrations simulating different coarseness, we show that layer 2–3 neurons within barrel boundaries differentially respond to specific texture coarsenesses, while only a minority of neurons responded monotonically with increased or decreased surface coarseness. Neurons with similar preferred texture coarseness were spatially clustered. Multi-contact single unit recordings showed a vertical columnar organization of texture coarseness preference in layer 2–3. These findings indicate that layer 2–3 neurons perform high hierarchical processing of tactile information, with surface coarseness embodied by distinct neuronal subpopulations that are spatially mapped onto the barrel cortex. DOI: http://dx.doi.org/10.7554/eLife.03405.001 PMID:25233151

Dual-scale Galerkin methods for Darcy flow

NASA Astrophysics Data System (ADS)

Wang, Guoyin; Scovazzi, Guglielmo; Nouveau, Léo; Kees, Christopher E.; Rossi, Simone; Colomés, Oriol; Main, Alex

2018-02-01

The discontinuous Galerkin (DG) method has found widespread application in elliptic problems with rough coefficients, of which the Darcy flow equations are a prototypical example. One of the long-standing issues of DG approximations is the overall computational cost, and many different strategies have been proposed, such as the variational multiscale DG method, the hybridizable DG method, the multiscale DG method, the embedded DG method, and the Enriched Galerkin method. In this work, we propose a mixed dual-scale Galerkin method, in which the degrees-of-freedom of a less computationally expensive coarse-scale approximation are linked to the degrees-of-freedom of a base DG approximation. We show that the proposed approach has always similar or improved accuracy with respect to the base DG method, with a considerable reduction in computational cost. For the specific definition of the coarse-scale space, we consider Raviart-Thomas finite elements for the mass flux and piecewise-linear continuous finite elements for the pressure. We provide a complete analysis of stability and convergence of the proposed method, in addition to a study on its conservation and consistency properties. We also present a battery of numerical tests to verify the results of the analysis, and evaluate a number of possible variations, such as using piecewise-linear continuous finite elements for the coarse-scale mass fluxes.

The pharmacopeial evolution of intralipid injectable emulsion in plastic containers: from a coarse to a fine dispersion.

PubMed

Driscoll, David F

2009-02-23

On December 1, 2007, the United States Pharmacopeia (USP) adopted Chapter 729 entitled Globule Size Distribution in Lipid Injectable Emulsions that contains two globule sizing methods and criteria to measure the mean droplet diameter (MDD) and the large-diameter tail of the globule size distribution to meet pharmacopeial specifications. The first of these measures, as the intensity-weighted MDD expressed in nanometers, must be less than 500 nm. The second measure, as the volume-weighted percentage of fat greater than 5 microm or PFAT(5), must be less than 0.05%. These limits were first suggested in 2001 based on an analysis of 16 lipid injectable emulsions available worldwide. In 2004, the packaging of the innovator lipid emulsion product Intralipid was changed from conventional glass bottles to plastic containers in the U.S. A subsequent analysis of the emulsion in its new container showed it to be more coarse than its previous glass counterpart and now failed the PFAT(5) limit. In 2007, it was announced that Intralipid in plastic containers was reformulated to meet the pharmacopeial limits. To track the time course of its transition from a coarse to a fine dispersion, 31 lots of Intralipid with expiration dates spanning five years were investigated.

Distributions of experimental protein structures on coarse-grained free energy landscapes

PubMed Central

Liu, Jie; Jernigan, Robert L.

2015-01-01

Predicting conformational changes of proteins is needed in order to fully comprehend functional mechanisms. With the large number of available structures in sets of related proteins, it is now possible to directly visualize the clusters of conformations and their conformational transitions through the use of principal component analysis. The most striking observation about the distributions of the structures along the principal components is their highly non-uniform distributions. In this work, we use principal component analysis of experimental structures of 50 diverse proteins to extract the most important directions of their motions, sample structures along these directions, and estimate their free energy landscapes by combining knowledge-based potentials and entropy computed from elastic network models. When these resulting motions are visualized upon their coarse-grained free energy landscapes, the basis for conformational pathways becomes readily apparent. Using three well-studied proteins, T4 lysozyme, serum albumin, and sarco-endoplasmic reticular Ca2+ adenosine triphosphatase (SERCA), as examples, we show that such free energy landscapes of conformational changes provide meaningful insights into the functional dynamics and suggest transition pathways between different conformational states. As a further example, we also show that Monte Carlo simulations on the coarse-grained landscape of HIV-1 protease can directly yield pathways for force-driven conformational changes. PMID:26723638

Species Composition of Down Dead and Standing Live Trees: Implications for Forest Inventory Analysis

Treesearch

Christopher W. Woodall; Linda Nagel

2005-01-01

The assessment of species composition in most forest inventory analysis relies solely on standing live tree information characterized by current forest type. With the implementation of the third phase of the U.S. Department of Agriculture Forest Service's Forest Inventory and Analysis program, the species composition of down dead trees, otherwise termed coarse...

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

[Intervention of coarse cereals on lipid metabolism in rats].

PubMed

Guo, Yanbo; Zhai, Chengkai; Wang, Yanli; Zhang, Qun; Ding, Zhoubo; Jin, Xin

2010-03-01

To observe the effect of coarse cereals on improving the disorder of lipid metabolism and the expression of PPARgamma mRNA in white adipose tissue in rats to investigate the mechanism of coarse cereals on lipid metabolism disorder. Forty four SPF rats were randomly divided into 4 groups: the negative control group was fed with normal diet and 3 experimental groups were fed with high-fat modeling diet for 6 weeks for model building. The 3 experimental groups, the coarse cereals group,rice-flour group and the hyperlipemia model group, were then fed with coarse cereals high-fat diet,rice-flour high-diet and high-fat modeling diet respectively for another 15 weeks. Compared with the hyperlipemia modeling group, serum TG, TC, IL-6 and TNF-alpha in the coarse cereals group were declined significantly (P < 0.05), serum HDL-C in coarse cereals group was higher than that in rice-flour group and hyperlipemia model group (P < 0.05), LPL, HL and TNF-alpha in coarse cereal group were close to the negative control group. Moreover, the expression of PPAR-gamma mRNA in white adipose tissue of the coarse cereals group was higher than other groups. The coarse cereals could activate PPARgamma and enhance the activity of key enzymes in lipids metabolism, so as to reduce the level of TG relieve inflammation and improve lipid dysmetabolism eventually.

An equation-free approach to agent-based computation: Bifurcation analysis and control of stationary states

NASA Astrophysics Data System (ADS)

Siettos, C. I.; Gear, C. W.; Kevrekidis, I. G.

2012-08-01

We show how the equation-free approach can be exploited to enable agent-based simulators to perform system-level computations such as bifurcation, stability analysis and controller design. We illustrate these tasks through an event-driven agent-based model describing the dynamic behaviour of many interacting investors in the presence of mimesis. Using short bursts of appropriately initialized runs of the detailed, agent-based simulator, we construct the coarse-grained bifurcation diagram of the (expected) density of agents and investigate the stability of its multiple solution branches. When the mimetic coupling between agents becomes strong enough, the stable stationary state loses its stability at a coarse turning point bifurcation. We also demonstrate how the framework can be used to design a wash-out dynamic controller that stabilizes open-loop unstable stationary states even under model uncertainty.

Assessing the Predictability of Convection using Ensemble Data Assimilation of Simulated Radar Observations in an LETKF system

NASA Astrophysics Data System (ADS)

Lange, Heiner; Craig, George

2014-05-01

This study uses the Local Ensemble Transform Kalman Filter (LETKF) to perform storm-scale Data Assimilation of simulated Doppler radar observations into the non-hydrostatic, convection-permitting COSMO model. In perfect model experiments (OSSEs), it is investigated how the limited predictability of convective storms affects precipitation forecasts. The study compares a fine analysis scheme with small RMS errors to a coarse scheme that allows for errors in position, shape and occurrence of storms in the ensemble. The coarse scheme uses superobservations, a coarser grid for analysis weights, a larger localization radius and larger observation error that allow a broadening of the Gaussian error statistics. Three hour forecasts of convective systems (with typical lifetimes exceeding 6 hours) from the detailed analyses of the fine scheme are found to be advantageous to those of the coarse scheme during the first 1-2 hours, with respect to the predicted storm positions. After 3 hours in the convective regime used here, the forecast quality of the two schemes appears indiscernible, judging by RMSE and verification methods for rain-fields and objects. It is concluded that, for operational assimilation systems, the analysis scheme might not necessarily need to be detailed to the grid scale of the model. Depending on the forecast lead time, and on the presence of orographic or synoptic forcing that enhance the predictability of storm occurrences, analyses from a coarser scheme might suffice.

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

PubMed

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

2013-12-19

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

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 at conditions that favor dimerization of gD-Crys. The resulting regions agree with previously found aggregation-prone sites, as well as suggesting new ones that may be important. PMID:24289039

Winter urban air particles from Rome (Italy): Effects on the monocytic-macrophagic RAW 264.7 cell line

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

Pozzi, Roberta; De Berardis, Barbara; Paoletti, Luigi

2005-11-15

Epidemiological data show an association between exposure to elevated levels of particulate matter (PM), in particular the fine fraction (<2.5{mu}m in diameter), and an increase in cardiovascular mortality and respiratory symptoms. The aim of this study was to compare the in vitro toxicity of coarse and fine particulate matter collected with a cascade impactor during winter in an urban area of Rome in relation to their physicochemical characterization (size distribution and chemical composition) as assessed by analytical electron microscopy (SEM/EDX). The X-ray microanalysis data of single particles of coarse and fine matter were analyzed by hierarchical cluster analysis to determinemore » the principal component of the two granulometric fractions. The main chemical difference between the two fractions was the greater abundance of carbonaceous particles in the fine fraction. We compared the ability of coarse and fine fractions, carbon black (CB), and residual oil fly ash (ROFA) to induce arachidonic acid release and tumor necrosis factor-{alpha} (TNF-{alpha}) production in the monocytic-macrophagic RAW 264.7 cell line at concentrations of 30 and 120{mu}g/mL. Our results showed that CB and ROFA were consistently less effective than both fractions of urban particles at inducing an inflammatory reaction in RAW 264.7 cells. Both PM fractions dose-dependently increased TNF-{alpha} production in RAW 264.7 cells after 5 and 24h of incubation, and only the TNF-{alpha} production induced by coarse particles at 30{mu}g/mL decreased significantly (P<0.01) after 24h of treatment. In our in vitro model the winter fine fraction was more reactive than the winter coarse fraction, in contrast to a previously examined summer sample. In the summer sample, coarse particles produced higher levels of inflammatory mediators than fine particles and the CB was consistently less effective than the urban particles. The different behaviors between summer and winter urban fractions may be due to their different physicochemical characteristics; in fact, the comparison of the two samples' characterization by SEM/EDX and X-ray photoelectron spectroscopy (XPS) analysis showed that in winter the carbonaceous particles are more abundant than in summer and that winter particles carry a greater quantity of organic compounds. We suggest that the higher concentration of organic compounds on fine carbonaceous particles may partially explain the higher activation of RAW 264.7 cells by fine particles.« less

Coarse-graining using the relative entropy and simplex-based optimization methods in VOTCA

NASA Astrophysics Data System (ADS)

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

2014-03-01

Coarse-grained (CG) simulations are an important tool to investigate systems on larger time and length scales. Several methods for systematic coarse-graining were developed, varying in complexity and the property of interest. Thus, the question arises which method best suits a specific class of system and desired application. The Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) provides a uniform platform for coarse-graining methods and allows for their direct comparison. We present recent advances of VOTCA, namely the implementation of the relative entropy method and downhill simplex optimization for coarse-graining. The methods are illustrated by coarse-graining SPC/E bulk water and a water-methanol mixture. Both CG models reproduce the pair distributions accurately. SYM is supported by AFOSR under grant 11157642 and by NSF under grant 1264282. CJ was supported in part by the NSF PHY11-25915 at KITP. K. Koschke acknowledges funding by the Nestle Research Center.

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....

Tracing the Origins of Coarse Sediment in Steep Mountain Catchments

NASA Astrophysics Data System (ADS)

Lukens, C. E.; Riebe, C. S.; Shuster, D. L.; Sklar, L. S.; Beyeler, J. D.

2011-12-01

Where does coarse sediment come from? How long does it persist in channels? What can the origins of sediment tell us about erosional processes and particle comminution in hillslope soils and mountain streams? To address these questions, we present new apatite-helium (AHe) ages from coarse sediment in steep streams of the Sierra Nevada, California. The evolution of grain size in sediment reflects both the physical and chemical breakdown of particles as they travel downstream. It also should reflect the dominant mechanisms of landscape evolution within a watershed. Previous studies have exploited detrital thermochronology in tracing the origins of sand-sized particles; the approach uses AHe age distributions in the sand as a geochemical fingerprint that can be compared with age-elevation relationships in bedrock as an indicator of provenance. In steep catchments, however, sand-sized particles comprise only a fraction of the sediment on the bed, and therefore tell only part of the erosional story. Much can be learned by examining age distributions of coarser grain sizes. Source elevations of coarse particles, for instance, may help reveal the relative importance of erosional mechanisms. For example, if boulders are sourced at high elevations, rock fall and debris flows likely dominate their transport. Conversely, if boulders are sourced only at lower elevations (nearer the sample location), they are more likely produced locally, and thus break down in place. We show how hypotheses such as these can be tested using detrital thermochronology on coarse sediment. We show how our analysis of detrital apatite can be coupled with a numerical model of the evolution of grain-size distributions by particle breakdown and input from slopes. We elaborate on how this approach can shed new quantitative light on processes of sediment production, transport, and breakdown in mountainous settings.

Domain-averaged snow depth over complex terrain from flat field measurements

NASA Astrophysics Data System (ADS)

Helbig, Nora; van Herwijnen, Alec

2017-04-01

Snow depth is an important parameter for a variety of coarse-scale models and applications, such as hydrological forecasting. Since high-resolution snow cover models are computational expensive, simplified snow models are often used. Ground measured snow depth at single stations provide a chance for snow depth data assimilation to improve coarse-scale model forecasts. Snow depth is however commonly recorded at so-called flat fields, often in large measurement networks. While these ground measurement networks provide a wealth of information, various studies questioned the representativity of such flat field snow depth measurements for the surrounding topography. We developed two parameterizations to compute domain-averaged snow depth for coarse model grid cells over complex topography using easy to derive topographic parameters. To derive the two parameterizations we performed a scale dependent analysis for domain sizes ranging from 50m to 3km using highly-resolved snow depth maps at the peak of winter from two distinct climatic regions in Switzerland and in the Spanish Pyrenees. The first, simpler parameterization uses a commonly applied linear lapse rate. For the second parameterization, we first removed the obvious elevation gradient in mean snow depth, which revealed an additional correlation with the subgrid sky view factor. We evaluated domain-averaged snow depth derived with both parameterizations using flat field measurements nearby with the domain-averaged highly-resolved snow depth. This revealed an overall improved performance for the parameterization combining a power law elevation trend scaled with the subgrid parameterized sky view factor. We therefore suggest the parameterization could be used to assimilate flat field snow depth into coarse-scale snow model frameworks in order to improve coarse-scale snow depth estimates over complex topography.

Coarse-graining errors and numerical optimization using a relative entropy framework

NASA Astrophysics Data System (ADS)

Chaimovich, Aviel; Shell, M. Scott

2011-03-01

The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise "first-principles") ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, Srel, that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework.

Graph-based analysis of kinetics on multidimensional potential-energy surfaces.

PubMed

Okushima, T; Niiyama, T; Ikeda, K S; Shimizu, Y

2009-09-01

The aim of this paper is twofold: one is to give a detailed description of an alternative graph-based analysis method, which we call saddle connectivity graph, for analyzing the global topography and the dynamical properties of many-dimensional potential-energy landscapes and the other is to give examples of applications of this method in the analysis of the kinetics of realistic systems. A Dijkstra-type shortest path algorithm is proposed to extract dynamically dominant transition pathways by kinetically defining transition costs. The applicability of this approach is first confirmed by an illustrative example of a low-dimensional random potential. We then show that a coarse-graining procedure tailored for saddle connectivity graphs can be used to obtain the kinetic properties of 13- and 38-atom Lennard-Jones clusters. The coarse-graining method not only reduces the complexity of the graphs, but also, with iterative use, reveals a self-similar hierarchical structure in these clusters. We also propose that the self-similarity is common to many-atom Lennard-Jones clusters.

A coarse-grained model for DNA origami.

PubMed

Reshetnikov, Roman V; Stolyarova, Anastasia V; Zalevsky, Arthur O; Panteleev, Dmitry Y; Pavlova, Galina V; Klinov, Dmitry V; Golovin, Andrey V; Protopopova, Anna D

2018-02-16

Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version.

Burst Testing and Analysis of Superalloy Disks With a Dual Grain Microstructure

NASA Technical Reports Server (NTRS)

Gayda, John; Kantzos, Pete

2006-01-01

Elastic-plastic finite element analyses of room temperature burst tests on four superalloy disks were conducted and reported in this paper. Two alloys, Rene 104 (General Electric Aircraft Engines) and Alloy 10 (Honeywell Engines & Systems), were studied. For both alloys an advanced dual microstructure disk, fine grain bore and coarse grain rim, were analyzed and compared with conventional disks with uniform microstructures, coarse grain for Rene 104 and fine grain for Alloy 10. The analysis and experimental data were in good agreement up to burst. At burst, the analysis underestimated the speed and growth of the Rene 104 disks, but overestimated the speed and growth of the Alloy 10 disks. Fractography revealed that the Alloy 10 disks displayed significant surface microcracking and coalescence in comparison to Rene 104 disks. This phenomenon may help explain the differences between the Alloy 10 disks and the Rene 104 disks, as well as the observed deviations between analytical and experimental data at burst.

A coarse-grained model for DNA origami

PubMed Central

Stolyarova, Anastasia V; Zalevsky, Arthur O; Panteleev, Dmitry Y; Pavlova, Galina V; Klinov, Dmitry V; Golovin, Andrey V; Protopopova, Anna D

2018-01-01

Abstract Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version. PMID:29267876

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.

Seeing through the Canopy: Relationship between Coarse Woody Debris and Forest Structure measured by Airborne Lidar in the Brazilian Amazon

NASA Astrophysics Data System (ADS)

Scaranello, M. A., Sr.; Keller, M. M.; dos-Santos, M. N.; Longo, M.; Pinagé, E. R.; Leitold, V.

2016-12-01

Coarse woody debris is an important but infrequently quantified carbon pool in tropical forests. Based on studies at 12 sites spread across the Brazilian Amazon, we quantified coarse woody debris stocks in intact forests and forests affected by different intensities of degradation by logging and/or fire. Measurement were made in-situ and for the first time field measurements of coarse woody debris were related to structural metrics derived from airborne lidar. Using the line-intercept method we established 84 transects for sampling fallen coarse woody debris and associated inventory plots for sampling standing dead wood in intact, conventional logging, reduced impact logging, burned and burned after logging forests. Overall mean and standard deviation of total coarse woody debris were 50.0 Mg ha-1 and 26.4 Mg ha-1 respectively. Forest degradation increased coarse woody debris stocks compared to intact forests by a factor of 1.7 in reduced impact logging forests and up to 3-fold in burned forests, in a side-by-side comparison of nearby areas. The ratio between coarse woody debris and biomass increased linearly with number of degradation events (R²: 0.67, p<0.01). Individual lidar-derived structural variables strongly correlated with coarse woody debris in intact and reduced impact logging forests: the 5th percentile of last returns for in intact forests (R²: 0.78, p<0.01) and forest gap area, mapped using lidar-derived canopy height model, for reduced impact logging forests (R²: 0.63, p<0.01). Individual gap area also played a weak but significant role in determining coarse woody debris in burned forests (R2: 0.21, p<0.05), but with contrasting trend. Both degradation-specific and general multiple models using lidar-derived variables were good predictor of coarse woody debris stocks in different degradation levels in the Brazilian Amazon. The strong relation of coarse woody debris with lidar derived structural variables suggests an approach for quantifying infrequently measured coarse woody debris over large areas.

Decision support system for the detection and grading of hard exudates from color fundus photographs

NASA Astrophysics Data System (ADS)

Jaafar, Hussain F.; Nandi, Asoke K.; Al-Nuaimy, Waleed

2011-11-01

Diabetic retinopathy is a major cause of blindness, and its earliest signs include damage to the blood vessels and the formation of lesions in the retina. Automated detection and grading of hard exudates from the color fundus image is a critical step in the automated screening system for diabetic retinopathy. We propose novel methods for the detection and grading of hard exudates and the main retinal structures. For exudate detection, a novel approach based on coarse-to-fine strategy and a new image-splitting method are proposed with overall sensitivity of 93.2% and positive predictive value of 83.7% at the pixel level. The average sensitivity of the blood vessel detection is 85%, and the success rate of fovea localization is 100%. For exudate grading, a polar fovea coordinate system is adopted in accordance with medical criteria. Because of its competitive performance and ability to deal efficiently with images of variable quality, the proposed technique offers promising and efficient performance as part of an automated screening system for diabetic retinopathy.

The relative influence of geographic location and reach-scale habitat on benthic invertebrate assemblages in six ecoregions

USGS Publications Warehouse

Munn, M.D.; Waite, I.R.; Larsen, D.P.; Herlihy, A.T.

2009-01-01

The objective of this study was to determine the relative influence of reach-specific habitat variables and geographic location on benthic invertebrate assemblages within six ecoregions across the Western USA. This study included 417 sites from six ecoregions. A total of 301 taxa were collected with the highest richness associated with ecoregions dominated by streams with coarse substrate (19-29 taxa per site). Lowest richness (seven to eight taxa per site) was associated with ecoregions dominated by fine-grain substrate. Principle component analysis (PCA) on reach-scale habitat separated the six ecoregions into those in high-gradient mountainous areas (Coast Range, Cascades, and Southern Rockies) and those in lower-gradient ecoregions (Central Great Plains and Central California Valley). Nonmetric multidimensional scaling (NMS) models performed best in ecoregions dominated by coarse-grain substrate and high taxa richness, along with coarse-grain substrates sites combined from multiple ecoregions regardless of location. In contrast, ecoregions or site combinations dominated by fine-grain substrate had poor model performance (high stress). Four NMS models showed that geographic location (i.e. latitude and longitude) was important for: (1) all ecoregions combined, (2) all sites dominated by coarse-grain sub strate combined, (3) Cascades Ecoregion, and (4) Columbia Ecoregion. Local factors (i.e. substrate or water temperature) seem to be overriding factors controlling invertebrate composition across the West, regardless of geographic location. ?? The Author(s) 2008.

Coarse Point Cloud Registration by Egi Matching of Voxel Clusters

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

Brain electric correlates of strong belief in paranormal phenomena: intracerebral EEG source and regional Omega complexity analyses.

PubMed

Pizzagalli, D; Lehmann, D; Gianotti, L; Koenig, T; Tanaka, H; Wackermann, J; Brugger, P

2000-12-22

The neurocognitive processes underlying the formation and maintenance of paranormal beliefs are important for understanding schizotypal ideation. Behavioral studies indicated that both schizotypal and paranormal ideation are based on an overreliance on the right hemisphere, whose coarse rather than focussed semantic processing may favor the emergence of 'loose' and 'uncommon' associations. To elucidate the electrophysiological basis of these behavioral observations, 35-channel resting EEG was recorded in pre-screened female strong believers and disbelievers during resting baseline. EEG data were subjected to FFT-Dipole-Approximation analysis, a reference-free frequency-domain dipole source modeling, and Regional (hemispheric) Omega Complexity analysis, a linear approach estimating the complexity of the trajectories of momentary EEG map series in state space. Compared to disbelievers, believers showed: more right-located sources of the beta2 band (18.5-21 Hz, excitatory activity); reduced interhemispheric differences in Omega complexity values; higher scores on the Magical Ideation scale; more general negative affect; and more hypnagogic-like reveries after a 4-min eyes-closed resting period. Thus, subjects differing in their declared paranormal belief displayed different active, cerebral neural populations during resting, task-free conditions. As hypothesized, believers showed relatively higher right hemispheric activation and reduced hemispheric asymmetry of functional complexity. These markers may constitute the neurophysiological basis for paranormal and schizotypal ideation.

Analysis of Silicones Released from Household Items and Baby Articles by Direct Analysis in Real Time-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Gross, Jürgen H.

2015-03-01

Direct analysis in real time-mass spectrometry (DART-MS) enables screening of articles of daily use made of polydimethylsiloxanes (PDMS), commonly known as silicone rubber, to assess their tendency to release low molecular weight silicone oligomers. DART-MS analyses were performed on a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Flexible silicone baking molds, a watch band, and a dough scraper, as baby articles different brands of pacifiers, nipples, and a teething ring have been examined. While somewhat arbitrarily chosen, the set can be regarded as representative of household items, baby articles, and other objects made of silicone rubber. For comparison, two brands of silicone septa and as blanks a glass slide and a latex pacifier were included. Differences between the objects were mainly observed in terms of molecular weight distribution and occasional release of other compounds in addition to PDMS. Other than that, all objects made of silicone rubber released significant amounts of PDMS during DART analysis. To provide a coarse quantification, a calibration based on silicone oil was established, which delivered PDMS losses from 20 μg to >100 μg during the 16-s period per measurement. Also, the extraction of baking molds in rapeseed oil demonstrated a PDMS release at the level of 1 μg mg-1. These findings indicate a potential health hazard from frequent or long-term use of such items. This work does not intend to blame certain brands of such articles. Nonetheless, a higher level of awareness of this source of daily silicone intake is suggested.

An automated system for the analysis of G protein-coupled receptor transmembrane binding pockets: alignment, receptor-based pharmacophores, and their application.

PubMed

Kratochwil, Nicole A; Malherbe, Pari; Lindemann, Lothar; Ebeling, Martin; Hoener, Marius C; Mühlemann, Andreas; Porter, Richard H P; Stahl, Martin; Gerber, Paul R

2005-01-01

G protein-coupled receptors (GPCRs) share a common architecture consisting of seven transmembrane (TM) domains. Various lines of evidence suggest that this fold provides a generic binding pocket within the TM region for hosting agonists, antagonists, and allosteric modulators. Here, a comprehensive and automated method allowing fast analysis and comparison of these putative binding pockets across the entire GPCR family is presented. The method relies on a robust alignment algorithm based on conservation indices, focusing on pharmacophore-like relationships between amino acids. Analysis of conservation patterns across the GPCR family and alignment to the rhodopsin X-ray structure allows the extraction of the amino acids lining the TM binding pocket in a so-called ligand binding pocket vector (LPV). In a second step, LPVs are translated to simple 3D receptor pharmacophore models, where each amino acid is represented by a single spherical pharmacophore feature and all atomic detail is omitted. Applications of the method include the assessment of selectivity issues, support of mutagenesis studies, and the derivation of rules for focused screening to identify chemical starting points in early drug discovery projects. Because of the coarseness of this 3D receptor pharmacophore model, however, meaningful scoring and ranking procedures of large sets of molecules are not justified. The LPV analysis of the trace amine-associated receptor family and its experimental validation is discussed as an example. The value of the 3D receptor model is demonstrated for a class C GPCR family, the metabotropic glutamate receptors.

Analysis of silicones released from household items and baby articles by direct analysis in real time-mass spectrometry.

PubMed

Gross, Jürgen H

2015-03-01

Direct analysis in real time-mass spectrometry (DART-MS) enables screening of articles of daily use made of polydimethylsiloxanes (PDMS), commonly known as silicone rubber, to assess their tendency to release low molecular weight silicone oligomers. DART-MS analyses were performed on a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Flexible silicone baking molds, a watch band, and a dough scraper, as baby articles different brands of pacifiers, nipples, and a teething ring have been examined. While somewhat arbitrarily chosen, the set can be regarded as representative of household items, baby articles, and other objects made of silicone rubber. For comparison, two brands of silicone septa and as blanks a glass slide and a latex pacifier were included. Differences between the objects were mainly observed in terms of molecular weight distribution and occasional release of other compounds in addition to PDMS. Other than that, all objects made of silicone rubber released significant amounts of PDMS during DART analysis. To provide a coarse quantification, a calibration based on silicone oil was established, which delivered PDMS losses from 20 μg to >100 μg during the 16-s period per measurement. Also, the extraction of baking molds in rapeseed oil demonstrated a PDMS release at the level of 1 μg mg(-1). These findings indicate a potential health hazard from frequent or long-term use of such items. This work does not intend to blame certain brands of such articles. Nonetheless, a higher level of awareness of this source of daily silicone intake is suggested.

Role of translational entropy in spatially inhomogeneous, coarse-grained models

NASA Astrophysics Data System (ADS)

Langenberg, Marcel; Jackson, Nicholas E.; de Pablo, Juan J.; Müller, Marcus

2018-03-01

Coarse-grained models of polymer and biomolecular systems have enabled the computational study of cooperative phenomena, e.g., self-assembly, by lumping multiple atomistic degrees of freedom along the backbone of a polymer, lipid, or DNA molecule into one effective coarse-grained interaction center. Such a coarse-graining strategy leaves the number of molecules unaltered. In order to treat the surrounding solvent or counterions on the same coarse-grained level of description, one can also stochastically group several of those small molecules into an effective, coarse-grained solvent bead or "fluid element." Such a procedure reduces the number of molecules, and we discuss how to compensate the concomitant loss of translational entropy by density-dependent interactions in spatially inhomogeneous systems.

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

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.

Three-Dimensional Viscous Alternating Direction Implicit Algorithm and Strategies for Shape Optimization

NASA Technical Reports Server (NTRS)

Pandya, Mohagna J.; Baysal, Oktay

1997-01-01

A gradient-based shape optimization based on quasi-analytical sensitivities has been extended for practical three-dimensional aerodynamic applications. The flow analysis has been rendered by a fully implicit, finite-volume formulation of the Euler and Thin-Layer Navier-Stokes (TLNS) equations. Initially, the viscous laminar flow analysis for a wing has been compared with an independent computational fluid dynamics (CFD) code which has been extensively validated. The new procedure has been demonstrated in the design of a cranked arrow wing at Mach 2.4 with coarse- and fine-grid based computations performed with Euler and TLNS equations. The influence of the initial constraints on the geometry and aerodynamics of the optimized shape has been explored. Various final shapes generated for an identical initial problem formulation but with different optimization path options (coarse or fine grid, Euler or TLNS), have been aerodynamically evaluated via a common fine-grid TLNS-based analysis. The initial constraint conditions show significant bearing on the optimization results. Also, the results demonstrate that to produce an aerodynamically efficient design, it is imperative to include the viscous physics in the optimization procedure with the proper resolution. Based upon the present results, to better utilize the scarce computational resources, it is recommended that, a number of viscous coarse grid cases using either a preconditioned bi-conjugate gradient (PbCG) or an alternating-direction-implicit (ADI) method, should initially be employed to improve the optimization problem definition, the design space and initial shape. Optimized shapes should subsequently be analyzed using a high fidelity (viscous with fine-grid resolution) flow analysis to evaluate their true performance potential. Finally, a viscous fine-grid-based shape optimization should be conducted, using an ADI method, to accurately obtain the final optimized shape.

Fracture Analysis of Cast Steel Sling

NASA Astrophysics Data System (ADS)

Li, Xinghui

2018-02-01

The fracture reasons of ZG270-500 cast steel sling are analyzed through such means as macroscopic morphology analysis, chemical composition analysis, and microscopic metallography analysis. Results: coarse Widmanstatten structure and casting defects occurring in casting and subsequent heat treatment process reduce the strength, plasticity and toughness of the steel, which is the main reason of brittle fracture of the sling during work, and corresponding improvement suggestions are proposed herein.

Effects of coarse chalk dust particles (2.5-10 μm) on respiratory burst and oxidative stress in alveolar macrophages.

PubMed

Zhang, Yuexia; Yang, Zhenhua; Feng, Yan; Li, Ruijin; Zhang, Quanxi; Geng, Hong; Dong, Chuan

2015-08-01

The main aim of the present study was to examine in vitro responses of rat alveolar macrophages (AMs) exposed to coarse chalk dust particles (particulate matter in the size range 2.5-10 μm, PM(coarse)) by respiratory burst and oxidative stress. Chalk PM(coarse)-induced respiratory burst in AMs was measured by using a luminol-dependent chemiluminescence (CL) method. Also, the cell viability; lactate dehydrogenase (LDH) release; levels of cellular superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), malondialdehyde (MDA), and acid phosphatase (ACP); plasma membrane ATPase; and extracellular nitric oxide (NO) level were determined 4 h following the treatment with the different dosages of chalk PM(coarse). The results showed that chalk PM(coarse) initiated the respiratory burst of AMs as indicated by strong CL, which was inhibited by diphenyleneiodonium chloride and L-N-nitro-L-arginine methyl ester hydrochloride. It suggested that chalk PM(coarse) induced the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in AMs. This hypothesis was confirmed by the fact that chalk PM(coarse) resulted in a significant decrease of intracellular SOD, GSH, ACP, and ATPase levels and a notable increase of intracellular CAT, MDA content, and extracellular NO level, consequently leading to a decrease of the cell viability and a increase of LDH release. It was concluded that AMs exposed to chalk PM(coarse) can suffer from cytotoxicity which may be mediated by generation of excessive ROS/RNS. Graphical Abstract The possible mechanism of coarse chalk particles-induced adverse effects in AMs.

Expeditious illustration of layer-cake models on and above a tactile surface

NASA Astrophysics Data System (ADS)

Lopes, Daniel Simões; Mendes, Daniel; Sousa, Maurício; Jorge, Joaquim

2016-05-01

Too often illustrating and visualizing 3D geological concepts are performed by sketching in 2D mediums, which may limit drawing performance of initial concepts. Here, the potential of expeditious geological modeling brought by hand gestures is explored. A spatial interaction system was developed to enable rapid modeling, editing, and exploration of 3D layer-cake objects. User interactions are acquired with motion capture and touch screen technologies. Virtual immersion is guaranteed by using stereoscopic technology. The novelty consists of performing expeditious modeling of coarse geological features with only a limited set of hand gestures. Results from usability-studies show that the proposed system is more efficient when compared to a windows-icon-menu-pointer modeling application.

Upscaling of Mixed Finite Element Discretization Problems by the Spectral AMGe Method

DOE PAGES

Kalchev, Delyan Z.; Lee, C. S.; Villa, U.; ...

2016-09-22

Here, we propose two multilevel spectral techniques for constructing coarse discretization spaces for saddle-point problems corresponding to PDEs involving a divergence constraint, with a focus on mixed finite element discretizations of scalar self-adjoint second order elliptic equations on general unstructured grids. We use element agglomeration algebraic multigrid (AMGe), which employs coarse elements that can have nonstandard shape since they are agglomerates of fine-grid elements. The coarse basis associated with each agglomerated coarse element is constructed by solving local eigenvalue problems and local mixed finite element problems. This construction leads to stable upscaled coarse spaces and guarantees the inf-sup compatibility ofmore » the upscaled discretization. Also, the approximation properties of these upscaled spaces improve by adding more local eigenfunctions to the coarse spaces. The higher accuracy comes at the cost of additional computational effort, as the sparsity of the resulting upscaled coarse discretization (referred to as operator complexity) deteriorates when we introduce additional functions in the coarse space. We also provide an efficient solver for the coarse (upscaled) saddle-point system by employing hybridization, which leads to a symmetric positive definite (s.p.d.) reduced system for the Lagrange multipliers, and to solve the latter s.p.d. system, we use our previously developed spectral AMGe solver. Numerical experiments, in both two and three dimensions, are provided to illustrate the efficiency of the proposed upscaling technique.« less

Upscaling of Mixed Finite Element Discretization Problems by the Spectral AMGe Method

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

Kalchev, Delyan Z.; Lee, C. S.; Villa, U.

Here, we propose two multilevel spectral techniques for constructing coarse discretization spaces for saddle-point problems corresponding to PDEs involving a divergence constraint, with a focus on mixed finite element discretizations of scalar self-adjoint second order elliptic equations on general unstructured grids. We use element agglomeration algebraic multigrid (AMGe), which employs coarse elements that can have nonstandard shape since they are agglomerates of fine-grid elements. The coarse basis associated with each agglomerated coarse element is constructed by solving local eigenvalue problems and local mixed finite element problems. This construction leads to stable upscaled coarse spaces and guarantees the inf-sup compatibility ofmore » the upscaled discretization. Also, the approximation properties of these upscaled spaces improve by adding more local eigenfunctions to the coarse spaces. The higher accuracy comes at the cost of additional computational effort, as the sparsity of the resulting upscaled coarse discretization (referred to as operator complexity) deteriorates when we introduce additional functions in the coarse space. We also provide an efficient solver for the coarse (upscaled) saddle-point system by employing hybridization, which leads to a symmetric positive definite (s.p.d.) reduced system for the Lagrange multipliers, and to solve the latter s.p.d. system, we use our previously developed spectral AMGe solver. Numerical experiments, in both two and three dimensions, are provided to illustrate the efficiency of the proposed upscaling technique.« less

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...

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...

Coarse-graining and self-dissimilarity of complex networks

NASA Astrophysics Data System (ADS)

Itzkovitz, Shalev; Levitt, Reuven; Kashtan, Nadav; Milo, Ron; Itzkovitz, Michael; Alon, Uri

2005-01-01

Can complex engineered and biological networks be coarse-grained into smaller and more understandable versions in which each node represents an entire pattern in the original network? To address this, we define coarse-graining units as connectivity patterns which can serve as the nodes of a coarse-grained network and present algorithms to detect them. We use this approach to systematically reverse-engineer electronic circuits, forming understandable high-level maps from incomprehensible transistor wiring: first, a coarse-grained version in which each node is a gate made of several transistors is established. Then the coarse-grained network is itself coarse-grained, resulting in a high-level blueprint in which each node is a circuit module made of many gates. We apply our approach also to a mammalian protein signal-transduction network, to find a simplified coarse-grained network with three main signaling channels that resemble multi-layered perceptrons made of cross-interacting MAP-kinase cascades. We find that both biological and electronic networks are “self-dissimilar,” with different network motifs at each level. The present approach may be used to simplify a variety of directed and nondirected, natural and designed networks.

Coarse-graining errors and numerical optimization using a relative entropy framework.

PubMed

Chaimovich, Aviel; Shell, M Scott

2011-03-07

The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise "first-principles") ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, S(rel), that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework. © 2011 American Institute of Physics.

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

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.

Effect of fly ash on the strength of porous concrete using recycled coarse aggregate to replace low-quality natural coarse aggregate

NASA Astrophysics Data System (ADS)

Arifi, Eva; Cahya, Evi Nur; Christin Remayanti, N.

2017-09-01

The performance of porous concrete made of recycled coarse aggregate was investigated. Fly ash was used as cement partial replacement. In this study, the strength of recycled aggregate was coMPared to low quality natural coarse aggregate which has high water absorption. Compression strength and tensile splitting strength test were conducted to evaluate the performance of porous concrete using fly ash as cement replacement. Results have shown that the utilization of recycled coarse aggregate up to 75% to replace low quality natural coarse aggregate with high water absorption increases compressive strength and splitting tensile strength of porous concrete. Using fly ash up to 25% as cement replacement improves compressive strength and splitting tensile strength of porous concrete.

Effects of Jet-Milled Defatted Soy Flour on the Physicochemical and Sensorial Properties of Hamburger Patties

PubMed Central

2017-01-01

We investigated the physicochemical and sensorial properties of hamburger patties made with three different defatted soybean flour (DSF) preparations which differed in particle size. Coarse (Dv50=259.3±0.6 µm), fine (Dv50=91.5±0.5 µm), and superfine (Dv50=3.7±0.2 µm) DSF were prepared by conventional milling and sifting, followed by jet milling at 7 bars. Hamburger patties containing 5% of each DSF were prepared for a property analysis. The hamburger patties made with 5% superfine DSF showed the lowest cooking loss among the treatment groups (p<0.05). The patties with superfine DSF also retained the texture profile values of the control patties in terms of hardness, gumminess, springiness, and chewiness, while the addition of coarse and fine DSF increased the hardness and chewiness significantly (p<0.05). The sensorial results of quantitative descriptive analysis (QDA) indicate that the patties containing superfine DSF were softer and tenderer than the controls (p<0.05). Although the overall acceptability of the patties made with coarse and fine DSF was poor, the overall acceptability of the superfine DSF patty was the same as that of the control patty. These results suggest that superfine DSF is an excellent food material that can supply dietary fiber, while maintaining the physical characteristics and texture of hamburger patty. PMID:29725205

Effects of Jet-Milled Defatted Soy Flour on the Physicochemical and Sensorial Properties of Hamburger Patties.

PubMed

Cho, Hyun-Woo; Jung, Young-Min; Auh, Joong-Hyuck; Lee, Dong-Un

2017-01-01

We investigated the physicochemical and sensorial properties of hamburger patties made with three different defatted soybean flour (DSF) preparations which differed in particle size. Coarse (Dv 50 =259.3±0.6 µm), fine (Dv 50 =91.5±0.5 µm), and superfine (Dv 50 =3.7±0.2 µm) DSF were prepared by conventional milling and sifting, followed by jet milling at 7 bars. Hamburger patties containing 5% of each DSF were prepared for a property analysis. The hamburger patties made with 5% superfine DSF showed the lowest cooking loss among the treatment groups ( p <0.05). The patties with superfine DSF also retained the texture profile values of the control patties in terms of hardness, gumminess, springiness, and chewiness, while the addition of coarse and fine DSF increased the hardness and chewiness significantly ( p <0.05). The sensorial results of quantitative descriptive analysis (QDA) indicate that the patties containing superfine DSF were softer and tenderer than the controls ( p <0.05). Although the overall acceptability of the patties made with coarse and fine DSF was poor, the overall acceptability of the superfine DSF patty was the same as that of the control patty. These results suggest that superfine DSF is an excellent food material that can supply dietary fiber, while maintaining the physical characteristics and texture of hamburger patty.

Principal component analysis acceleration of rovibrational coarse-grain models for internal energy excitation and dissociation

NASA Astrophysics Data System (ADS)

Bellemans, Aurélie; Parente, Alessandro; Magin, Thierry

2018-04-01

The present work introduces a novel approach for obtaining reduced chemistry representations of large kinetic mechanisms in strong non-equilibrium conditions. The need for accurate reduced-order models arises from compression of large ab initio quantum chemistry databases for their use in fluid codes. The method presented in this paper builds on existing physics-based strategies and proposes a new approach based on the combination of a simple coarse grain model with Principal Component Analysis (PCA). The internal energy levels of the chemical species are regrouped in distinct energy groups with a uniform lumping technique. Following the philosophy of machine learning, PCA is applied on the training data provided by the coarse grain model to find an optimally reduced representation of the full kinetic mechanism. Compared to recently published complex lumping strategies, no expert judgment is required before the application of PCA. In this work, we will demonstrate the benefits of the combined approach, stressing its simplicity, reliability, and accuracy. The technique is demonstrated by reducing the complex quantum N2(g+1Σ) -N(S4u ) database for studying molecular dissociation and excitation in strong non-equilibrium. Starting from detailed kinetics, an accurate reduced model is developed and used to study non-equilibrium properties of the N2(g+1Σ) -N(S4u ) system in shock relaxation simulations.

Simulation study of entropy production in the one-dimensional Vlasov system

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

Dai, Zongliang, E-mail: liangliang1223@gmail.com; Wang, Shaojie

2016-07-15

The coarse-grain averaged distribution function of the one-dimensional Vlasov system is obtained by numerical simulation. The entropy productions in cases of the random field, the linear Landau damping, and the bump-on-tail instability are computed with the coarse-grain averaged distribution function. The computed entropy production is converged with increasing length of coarse-grain average. When the distribution function differs slightly from a Maxwellian distribution, the converged value agrees with the result computed by using the definition of thermodynamic entropy. The length of the coarse-grain average to compute the coarse-grain averaged distribution function is discussed.

Neural mechanisms of coarse-to-fine discrimination in the visual cortex.

PubMed

Purushothaman, Gopathy; Chen, Xin; Yampolsky, Dmitry; Casagrande, Vivien A

2014-12-01

Vision is a dynamic process that refines the spatial scale of analysis over time, as evidenced by a progressive improvement in the ability to detect and discriminate finer details. To understand coarse-to-fine discrimination, we studied the dynamics of spatial frequency (SF) response using reverse correlation in the primary visual cortex (V1) of the primate. In a majority of V1 cells studied, preferred SF either increased monotonically with time (group 1) or changed nonmonotonically, with an initial increase followed by a decrease (group 2). Monotonic shift in preferred SF occurred with or without an early suppression at low SFs. Late suppression at high SFs always accompanied nonmonotonic SF dynamics. Bayesian analysis showed that SF discrimination performance and best discriminable SF frequencies changed with time in different ways in the two groups of neurons. In group 1 neurons, SF discrimination performance peaked on both left and right flanks of the SF tuning curve at about the same time. In group 2 neurons, peak discrimination occurred on the right flank (high SFs) later than on the left flank (low SFs). Group 2 neurons were also better discriminators of high SFs. We examined the relationship between the time at which SF discrimination performance peaked on either flank of the SF tuning curve and the corresponding best discriminable SFs in both neuronal groups. This analysis showed that the population best discriminable SF increased with time in V1. These results suggest neural mechanisms for coarse-to-fine discrimination behavior and that this process originates in V1 or earlier. Copyright © 2014 the American Physiological Society.

On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies

NASA Astrophysics Data System (ADS)

Degiacomi, Matteo T.

2018-05-01

Ion mobility mass spectrometry (IM/MS) can provide structural information on intact protein complexes. Such data, including connectivity and collision cross sections (CCS) of assemblies' subunits, can in turn be used as a guide to produce representative super coarse-grained models. These models are constituted by ensembles of overlapping spheres, each representing a protein subunit. A model is considered plausible if the CCS and sphere-overlap levels of its subunits fall within predetermined confidence intervals. While the first is determined by experimental error, the latter is based on a statistical analysis on a range of protein dimers. Here, we first propose a new expression to describe the overlap between two spheres. Then we analyze the effect of specific overlap cutoff choices on the precision and accuracy of super coarse-grained models. Finally, we propose a method to determine overlap cutoff levels on a per-case scenario, based on collected CCS data, and show that it can be applied to the characterization of the assembly topology of symmetrical homo-multimers. [Figure not available: see fulltext.

Comparative Performance Analysis of Coarse Solvers for Algebraic Multigrid on Multicore and Manycore Architectures

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

Druinsky, Alex; Ghysels, Pieter; Li, Xiaoye S.

In this paper, we study the performance of a two-level algebraic-multigrid algorithm, with a focus on the impact of the coarse-grid solver on performance. We consider two algorithms for solving the coarse-space systems: the preconditioned conjugate gradient method and a new robust HSS-embedded low-rank sparse-factorization algorithm. Our test data comes from the SPE Comparative Solution Project for oil-reservoir simulations. We contrast the performance of our code on one 12-core socket of a Cray XC30 machine with performance on a 60-core Intel Xeon Phi coprocessor. To obtain top performance, we optimized the code to take full advantage of fine-grained parallelism andmore » made it thread-friendly for high thread count. We also developed a bounds-and-bottlenecks performance model of the solver which we used to guide us through the optimization effort, and also carried out performance tuning in the solver’s large parameter space. Finally, as a result, significant speedups were obtained on both machines.« less

A Critical Study of Agglomerated Multigrid Methods for Diffusion

NASA Technical Reports Server (NTRS)

Nishikawa, Hiroaki; Diskin, Boris; Thomas, James L.

2011-01-01

Agglomerated multigrid techniques used in unstructured-grid methods are studied critically for a model problem representative of laminar diffusion in the incompressible limit. The studied target-grid discretizations and discretizations used on agglomerated grids are typical of current node-centered formulations. Agglomerated multigrid convergence rates are presented using a range of two- and three-dimensional randomly perturbed unstructured grids for simple geometries with isotropic and stretched grids. Two agglomeration techniques are used within an overall topology-preserving agglomeration framework. The results show that multigrid with an inconsistent coarse-grid scheme using only the edge terms (also referred to in the literature as a thin-layer formulation) provides considerable speedup over single-grid methods but its convergence deteriorates on finer grids. Multigrid with a Galerkin coarse-grid discretization using piecewise-constant prolongation and a heuristic correction factor is slower and also grid-dependent. In contrast, grid-independent convergence rates are demonstrated for multigrid with consistent coarse-grid discretizations. Convergence rates of multigrid cycles are verified with quantitative analysis methods in which parts of the two-grid cycle are replaced by their idealized counterparts.

A Critical Study of Agglomerated Multigrid Methods for Diffusion

NASA Technical Reports Server (NTRS)

Thomas, James L.; Nishikawa, Hiroaki; Diskin, Boris

2009-01-01

Agglomerated multigrid techniques used in unstructured-grid methods are studied critically for a model problem representative of laminar diffusion in the incompressible limit. The studied target-grid discretizations and discretizations used on agglomerated grids are typical of current node-centered formulations. Agglomerated multigrid convergence rates are presented using a range of two- and three-dimensional randomly perturbed unstructured grids for simple geometries with isotropic and highly stretched grids. Two agglomeration techniques are used within an overall topology-preserving agglomeration framework. The results show that multigrid with an inconsistent coarse-grid scheme using only the edge terms (also referred to in the literature as a thin-layer formulation) provides considerable speedup over single-grid methods but its convergence deteriorates on finer grids. Multigrid with a Galerkin coarse-grid discretization using piecewise-constant prolongation and a heuristic correction factor is slower and also grid-dependent. In contrast, grid-independent convergence rates are demonstrated for multigrid with consistent coarse-grid discretizations. Actual cycle results are verified using quantitative analysis methods in which parts of the cycle are replaced by their idealized counterparts.

Analysis of the Cytomorphological Features in Atypical Urine Specimens following Application of The Paris System for Reporting Urinary Cytology.

PubMed

Glass, Ryan; Rosen, Lisa; Chau, Karen; Sheikh-Fayyaz, Sylvat; Farmer, Peter; Coutsouvelis, Constantinos; Slim, Farah; Brenkert, Ryan; Das, Kasturi; Raab, Stephen; Cocker, Rubina

2018-01-01

This study investigates the use of The Paris System (TPS) for Reporting Urinary Cytopathology and examines the performance of individual and combined morphological features in atypical urine cytologies. We reviewed 118 atypical cytologies with subsequent bladder biopsies for the presence of several morphological features and reclassified them into Paris System categories. The sensitivity and specificity of individual and combined features were calculated along with the risk of malignancy. An elevated nuclear-to-cytoplasmic ratio was only predictive of malignancy if seen in single cells, while irregular nuclear borders, hyperchromasia, and coarse granular chromatin were predictive in single cells and in groups. Identification of coarse chromatin alone yielded a malignancy risk comparable to 2-feature combinations. The use of TPS criteria identified the specimens at a higher risk of malignancy. Our findings support the use of TPS criteria, suggesting that the presence of coarse chromatin is more specific than other individual features, and confirming that cytologic atypia is more worrisome in single cells than in groups. © 2017 S. Karger AG, Basel.

A rapid solvent accessible surface area estimator for coarse grained molecular simulations.

PubMed

Wei, Shuai; Brooks, Charles L; Frank, Aaron T

2017-06-05

The rapid and accurate calculation of solvent accessible surface area (SASA) is extremely useful in the energetic analysis of biomolecules. For example, SASA models can be used to estimate the transfer free energy associated with biophysical processes, and when combined with coarse-grained simulations, can be particularly useful for accounting for solvation effects within the framework of implicit solvent models. In such cases, a fast and accurate, residue-wise SASA predictor is highly desirable. Here, we develop a predictive model that estimates SASAs based on Cα-only protein structures. Through an extensive comparison between this method and a comparable method, POPS-R, we demonstrate that our new method, Protein-C α Solvent Accessibilities or PCASA, shows better performance, especially for unfolded conformations of proteins. We anticipate that this model will be quite useful in the efficient inclusion of SASA-based solvent free energy estimations in coarse-grained protein folding simulations. PCASA is made freely available to the academic community at https://github.com/atfrank/PCASA. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Stochastic entangled chain dynamics of dense polymer solutions.

PubMed

Kivotides, Demosthenes; Wilkin, S Louise; Theofanous, Theo G

2010-10-14

We propose an adjustable-parameter-free, entangled chain dynamics model of dense polymer solutions. The model includes the self-consistent dynamics of molecular chains and solvent by describing the former via coarse-grained polymer dynamics that incorporate hydrodynamic interaction effects, and the latter via the forced Stokes equation. Real chain elasticity is modeled via the inclusion of a Pincus regime in the polymer's force-extension curve. Excluded volume effects are taken into account via the combined action of coarse-grained intermolecular potentials and explicit geometric tracking of chain entanglements. We demonstrate that entanglements are responsible for a new (compared to phantom chain dynamics), slow relaxation mode whose characteristic time scale agrees very well with experiment. Similarly good agreement between theory and experiment is also obtained for the equilibrium chain size. We develop methods for the solution of the model in periodic flow domains and apply them to the computation of entangled polymer solutions in equilibrium. We show that the number of entanglements Π agrees well with the number of entanglements expected on the basis of tube theory, satisfactorily reproducing the latter's scaling of Π with the polymer volume fraction φ. Our model predicts diminishing chain size with concentration, thus vindicating Flory's suggestion of excluded volume effects screening in dense solutions. The predicted scaling of chain size with φ is consistent with the heuristic, Flory theory based value.

Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

PubMed

Shen, Lin; Yang, Weitao

2016-04-12

We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

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

PubMed

Wei, Dongshan; Wang, Feng

2010-08-28

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.

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.

Sensitivity of aerosol radiative forcing efficiency to the coarse mode contributions across aerosol regimes

NASA Astrophysics Data System (ADS)

McComiskey, A. C.; Telg, H.; Sheridan, P. J.; Kassianov, E.

2017-12-01

The coarse mode contribution to the aerosol radiative effect in a range of clean and turbid aerosol regimes has not been well quantified. While the coarse-mode radiative effect in turbid conditions is generally assumed to be consequential, the effect in clean conditions has likely been underestimated. We survey ground-based in situ measurements of the coarse mode fraction of aerosol optical properties measured around the globe over the past 20 years by the DOE Atmospheric Radiation Measurement Facility and the NOAA Global Monitoring Division. The aerosol forcing efficiency is presented, allowing an evaluation of where the aerosol coarse mode might be climatologically significant.

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.

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.

Resolving Properties of Polymers and Nanoparticle Assembly through Coarse-Grained Computational Studies.

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

Grest, Gary S.

2017-09-01

Coupled length and time scales determine the dynamic behavior of polymers and polymer nanocomposites and underlie their unique properties. To resolve the properties over large time and length scales it is imperative to develop coarse grained models which retain the atomistic specificity. Here we probe the degree of coarse graining required to simultaneously retain significant atomistic details a nd access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using polyethylene as a model system, we probe how the coarse - graining scale affects themore » measured dynamics with different number methylene group s per coarse - grained beads. Using these models we simulate polyethylene melts for times over 500 ms to study the viscoelastic properties of well - entangled polymer melts and large nanoparticle assembly as the nanoparticles are driven close enough to form nanostructures.« less

Refinement of Out of Circularity and Thickness Measurements of a Cylinder for Finite Element Analysis

DTIC Science & Technology

2016-09-01

UNCLASSIFIED UNCLASSIFIED Refinement of Out of Circularity and Thickness Measurements of a Cylinder for Finite Element Analysis...significant effect on the collapse strength and must be accurately represented in finite element analysis to obtain accurate results. Often it is necessary...to interpolate measurements from a relatively coarse grid to a refined finite element model and methods that have wide general acceptance are

Evaluation of various coarse aggregate concretes : final report.

DOT National Transportation Integrated Search

1983-10-01

This study was initiated to determine the properties of concrete using three types of coarse aggregate. The coarse aggregates evaluated in this study included silicious gravel, the standard aggregate for concrete in the state, with sandstone and lime...

Audio-guided audiovisual data segmentation, indexing, and retrieval

NASA Astrophysics Data System (ADS)

Zhang, Tong; Kuo, C.-C. Jay

1998-12-01

While current approaches for video segmentation and indexing are mostly focused on visual information, audio signals may actually play a primary role in video content parsing. In this paper, we present an approach for automatic segmentation, indexing, and retrieval of audiovisual data, based on audio content analysis. The accompanying audio signal of audiovisual data is first segmented and classified into basic types, i.e., speech, music, environmental sound, and silence. This coarse-level segmentation and indexing step is based upon morphological and statistical analysis of several short-term features of the audio signals. Then, environmental sounds are classified into finer classes, such as applause, explosions, bird sounds, etc. This fine-level classification and indexing step is based upon time- frequency analysis of audio signals and the use of the hidden Markov model as the classifier. On top of this archiving scheme, an audiovisual data retrieval system is proposed. Experimental results show that the proposed approach has an accuracy rate higher than 90 percent for the coarse-level classification, and higher than 85 percent for the fine-level classification. Examples of audiovisual data segmentation and retrieval are also provided.

A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization

NASA Astrophysics Data System (ADS)

Li, Zhen; Bian, Xin; Yang, Xiu; Karniadakis, George Em

2016-07-01

We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of a star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models cannot be selected arbitrarily. If the free parameters are properly defined, the reverse CG procedure also yields an accurate effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces the many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn.

Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

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

Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr; Schnell, Benoît

2014-04-07

We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining levelmore » on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.« less

A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization.

PubMed

Li, Zhen; Bian, Xin; Yang, Xiu; Karniadakis, George Em

2016-07-28

We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of a star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models cannot be selected arbitrarily. If the free parameters are properly defined, the reverse CG procedure also yields an accurate effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces the many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn.

Recognition of units in coarse, unconsolidated braided-stream deposits from geophysical log data with principal components analysis

USGS Publications Warehouse

Morin, R.H.

1997-01-01

Returns from drilling in unconsolidated cobble and sand aquifers commonly do not identify lithologic changes that may be meaningful for Hydrogeologic investigations. Vertical resolution of saturated, Quaternary, coarse braided-slream deposits is significantly improved by interpreting natural gamma (G), epithermal neutron (N), and electromagnetically induced resistivity (IR) logs obtained from wells at the Capital Station site in Boise, Idaho. Interpretation of these geophysical logs is simplified because these sediments are derived largely from high-gamma-producing source rocks (granitics of the Boise River drainage), contain few clays, and have undergone little diagenesis. Analysis of G, N, and IR data from these deposits with principal components analysis provides an objective means to determine if units can be recognized within the braided-stream deposits. In particular, performing principal components analysis on G, N, and IR data from eight wells at Capital Station (1) allows the variable system dimensionality to be reduced from three to two by selecting the two eigenvectors with the greatest variance as axes for principal component scatterplots, (2) generates principal components with interpretable physical meanings, (3) distinguishes sand from cobble-dominated units, and (4) provides a means to distinguish between cobble-dominated units.

Effects of coarse aggregate on the physical properties of Florida concrete mixes.

DOT National Transportation Integrated Search

2015-10-01

Portland cement concrete is a heterogeneous, composite material composed of coarse and fine granular material : embedded in a matrix of hardened paste. The coarse material is aggregate, which is primarily used as inexpensive filler : and comprises th...

Pb, Sr and Nd isotopic composition and trace element characteristics of coarse airborne particles collected with passive samplers

NASA Astrophysics Data System (ADS)

Hoàng-Hòa, Thi Bich; Stille, Peter; Dietze, Volker; Guéguen, Florence; Perrone, Thierry; Gieré, Reto

2015-09-01

Passive samplers for collection of coarse airborne particulate matter have been installed in and around the coal-mining town of Cam Pha, Quang Ninh Province (Vietnam). Analysis of Pb, Sr, and Nd isotope ratios and of major and trace element distribution patterns in atmospheric particulates collected at three stations allowed for the identification of four important dust components: (1) coal dust from an open-pit mine and fly ash particles from a coal-fired power station, (2) diesel soot, (3) traffic dust from metal, tire and pavement abrasion, and (4) limestone-derived dust. Outside of the coal-mining area, traffic-derived dust defines the atmospheric baseline composition of the studied environment.

High diversity of fungi in air particulate matter.

PubMed

Fröhlich-Nowoisky, Janine; Pickersgill, Daniel A; Després, Viviane R; Pöschl, Ulrich

2009-08-04

Fungal spores can account for large proportions of air particulate matter, and they may potentially influence the hydrological cycle and climate as nuclei for water droplets and ice crystals in clouds, fog, and precipitation. Moreover, some fungi are major pathogens and allergens. The diversity of airborne fungi is, however, not well-known. By DNA analysis we found pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter, with more plant pathogens in the coarse fraction and more human pathogens and allergens in the respirable fine particle fraction (<3 microm). Moreover, the ratio of Basidiomycota to Ascomycota was found to be much higher than previously assumed, which might also apply to the biosphere.

Multigrid methods for differential equations with highly oscillatory coefficients

NASA Technical Reports Server (NTRS)

Engquist, Bjorn; Luo, Erding

1993-01-01

New coarse grid multigrid operators for problems with highly oscillatory coefficients are developed. These types of operators are necessary when the characters of the differential equations on coarser grids or longer wavelengths are different from that on the fine grid. Elliptic problems for composite materials and different classes of hyperbolic problems are practical examples. The new coarse grid operators can be constructed directly based on the homogenized differential operators or hierarchically computed from the finest grid. Convergence analysis based on the homogenization theory is given for elliptic problems with periodic coefficients and some hyperbolic problems. These are classes of equations for which there exists a fairly complete theory for the interaction between shorter and longer wavelengths in the problems. Numerical examples are presented.

Evaluating lubricant performance by 3D profilometry of wear scars

NASA Astrophysics Data System (ADS)

Georgescu, C.; Deleanu, L.; Pirvu, C.

2016-08-01

Due to improvement in analysing surface texture and optical instruments for investigating the texture surface, the authors propose to evaluate the lubricant performance by analysing the change in several 3D parameters in comparison to an analysis on 2D profile. All the surface of the wear scar generated on the four ball machine is investigated and the conclusion is that from the tribological point of view, the 3D parameters reflect better the surface quality evolution after testing. Investigation was done on the wear scars generated on the three fixed balls, for five lubricants: a non-additivated transmission mineral oil (T90), two grades of rapeseed oil (coarse degummed and refined) and two grades of soybean oil (coarse and degummed).

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 variability of these pollutants.

Scalable parallel communications

NASA Technical Reports Server (NTRS)

Maly, K.; Khanna, S.; Overstreet, C. M.; Mukkamala, R.; Zubair, M.; Sekhar, Y. S.; Foudriat, E. C.

1992-01-01

Coarse-grain parallelism in networking (that is, the use of multiple protocol processors running replicated software sending over several physical channels) can be used to provide gigabit communications for a single application. Since parallel network performance is highly dependent on real issues such as hardware properties (e.g., memory speeds and cache hit rates), operating system overhead (e.g., interrupt handling), and protocol performance (e.g., effect of timeouts), we have performed detailed simulations studies of both a bus-based multiprocessor workstation node (based on the Sun Galaxy MP multiprocessor) and a distributed-memory parallel computer node (based on the Touchstone DELTA) to evaluate the behavior of coarse-grain parallelism. Our results indicate: (1) coarse-grain parallelism can deliver multiple 100 Mbps with currently available hardware platforms and existing networking protocols (such as Transmission Control Protocol/Internet Protocol (TCP/IP) and parallel Fiber Distributed Data Interface (FDDI) rings); (2) scale-up is near linear in n, the number of protocol processors, and channels (for small n and up to a few hundred Mbps); and (3) since these results are based on existing hardware without specialized devices (except perhaps for some simple modifications of the FDDI boards), this is a low cost solution to providing multiple 100 Mbps on current machines. In addition, from both the performance analysis and the properties of these architectures, we conclude: (1) multiple processors providing identical services and the use of space division multiplexing for the physical channels can provide better reliability than monolithic approaches (it also provides graceful degradation and low-cost load balancing); (2) coarse-grain parallelism supports running several transport protocols in parallel to provide different types of service (for example, one TCP handles small messages for many users, other TCP's running in parallel provide high bandwidth service to a single application); and (3) coarse grain parallelism will be able to incorporate many future improvements from related work (e.g., reduced data movement, fast TCP, fine-grain parallelism) also with near linear speed-ups.

Source characterization of fine and coarse particles at the East Mediterranean coast

NASA Astrophysics Data System (ADS)

Mamane, Yaacov; Perrino, Cinzia; Yossef, Osnat; Catrambone, Maria

Fine and coarse atmospheric particles were collected in Ashdod—a midsize industrial city on the southeastern Mediterranean coast, and in Gedera—a rural site, to characterize ambient particles and to determine their long-range transport during two major seasons—winter and summer. Manual PM2.5 and PM10 samplers, dichotomous samplers, continuous automated PM10 samplers, and denuders were used to sample particulate and gaseous pollutants. Fine and coarse concentrations in Ashdod were 21.2 and 39.6 μg m -3, and 23.9 and 30.5 μg m -3 in the fall-winter and summer campaigns, respectively. Crustal material, as calcites or dolomites mixed with silicates, dominated the coarse fraction and also the fine fraction on dusty days. In the fall-winter, S, P, and Ni were coupled with minerals. Coarse Ni was associated with crustal material during dust storms, while P originated from shipping and deposition of phosphates in the urban area around. Sulfates dominated the fine fractions in the summer season averaging 12 μg m -3. Multivariate analysis indicated that S was associated with As and Se, V and Ni, both associated with heavy fuel combustion, and Zn and Pb. In winter, those mixed sources were local, but in summer they were part of long-range transport. In the fall-winter, Zn and Pb were strongly associated with Mn, Ga, and Cu—elements emitted from either traffic or metal processing plants. Although the influence of crustal material on both size fractions was significant, most heavy metals were associated with PM2.5. Higher concentrations were linked to a larger number of particles in this fraction, to a larger surface area available for biochemical reaction [Harrison, R., Shi, J., Xi, S., Khan, A., Mark, D., Kinnersley, R., Yin, J., Philos, T., 2000. Measurement of number, mass and size distribution of particles in the atmosphere. Philosophical Transactions of the Royal Society 358, 2567-2579], and finally to a larger concern in regards to health effects.

Aerosol characteristics and sources for the Amazon basin during the wet season

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

Artaxo, P.; Maenhaut, W.; Storms, H.

1990-09-20

Fine (< 2.0 {mu}m) and coarse (2.0 - 15 {mu}m) aerosol fractions were collected using stacked filter units, at three sites under the forest canopy and at three levels of a tower inside the jungle. Particle-induced x-ray emission (PIXE) was used to measure concentrations Na, Mg, Al, Si, P, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Ni, Cu, Zn, Br, Rb, Sr, Zr, and Pb. Morphological and trace element measurements of individual particles were carried out by automated electron probe x-ray microanalysis. Gravimetric analysis was performed to obtain the fine and coarse aerosol mass concentration. The concentrations ofmore » soil dust related elements (Al, Si, Ti, Fe, Mn) were 5 times larger in the wet season compared to the 1985 ABLE 2A dry season experiment. Biogenic aerosol related elements in the fine fraction showed lower concentrations in the wet season. Fine aerosol mass concentration averaged only 2.1 {plus minus} 0.7 {mu}g m{sup {minus}3}, while the average coarse mass concentration was 6.1 {plus minus} 1.8 {mu}g m{sup {minus}3}. Sulfur concentrations averaged 76 {plus minus} 14 ng m{sup {minus}3} in the fine fraction and 37 {plus minus} 9 ng m{sup {minus}3} in the coarse fraction. Only two factors explained about 90% of the data variability for the fine and coarse aerosol fractions. These were soil dust (represented mainly by Al, Si, Ti, Mn, and Fe) and biogenic aerosol (represented by K, P, Cl, S, Zn, and the aerosol mass concentration). Biogenic particles account for 55-95% of the airborne concentrations and consisted of leaf fragments, pollen grains, fungi, algae, and other types of particles. It is possible that biogenic particles can play an important role in the global aerosol budget and in the global biogeochemical cycles of various elements.« less

Quantifying uncertainty in carbon and nutrient pools of coarse woody debris

NASA Astrophysics Data System (ADS)

See, C. R.; Campbell, J. L.; Fraver, S.; Domke, G. M.; Harmon, M. E.; Knoepp, J. D.; Woodall, C. W.

2016-12-01

Woody detritus constitutes a major pool of both carbon and nutrients in forested ecosystems. Estimating coarse wood stocks relies on many assumptions, even when full surveys are conducted. Researchers rarely report error in coarse wood pool estimates, despite the importance to ecosystem budgets and modelling efforts. To date, no study has attempted a comprehensive assessment of error rates and uncertainty inherent in the estimation of this pool. Here, we use Monte Carlo analysis to propagate the error associated with the major sources of uncertainty present in the calculation of coarse wood carbon and nutrient (i.e., N, P, K, Ca, Mg, Na) pools. We also evaluate individual sources of error to identify the importance of each source of uncertainty in our estimates. We quantify sampling error by comparing the three most common field methods used to survey coarse wood (two transect methods and a whole-plot survey). We quantify the measurement error associated with length and diameter measurement, and technician error in species identification and decay class using plots surveyed by multiple technicians. We use previously published values of model error for the four most common methods of volume estimation: Smalian's, conical frustum, conic paraboloid, and average-of-ends. We also use previously published values for error in the collapse ratio (cross-sectional height/width) of decayed logs that serves as a surrogate for the volume remaining. We consider sampling error in chemical concentration and density for all decay classes, using distributions from both published and unpublished studies. Analytical uncertainty is calculated using standard reference plant material from the National Institute of Standards. Our results suggest that technician error in decay classification can have a large effect on uncertainty, since many of the error distributions included in the calculation (e.g. density, chemical concentration, volume-model selection, collapse ratio) are decay-class specific.

Theory of wavelet-based coarse-graining hierarchies for molecular dynamics.

PubMed

Rinderspacher, Berend Christopher; Bardhan, Jaydeep P; Ismail, Ahmed E

2017-07-01

We present a multiresolution approach to compressing the degrees of freedom and potentials associated with molecular dynamics, such as the bond potentials. The approach suggests a systematic way to accelerate large-scale molecular simulations with more than two levels of coarse graining, particularly applications of polymeric materials. In particular, we derive explicit models for (arbitrarily large) linear (homo)polymers and iterative methods to compute large-scale wavelet decompositions from fragment solutions. This approach does not require explicit preparation of atomistic-to-coarse-grained mappings, but instead uses the theory of diffusion wavelets for graph Laplacians to develop system-specific mappings. Our methodology leads to a hierarchy of system-specific coarse-grained degrees of freedom that provides a conceptually clear and mathematically rigorous framework for modeling chemical systems at relevant model scales. The approach is capable of automatically generating as many coarse-grained model scales as necessary, that is, to go beyond the two scales in conventional coarse-grained strategies; furthermore, the wavelet-based coarse-grained models explicitly link time and length scales. Furthermore, a straightforward method for the reintroduction of omitted degrees of freedom is presented, which plays a major role in maintaining model fidelity in long-time simulations and in capturing emergent behaviors.

Mechanical response of two polyimides through coarse-grained molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sudarkodi, V.; Sooraj, K.; Nair, Nisanth N.; Basu, Sumit; Parandekar, Priya V.; Sinha, Nishant K.; Prakash, Om; Tsotsis, Tom

2018-03-01

Coarse-grained molecular dynamics (MD) simulations allow us to predict the mechanical responses of polymers, starting merely with a description of their molecular architectures. It is interesting to ask whether, given two competing molecular architectures, coarse-grained MD simulations can predict the differences that can be expected in their mechanical responses. We have studied two crosslinked polyimides PMR15 and HFPE52—both used in high- temperature applications—to assess whether the subtle differences in their uniaxial stress-strain responses, revealed by experiments, can be reproduced by carefully coarse-grained MD models. The coarse graining procedure for PMR15 is outlined in this work, while the coarse grain forcefields for HFPE52 are borrowed from an earlier one (Pandiyan et al 2015 Macromol. Theory Simul. 24 513-20). We show that the stress-strain responses of both these polyimides are qualitatively reproduced, and important insights into their deformation and failure mechanisms are obtained. More importantly, the differences in the molecular architecture between the polyimides carry over to the differences in the stress-strain responses in a manner that parallels the experimental results. A critical assessment of the successes and shortcomings of predicting mechanical responses through coarse-grained MD simulations has been made.

Modeling disease transmission near eradication: An equation free approach

NASA Astrophysics Data System (ADS)

Williams, Matthew O.; Proctor, Joshua L.; Kutz, J. Nathan

2015-01-01

Although disease transmission in the near eradication regime is inherently stochastic, deterministic quantities such as the probability of eradication are of interest to policy makers and researchers. Rather than running large ensembles of discrete stochastic simulations over long intervals in time to compute these deterministic quantities, we create a data-driven and deterministic "coarse" model for them using the Equation Free (EF) framework. In lieu of deriving an explicit coarse model, the EF framework approximates any needed information, such as coarse time derivatives, by running short computational experiments. However, the choice of the coarse variables (i.e., the state of the coarse system) is critical if the resulting model is to be accurate. In this manuscript, we propose a set of coarse variables that result in an accurate model in the endemic and near eradication regimes, and demonstrate this on a compartmental model representing the spread of Poliomyelitis. When combined with adaptive time-stepping coarse projective integrators, this approach can yield over a factor of two speedup compared to direct simulation, and due to its lower dimensionality, could be beneficial when conducting systems level tasks such as designing eradication or monitoring campaigns.

Segmentation and Quantitative Analysis of Apoptosis of Chinese Hamster Ovary Cells from Fluorescence Microscopy Images.

PubMed

Du, Yuncheng; Budman, Hector M; Duever, Thomas A

2017-06-01

Accurate and fast quantitative analysis of living cells from fluorescence microscopy images is useful for evaluating experimental outcomes and cell culture protocols. An algorithm is developed in this work to automatically segment and distinguish apoptotic cells from normal cells. The algorithm involves three steps consisting of two segmentation steps and a classification step. The segmentation steps are: (i) a coarse segmentation, combining a range filter with a marching square method, is used as a prefiltering step to provide the approximate positions of cells within a two-dimensional matrix used to store cells' images and the count of the number of cells for a given image; and (ii) a fine segmentation step using the Active Contours Without Edges method is applied to the boundaries of cells identified in the coarse segmentation step. Although this basic two-step approach provides accurate edges when the cells in a given image are sparsely distributed, the occurrence of clusters of cells in high cell density samples requires further processing. Hence, a novel algorithm for clusters is developed to identify the edges of cells within clusters and to approximate their morphological features. Based on the segmentation results, a support vector machine classifier that uses three morphological features: the mean value of pixel intensities in the cellular regions, the variance of pixel intensities in the vicinity of cell boundaries, and the lengths of the boundaries, is developed for distinguishing apoptotic cells from normal cells. The algorithm is shown to be efficient in terms of computational time, quantitative analysis, and differentiation accuracy, as compared with the use of the active contours method without the proposed preliminary coarse segmentation step.

Effect of grinding with diamond-disc and -bur on the mechanical behavior of a Y-TZP ceramic.

PubMed

Pereira, G K R; Amaral, M; Simoneti, R; Rocha, G C; Cesar, P F; Valandro, L F

2014-09-01

This study compared the effects of grinding on the surface micromorphology, phase transformation (t→m), biaxial flexural strength and structural reliability (Weibull analysis) of a Y-TZP (Lava) ceramic using diamond-discs and -burs. 170 discs (15×1.2mm) were produced and divided into 5 groups: without treatment (Ctrl, as-sintered), and ground with 4 different systems: extra-fine (25µm, Xfine) and coarse diamond-bur (181µm, Coarse), 600-grit (25µm, D600) and 120-grit diamond-disc (160µm, D120). Grinding with burs was performed using a contra-angle handpiece (T2-Revo R170, Sirona), while for discs (Allied) a Polishing Machine (Ecomet, Buehler) was employed, both under water-cooling. Micromorphological analysis showed distinct patterns generated by grinding with discs and burs, independent of grit size. There was no statistical difference for characteristic strength values (MPa) between smaller grit sizes (D600 - 1050.08 and Xfine - 1171.33), although they presented higher values compared to Ctrl (917.58). For bigger grit sizes, a significant difference was observed (Coarse - 1136.32>D120 - 727.47). Weibull Modules were statistically similar between the tested groups. Within the limits of this study, from a micromorphological point-of-view, the treatments performed did not generate similar effects, so from a methodological point-of-view, diamond-discs should not be employed to simulate clinical abrasion performed with diamond-burs on Y-TZP ceramics. Copyright © 2014 Elsevier Ltd. All rights reserved.

Visual recovery in cortical blindness is limited by high internal noise

PubMed Central

Cavanaugh, Matthew R.; Zhang, Ruyuan; Melnick, Michael D.; Das, Anasuya; Roberts, Mariel; Tadin, Duje; Carrasco, Marisa; Huxlin, Krystel R.

2015-01-01

Damage to the primary visual cortex typically causes cortical blindness (CB) in the hemifield contralateral to the damaged hemisphere. Recent evidence indicates that visual training can partially reverse CB at trained locations. Whereas training induces near-complete recovery of coarse direction and orientation discriminations, deficits in fine motion processing remain. Here, we systematically disentangle components of the perceptual inefficiencies present in CB fields before and after coarse direction discrimination training. In seven human CB subjects, we measured threshold versus noise functions before and after coarse direction discrimination training in the blind field and at corresponding intact field locations. Threshold versus noise functions were analyzed within the framework of the linear amplifier model and the perceptual template model. Linear amplifier model analysis identified internal noise as a key factor differentiating motion processing across the tested areas, with visual training reducing internal noise in the blind field. Differences in internal noise also explained residual perceptual deficits at retrained locations. These findings were confirmed with perceptual template model analysis, which further revealed that the major residual deficits between retrained and intact field locations could be explained by differences in internal additive noise. There were no significant differences in multiplicative noise or the ability to process external noise. Together, these results highlight the critical role of altered internal noise processing in mediating training-induced visual recovery in CB fields, and may explain residual perceptual deficits relative to intact regions of the visual field. PMID:26389544

COARSEMAP: synthesis of observations and models for coarse-mode aerosols

NASA Astrophysics Data System (ADS)

Wiedinmyer, C.; Lihavainen, H.; Mahowald, N. M.; Alastuey, A.; Albani, S.; Artaxo, P.; Bergametti, G.; Batterman, S.; Brahney, J.; Duce, R. A.; Feng, Y.; Buck, C.; Ginoux, P. A.; Chen, Y.; Guieu, C.; Cohen, D.; Hand, J. L.; Harrison, R. M.; Herut, B.; Ito, A.; Losno, R.; Gomez, D.; Kanakidou, M.; Landing, W. M.; Laurent, B.; Mihalopoulos, N.; Mackey, K.; Maenhaut, W.; Hueglin, C.; Milando, C.; Miller, R. L.; Myriokefaitakis, S.; Neff, J. C.; Pandolfi, M.; Paytan, A.; Perez Garcia-Pando, C.; Prank, M.; Prospero, J. M.; Tamburo, E.; Varrica, D.; Wong, M.; Zhang, Y.

2017-12-01

Coarse mode aerosols influence Earth's climate and biogeochemistry by interacting with long-wave radiation, promoting ice nucleation, and contributing important elements to biogeochemical cycles during deposition. Yet coarse mode aerosols have received less emphasis in the scientific literature. Here we present first efforts to globally synthesize available mass concentration, composition and optical depth data and modeling for the coarse mode aerosols (<10 µm) in a new project called "COARSEMAP" (http://www.geo.cornell.edu/eas/PeoplePlaces/Faculty/mahowald/COARSEMAP/). We seek more collaborators who have observational data, especially including elemental or composition data, and/or who are interested in detailed modeling of the coarse mode. The goal will be publications synthesizing data with models, as well as providing synthesized results to the wider community.

[Effects, safety and cost-benefit analysis of Down syndrome screening in first trimester].

PubMed

Shengmou, Lin; Min, Chen; Chenhong, Wang; Shengli, Li; Jiansheng, Xie; Hui, Yuan; Dinghao, Lin; Xiaoxia, Wu; Wei, Wang; Hongyun, Zhang; Haiyan, Tang

2014-05-01

To investigate the effects, safety and cost-benefit analysis of Down syndrome screening in first trimester. From January 2009 to December 2012, 43 729 pregnant women undergoing 3 methods of Down syndrome traditional screening strategies in Shenzhen Maternity and Child Healthcare Hospital were studied retrospectively, including in 17 502 cases in pregnancy associated plasma protein A (PAPP-A) and free β-hCG measured biochemistry screening, 14 080 cases in nuchal translucency (NT) screening and 12 147 cases in combined screening, meanwhile, 7 389 cases on non-invasive fetal trisomy test (NIFTY) were performed in Huada Gene Research Institute(BGI). The effects and safety of four screening strategies were assessed throughout a decision tree. The economical characters of each screening strategy were compared by cost-effectiveness analysis as well as cost-benefit analysis. (1) The effects of four strategies are: NIFTY > combined screening > NT screening > biochemistry screening. (2) The safety of four strategies are: NIFTY > combined screening > NT screening > biochemistry screening. (3) Cost-effectiveness analysis and cost-benefit analysis:the biochemistry screening has lowest cost-effectiveness ratio (CER) and highest cost-benefit ratio (CBR), which performed a better economical efficiency. The incremental CER of three traditional screening strategies are all less than the economical burden of Down syndrome.NIFTY has highest CER and negative net present value (NPV), NPV would be positive and CBR would be more than 1 if the price of NIFTY reduce to 1 434 Yuan. Combined screening possess best screening efficiency, while biochemistry screening was demonstrated more economical in traditional screening.NIFTY is the future of Down syndrome screening.

Cognitive-Developmental Learning for a Humanoid Robot: A Caregiver’s Gift

DTIC Science & Technology

2004-05-01

system . We propose a real- time algorithm to infer depth and build 3-dimensional coarse maps for objects through the analysis of cues provided by an... system is well defined at the boundary of these regions (although the derivatives are not). A time domain analysis is presented for a piece-linear... Analysis of Multivariable Systems ......................... 266 D.3.1 Networks of Multiple Neural Oscillators ................. 266 D.3.2 Networks of

Development of new test procedures for measuring fine and coarse aggregates specific gravity.

DOT National Transportation Integrated Search

2009-09-01

The objective of the research is to develop and evaluate new test methods at determining the specific gravity and absorption of both fine and coarse aggregates. Current methods at determining the specific gravity and absorption of fine and coarse agg...

Resolving Dynamic Properties of Polymers through Coarse-Grained Computational Studies

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

Salerno, K. Michael; Agrawal, Anupriya; Perahia, Dvora

2016-02-05

Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly modeled. In this paper, we probe the degree of coarse graining required to simultaneously retain significant atomistic details and access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using linear polyethylene as a model system, we probe how the coarse-graining scale affects the measured dynamics. Iterative Boltzmann inversion ismore » used to derive coarse-grained potentials with 2–6 methylene groups per coarse-grained bead from a fully atomistic melt simulation. We show that atomistic detail is critical to capturing large-scale dynamics. Finally, using these models we simulate polyethylene melts for times over 500 μs to study the viscoelastic properties of well-entangled polymer melts.« less

Structure and osmotic pressure of ionic microgel dispersions

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

Hedrick, Mary M.; Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050; Chung, Jun Kyung

We investigate structural and thermodynamic properties of aqueous dispersions of ionic microgels—soft colloidal gel particles that exhibit unusual phase behavior. Starting from a coarse-grained model of microgel macroions as charged spheres that are permeable to microions, we perform simulations and theoretical calculations using two complementary implementations of Poisson-Boltzmann (PB) theory. Within a one-component model, based on a linear-screening approximation for effective electrostatic pair interactions, we perform molecular dynamics simulations to compute macroion-macroion radial distribution functions, static structure factors, and macroion contributions to the osmotic pressure. For the same model, using a variational approximation for the free energy, we compute bothmore » macroion and microion contributions to the osmotic pressure. Within a spherical cell model, which neglects macroion correlations, we solve the nonlinear PB equation to compute microion distributions and osmotic pressures. By comparing the one-component and cell model implementations of PB theory, we demonstrate that the linear-screening approximation is valid for moderately charged microgels. By further comparing cell model predictions with simulation data for osmotic pressure, we chart the cell model’s limits in predicting osmotic pressures of salty dispersions.« less

Coarse and fine sediment transportation patterns and causes downstream of the Three Gorges Dam

NASA Astrophysics Data System (ADS)

Li, Songzhe; Yang, Yunping; Zhang, Mingjin; Sun, Zhaohua; Zhu, Lingling; You, Xingying; Li, Kanyu

2017-11-01

Reservoir construction within a basin affects the process of water and sediment transport downstream of the dam. The Three Gorges Reservoir (TGR) affects the sediment transport downstream of the dam. The impoundment of the TGR reduced total downstream sediment. The sediment group d≤0.125 mm (fine particle) increased along the path, but the average was still below what existed before the reservoir impoundment. The sediments group d>0.125 mm (coarse particle) was recharged in the Yichang to Jianli reach, but showed a deposition trend downstream of Jianli. The coarse sediment in the Yichang to Jianli section in 2003 to 2007 was above the value before the TGR impoundment. However, the increase of both coarse and fine sediments in 2008 to 2014 was less than that in 2003 to 2007. The sediment retained in the dam is the major reason for the sediment reduction downstream. However, the retention in different river reaches is affected by riverbed coarsening, discharge, flow process, and conditions of lake functioning and recharging from the tributaries. The main conclusions derived from our study are as follows: 1) The riverbed in the Yichang to Shashi section was relatively coarse, thereby limiting the supply of fine and coarse sediments. The fine sediment supply was mainly controlled by TGR discharge, whereas the coarse sediment supply was controlled by the duration of high flow and its magnitude. 2) The supply of both coarse and fine sediments in the Shashi to Jianli section was controlled by the amount of total discharge. The sediment supply from the riverbed was higher in flood years than that in the dry years. The coarse sediment tended to deposit, and the deposition in the dry years was larger than that in the flood years. 3) The feeding of the fine sediment in the Luoshan to Hankou section was mainly from the riverbed. The supply in 2008 to 2014 was more than that in 2003 to 2007. Around 2010, the coarse sediments transited from depositing to scouring that was probably caused by the increased duration of high flow days. 4) Fine sediments appeared to be deposited in large amounts in the Hankou to Jiujiang section. The coarse sediment was fed by the riverbed scouring, and much more coarse sediments were recharged from the riverbed in the flood years than in the dry years. 5) In the Jiujiang to Datong section, the ratio of fine sediments from the Poyang Lake and that from the riverbed was 1: 2.82. The sediment from the riverbed scouring contributed more to the coarse sediment transportation. The contribution was mainly affected by the input by magnitude and duration of high flows.

Investigation of Pier Scour in Coarse-Bed Streams in Montana, 2001 through 2007

DOT National Transportation Integrated Search

2011-01-01

Determination of pier-scour potential is an important consideration in the hydraulic analysis and design of highway bridges that cross streams, rivers, and other waterways in the United States. A primary goal of ongoing research in the field of bridg...

A new algorithm for construction of coarse-grained sites of large biomolecules.

PubMed

Li, Min; Zhang, John Z H; Xia, Fei

2016-04-05

The development of coarse-grained (CG) models for large biomolecules remains a challenge in multiscale simulations, including a rigorous definition of CG representations for them. In this work, we proposed a new stepwise optimization imposed with the boundary-constraint (SOBC) algorithm to construct the CG sites of large biomolecules, based on the s cheme of essential dynamics CG. By means of SOBC, we can rigorously derive the CG representations of biomolecules with less computational cost. The SOBC is particularly efficient for the CG definition of large systems with thousands of residues. The resulted CG sites can be parameterized as a CG model using the normal mode analysis based fluctuation matching method. Through normal mode analysis, the obtained modes of CG model can accurately reflect the functionally related slow motions of biomolecules. The SOBC algorithm can be used for the construction of CG sites of large biomolecules such as F-actin and for the study of mechanical properties of biomaterials. © 2015 Wiley Periodicals, Inc.

Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: does a stronger acid make a stiffer hydrogen bond?

PubMed

Houjou, Hirohiko

2011-10-21

Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m(-1) for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules. © 2011 American Institute of Physics

Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: Does a stronger acid make a stiffer hydrogen bond?

NASA Astrophysics Data System (ADS)

Houjou, Hirohiko

2011-10-01

Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m-1 for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.

Detecting synchronization clusters in multivariate time series via coarse-graining of Markov chains.

PubMed

Allefeld, Carsten; Bialonski, Stephan

2007-12-01

Synchronization cluster analysis is an approach to the detection of underlying structures in data sets of multivariate time series, starting from a matrix R of bivariate synchronization indices. A previous method utilized the eigenvectors of R for cluster identification, analogous to several recent attempts at group identification using eigenvectors of the correlation matrix. All of these approaches assumed a one-to-one correspondence of dominant eigenvectors and clusters, which has however been shown to be wrong in important cases. We clarify the usefulness of eigenvalue decomposition for synchronization cluster analysis by translating the problem into the language of stochastic processes, and derive an enhanced clustering method harnessing recent insights from the coarse-graining of finite-state Markov processes. We illustrate the operation of our method using a simulated system of coupled Lorenz oscillators, and we demonstrate its superior performance over the previous approach. Finally we investigate the question of robustness of the algorithm against small sample size, which is important with regard to field applications.

Refined composite multivariate generalized multiscale fuzzy entropy: A tool for complexity analysis of multichannel signals

NASA Astrophysics Data System (ADS)

Azami, Hamed; Escudero, Javier

2017-01-01

Multiscale entropy (MSE) is an appealing tool to characterize the complexity of time series over multiple temporal scales. Recent developments in the field have tried to extend the MSE technique in different ways. Building on these trends, we propose the so-called refined composite multivariate multiscale fuzzy entropy (RCmvMFE) whose coarse-graining step uses variance (RCmvMFEσ2) or mean (RCmvMFEμ). We investigate the behavior of these multivariate methods on multichannel white Gaussian and 1/ f noise signals, and two publicly available biomedical recordings. Our simulations demonstrate that RCmvMFEσ2 and RCmvMFEμ lead to more stable results and are less sensitive to the signals' length in comparison with the other existing multivariate multiscale entropy-based methods. The classification results also show that using both the variance and mean in the coarse-graining step offers complexity profiles with complementary information for biomedical signal analysis. We also made freely available all the Matlab codes used in this paper.

Fractal dimension analysis for robust ultrasonic non-destructive evaluation (NDE) of coarse grained materials

NASA Astrophysics Data System (ADS)

Li, Minghui; Hayward, Gordon

2018-04-01

Over the recent decades, there has been a growing demand on reliable and robust non-destructive evaluation (NDE) of structures and components made from coarse grained materials such as alloys, stainless steels, carbon-reinforced composites and concrete; however, when inspected using ultrasound, the flaw echoes are usually contaminated by high-level, time-invariant, and correlated grain noise originating from the microstructure and grain boundaries, leading to pretty low signal-to-noise ratio (SNR) and the flaw information being obscured or completely hidden by the grain noise. In this paper, the fractal dimension analysis of the A-scan echoes is investigated as a measure of complexity of the time series to distinguish the echoes originating from the real defects and the grain noise, and then the normalized fractal dimension coefficients are applied to the amplitudes as the weighting factor to enhance the SNR and defect detection. Experiments on industrial samples of the mild steel and the stainless steel are conducted and the results confirm the great benefits of the method.

Modal density of rectangular structures in a wide frequency range

NASA Astrophysics Data System (ADS)

Parrinello, A.; Ghiringhelli, G. L.

2018-04-01

A novel approach to investigate the modal density of a rectangular structure in a wide frequency range is presented. First, the modal density is derived, in the whole frequency range of interest, on the basis of sound transmission through the infinite counterpart of the structure; then, it is corrected by means of the low-frequency modal behavior of the structure, taking into account actual size and boundary conditions. A statistical analysis reveals the connection between the modal density of the structure and the transmission of sound through its thickness. A transfer matrix approach is used to compute the required acoustic parameters, making it possible to deal with structures having arbitrary stratifications of different layers. A finite element method is applied on coarse grids to derive the first few eigenfrequencies required to correct the modal density. Both the transfer matrix approach and the coarse grids involved in the finite element analysis grant high efficiency. Comparison with alternative formulations demonstrates the effectiveness of the proposed methodology.

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.

Predictive coarse-graining

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

Schöberl, Markus, E-mail: m.schoeberl@tum.de; Zabaras, Nicholas; Department of Aerospace and Mechanical Engineering, University of Notre Dame, 365 Fitzpatrick Hall, Notre Dame, IN 46556

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 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 extendedmore » 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.« less

Coarse-grained stochastic processes and kinetic Monte Carlo simulators for the diffusion of interacting particles

NASA Astrophysics Data System (ADS)

Katsoulakis, Markos A.; Vlachos, Dionisios G.

2003-11-01

We derive a hierarchy of successively coarse-grained stochastic processes and associated coarse-grained Monte Carlo (CGMC) algorithms directly from the microscopic processes as approximations in larger length scales for the case of diffusion of interacting particles on a lattice. This hierarchy of models spans length scales between microscopic and mesoscopic, satisfies a detailed balance, and gives self-consistent fluctuation mechanisms whose noise is asymptotically identical to the microscopic MC. Rigorous, detailed asymptotics justify and clarify these connections. Gradient continuous time microscopic MC and CGMC simulations are compared under far from equilibrium conditions to illustrate the validity of our theory and delineate the errors obtained by rigorous asymptotics. Information theory estimates are employed for the first time to provide rigorous error estimates between the solutions of microscopic MC and CGMC, describing the loss of information during the coarse-graining process. Simulations under periodic boundary conditions are used to verify the information theory error estimates. It is shown that coarse-graining in space leads also to coarse-graining in time by q2, where q is the level of coarse-graining, and overcomes in part the hydrodynamic slowdown. Operation counting and CGMC simulations demonstrate significant CPU savings in continuous time MC simulations that vary from q3 for short potentials to q4 for long potentials. Finally, connections of the new coarse-grained stochastic processes to stochastic mesoscopic and Cahn-Hilliard-Cook models are made.

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

PubMed

Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam

2018-04-30

A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.

Evaluation of an improved finite-element thermal stress calculation technique

NASA Technical Reports Server (NTRS)

Camarda, C. J.

1982-01-01

A procedure for generating accurate thermal stresses with coarse finite element grids (Ojalvo's method) is described. The procedure is based on the observation that for linear thermoelastic problems, the thermal stresses may be envisioned as being composed of two contributions; the first due to the strains in the structure which depend on the integral of the temperature distribution over the finite element and the second due to the local variation of the temperature in the element. The first contribution can be accurately predicted with a coarse finite-element mesh. The resulting strain distribution can then be combined via the constitutive relations with detailed temperatures from a separate thermal analysis. The result is accurate thermal stresses from coarse finite element structural models even where the temperature distributions have sharp variations. The range of applicability of the method for various classes of thermostructural problems such as in-plane or bending type problems and the effect of the nature of the temperature distribution and edge constraints are addressed. Ojalvo's method is used in conjunction with the SPAR finite element program. Results are obtained for rods, membranes, a box beam and a stiffened panel.

Registration of Laser Scanning Point Clouds: A Review.

PubMed

Cheng, Liang; Chen, Song; Liu, Xiaoqiang; Xu, Hao; Wu, Yang; Li, Manchun; Chen, Yanming

2018-05-21

The integration of multi-platform, multi-angle, and multi-temporal LiDAR data has become important for geospatial data applications. This paper presents a comprehensive review of LiDAR data registration in the fields of photogrammetry and remote sensing. At present, a coarse-to-fine registration strategy is commonly used for LiDAR point clouds registration. The coarse registration method is first used to achieve a good initial position, based on which registration is then refined utilizing the fine registration method. According to the coarse-to-fine framework, this paper reviews current registration methods and their methodologies, and identifies important differences between them. The lack of standard data and unified evaluation systems is identified as a factor limiting objective comparison of different methods. The paper also describes the most commonly-used point cloud registration error analysis methods. Finally, avenues for future work on LiDAR data registration in terms of applications, data, and technology are discussed. In particular, there is a need to address registration of multi-angle and multi-scale data from various newly available types of LiDAR hardware, which will play an important role in diverse applications such as forest resource surveys, urban energy use, cultural heritage protection, and unmanned vehicles.

Variable-free exploration of stochastic models: a gene regulatory network example.

PubMed

Erban, Radek; Frewen, Thomas A; Wang, Xiao; Elston, Timothy C; Coifman, Ronald; Nadler, Boaz; Kevrekidis, Ioannis G

2007-04-21

Finding coarse-grained, low-dimensional descriptions is an important task in the analysis of complex, stochastic models of gene regulatory networks. This task involves (a) identifying observables that best describe the state of these complex systems and (b) characterizing the dynamics of the observables. In a previous paper [R. Erban et al., J. Chem. Phys. 124, 084106 (2006)] the authors assumed that good observables were known a priori, and presented an equation-free approach to approximate coarse-grained quantities (i.e., effective drift and diffusion coefficients) that characterize the long-time behavior of the observables. Here we use diffusion maps [R. Coifman et al., Proc. Natl. Acad. Sci. U.S.A. 102, 7426 (2005)] to extract appropriate observables ("reduction coordinates") in an automated fashion; these involve the leading eigenvectors of a weighted Laplacian on a graph constructed from network simulation data. We present lifting and restriction procedures for translating between physical variables and these data-based observables. These procedures allow us to perform equation-free, coarse-grained computations characterizing the long-term dynamics through the design and processing of short bursts of stochastic simulation initialized at appropriate values of the data-based observables.

Registration of Laser Scanning Point Clouds: A Review

PubMed Central

Cheng, Liang; Chen, Song; Xu, Hao; Wu, Yang; Li, Manchun

2018-01-01

The integration of multi-platform, multi-angle, and multi-temporal LiDAR data has become important for geospatial data applications. This paper presents a comprehensive review of LiDAR data registration in the fields of photogrammetry and remote sensing. At present, a coarse-to-fine registration strategy is commonly used for LiDAR point clouds registration. The coarse registration method is first used to achieve a good initial position, based on which registration is then refined utilizing the fine registration method. According to the coarse-to-fine framework, this paper reviews current registration methods and their methodologies, and identifies important differences between them. The lack of standard data and unified evaluation systems is identified as a factor limiting objective comparison of different methods. The paper also describes the most commonly-used point cloud registration error analysis methods. Finally, avenues for future work on LiDAR data registration in terms of applications, data, and technology are discussed. In particular, there is a need to address registration of multi-angle and multi-scale data from various newly available types of LiDAR hardware, which will play an important role in diverse applications such as forest resource surveys, urban energy use, cultural heritage protection, and unmanned vehicles. PMID:29883397

Preliminary Analysis of Night-time Aerosol Optical Depth Retrievals at a Rural, Near-urban Site in Southern Canada

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

Baibakov, K.; O'Neill, N. T.; Firanski, B.

2009-03-11

In the summer of 2007, a SPSTAR03 starphotometer was installed at Egbert, Canada (44 deg. 13' N, 79 deg. 45' W, alt 264 m) and a continuous series of initial measurements was performed between August 26 and September 19. Several sunphotometry parameters such as the aerosol optical depth (AOD) and the 'fine' and 'coarse' optical depths were extracted from the SPSTAR03 extinction spectra. The SPSTAR03 data was analyzed in conjunction with sunphotometry and zenith-pointing lidar data acquired during the same time period. Preliminary results show coarse continuity between the day- and night time AOD values (with the mean difference betweenmore » the measured and the interpolated values being 0.05) as well as a qualitative correlation between the 'fine' and 'coarse' optical depths and the normalized lidar backscatter coefficient profiles. It was also found that the spectra produced with the differential two-star measurement method were sensitive to non-horizontally homogeneous differences in the line-of-sight conditions of both stars. The one-star method helps to reduce the uncertainties but requires the determination of a calibration constant.« less

Effects of temperature segregation on the volumetric and mechanistic properties of asphalt mixtures : research project capsule.

DOT National Transportation Integrated Search

2015-02-01

Material segregation in asphalt mixtures is a non-uniform distribution of coarse : and fine aggregates through its masses, i.e., concentration of coarse materials : in some area and fine materials in others. During construction, the coarse and : fine...

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 ...

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...

TRAC-PD2 posttest analysis of the CCTF Evaluation-Model Test C1-19 (Run 38). [PWR

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

Motley, F.

The results of a Transient Reactor Analysis Code posttest analysis of the Cylindral Core Test Facility Evaluation-Model Test agree very well with the results of the experiment. The good agreement obtained verifies the multidimensional analysis capability of the TRAC code. Because of the steep radial power profile, the importance of using fine noding in the core region was demonstrated (as compared with poorer results obtained from an earlier pretest prediction that used a coarsely noded model).

A variational principle for compressible fluid mechanics: Discussion of the multi-dimensional theory

NASA Technical Reports Server (NTRS)

Prozan, R. J.

1982-01-01

The variational principle for compressible fluid mechanics previously introduced is extended to two dimensional flow. The analysis is stable, exactly conservative, adaptable to coarse or fine grids, and very fast. Solutions for two dimensional problems are included. The excellent behavior and results lend further credence to the variational concept and its applicability to the numerical analysis of complex flow fields.

Parallel processing for nonlinear dynamics simulations of structures including rotating bladed-disk assemblies

NASA Technical Reports Server (NTRS)

Hsieh, Shang-Hsien

1993-01-01

The principal objective of this research is to develop, test, and implement coarse-grained, parallel-processing strategies for nonlinear dynamic simulations of practical structural problems. There are contributions to four main areas: finite element modeling and analysis of rotational dynamics, numerical algorithms for parallel nonlinear solutions, automatic partitioning techniques to effect load-balancing among processors, and an integrated parallel analysis system.

Coarse particle speciation at selected locations in the rural continental United States

NASA Astrophysics Data System (ADS)

Malm, William C.; Pitchford, Marc L.; McDade, Charles; Ashbaugh, Lowell L.

A few short-term special studies at National Parks have shown that coarse mass (CM) (2.5- 10μm) may not be just crustal minerals but may consist of a substantial amount ( ≈40-50%) of carbonaceous material and inorganic salts such as calcium nitrate and sodium nitrate. To more fully investigate the composition of coarse particles, a program of coarse particle sampling and speciation analysis at nine of the Interagency Monitoring of Protected Visual Environments (IMPROVE) sites was initiated 19 March 2003 and operated through the year 2004. Only the data for 2004 are reported here. Sites were selected to be representative of the continental United States and were operated according to IMPROVE protocol analytical procedures. Crustal minerals (soil) are the single largest contributor to CM at all but one monitoring location. The average fractional contributions range from a high of 76% at Grand Canyon National Park to a low of 34% at Mount Rainier National Park. The second largest contributor to CM is organic mass, which on an average annual fractional basis is highest at Mount Rainier at 59%. At Great Smoky Mountains National Park, organic mass contributes 40% on average, while at four sites organic mass concentrations contribute between 20% and 30% of the CM. Nitrates are on average the third largest contributor to CM concentrations. The highest fractional contributions of nitrates to CM are at Brigantine National Wildlife Refuge, Great Smoky Mountains, and San Gorgonio wilderness area at 10-12%. Sulfates contribute less than about 5% at all sites.

A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

PubMed Central

Qin, Feng

2015-01-01

The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362

Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information

PubMed Central

Lopes, Anne; Sacquin-Mora, Sophie; Dimitrova, Viktoriya; Laine, Elodie; Ponty, Yann; Carbone, Alessandra

2013-01-01

Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis, are possible and realizable on hundreds of proteins with variate structures and interfaces. We demonstrated this on the 168 proteins of the Mintseris Benchmark 2.0. On the one hand, we evaluated the quality of the interaction signal and the contribution of docking information compared to evolutionary information showing that the combination of the two improves partner identification. On the other hand, since protein interactions usually occur in crowded environments with several competing partners, we realized a thorough analysis of the interactions of proteins with true partners but also with non-partners to evaluate whether proteins in the environment, competing with the true partner, affect its identification. We found three populations of proteins: strongly competing, never competing, and interacting with different levels of strength. Populations and levels of strength are numerically characterized and provide a signature for the behavior of a protein in the crowded environment. We showed that partner identification, to some extent, does not depend on the competing partners present in the environment, that certain biochemical classes of proteins are intrinsically easier to analyze than others, and that small proteins are not more promiscuous than large ones. Our approach brings to light that the knowledge of the binding site can be used to reduce the high computational cost of docking simulations with no consequence in the quality of the results, demonstrating the possibility to apply coarse-grain docking to datasets made of thousands of proteins. Comparison with all available large-scale analyses aimed to partner predictions is realized. We release the complete decoys set issued by coarse-grain docking simulations of both true and false interacting partners, and their evolutionary sequence analysis leading to binding site predictions. Download site: http://www.lgm.upmc.fr/CCDMintseris/ PMID:24339765

Dispersed Fringe Sensing Analysis - DFSA

NASA Technical Reports Server (NTRS)

Sigrist, Norbert; Shi, Fang; Redding, David C.; Basinger, Scott A.; Ohara, Catherine M.; Seo, Byoung-Joon; Bikkannavar, Siddarayappa A.; Spechler, Joshua A.

2012-01-01

Dispersed Fringe Sensing (DFS) is a technique for measuring and phasing segmented telescope mirrors using a dispersed broadband light image. DFS is capable of breaking the monochromatic light ambiguity, measuring absolute piston errors between segments of large segmented primary mirrors to tens of nanometers accuracy over a range of 100 micrometers or more. The DFSA software tool analyzes DFS images to extract DFS encoded segment piston errors, which can be used to measure piston distances between primary mirror segments of ground and space telescopes. This information is necessary to control mirror segments to establish a smooth, continuous primary figure needed to achieve high optical quality. The DFSA tool is versatile, allowing precise piston measurements from a variety of different optical configurations. DFSA technology may be used for measuring wavefront pistons from sub-apertures defined by adjacent segments (such as Keck Telescope), or from separated sub-apertures used for testing large optical systems (such as sub-aperture wavefront testing for large primary mirrors using auto-collimating flats). An experimental demonstration of the coarse-phasing technology with verification of DFSA was performed at the Keck Telescope. DFSA includes image processing, wavelength and source spectral calibration, fringe extraction line determination, dispersed fringe analysis, and wavefront piston sign determination. The code is robust against internal optical system aberrations and against spectral variations of the source. In addition to the DFSA tool, the software package contains a simple but sophisticated MATLAB model to generate dispersed fringe images of optical system configurations in order to quickly estimate the coarse phasing performance given the optical and operational design requirements. Combining MATLAB (a high-level language and interactive environment developed by MathWorks), MACOS (JPL s software package for Modeling and Analysis for Controlled Optical Systems), and DFSA provides a unique optical development, modeling and analysis package to study current and future approaches to coarse phasing controlled segmented optical systems.

Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization.

PubMed

Li, Min; Zhang, John Zenghui; Xia, Fei

2016-04-12

Coarse-grained (CG) models are valuable tools for the study of functions of large biomolecules on large length and time scales. The definition of CG representations for huge biomolecules is always a formidable challenge. In this work, we propose a new method called fluctuation maximization coarse-graining (FM-CG) to construct the CG sites of biomolecules. The defined residual in FM-CG converges to a maximal value as the number of CG sites increases, allowing an optimal CG model to be rigorously defined on the basis of the maximum. More importantly, we developed a robust algorithm called stepwise local iterative optimization (SLIO) to accelerate the process of coarse-graining large biomolecules. By means of the efficient SLIO algorithm, the computational cost of coarse-graining large biomolecules is reduced to within the time scale of seconds, which is far lower than that of conventional simulated annealing. The coarse-graining of two huge systems, chaperonin GroEL and lengsin, indicates that our new methods can coarse-grain huge biomolecular systems with up to 10,000 residues within the time scale of minutes. The further parametrization of CG sites derived from FM-CG allows us to construct the corresponding CG models for studies of the functions of huge biomolecular systems.

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

Li, Zhen; Bian, Xin; Yang, Xiu

We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics basedmore » on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models are not interchangeable. If the free parameters are properly selected, the reverse CG procedure also yields an effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn.« less

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

Li, Zhen; Bian, Xin; Karniadakis, George Em, E-mail: george-karniadakis@brown.edu

We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of a star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamicsmore » based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models cannot be selected arbitrarily. If the free parameters are properly defined, the reverse CG procedure also yields an accurate effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces the many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn.« less

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

NASA Astrophysics Data System (ADS)

Farrell, Kathryn; Oden, J. Tinsley

2014-07-01

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

Coarse coding and discourse comprehension in adults with right hemisphere brain damage

PubMed Central

Tompkins, Connie A.; Scharp, Victoria L.; Meigh, Kimberly M.; Fassbinder, Wiltrud

2009-01-01

Background Various investigators suggest that some discourse-level comprehension difficulties in adults with right hemisphere brain damage (RHD) have a lexical-semantic basis. As words are processed, the intact right hemisphere arouses and sustains activation of a wide-ranging network of secondary or peripheral meanings and features—a phenomenon dubbed “coarse coding”. Coarse coding impairment has been postulated to underpin some prototypical RHD comprehension deficits, such as difficulties with nonliteral language interpretation, discourse integration, some kinds of inference generation, and recovery when a reinterpretation is needed. To date, however, no studies have addressed the hypothesised link between coarse coding deficit and discourse comprehension in RHD. Aims The current investigation examined whether coarse coding was related to performance on two measures of narrative comprehension in adults with RHD. Methods & Procedures Participants were 32 adults with unilateral RHD from cerebrovascular accident, and 38 adults without brain damage. Coarse coding was operationalised as poor activation of peripheral/weakly related semantic features of words. For the coarse coding assessment, participants listened to spoken sentences that ended in a concrete noun. Each sentence was followed by a spoken target phoneme string. Targets were subordinate semantic features of the sentence-final nouns that were incompatible with their dominant mental representations (e.g., “rotten” for apple). Targets were presented at two post-noun intervals. A lexical decision task was used to gauge both early activation and maintenance of activation of these weakly related semantic features. One of the narrative tasks assessed comprehension of implied main ideas and details, while the other indexed high-level inferencing and integration. Both comprehension tasks were presented auditorily. For all tasks, accuracy of performance was the dependent measure. Correlations were computed within the RHD group between both the early and late coarse coding measures and the two discourse measures. Additionally, ANCOVA and independent t-tests were used to compare both early and sustained coarse coding in subgroups of good and poor RHD comprehenders. Outcomes & Results The group with RHD was less accurate than the control group on all measures. The finding of coarse coding impairment (difficulty activating/sustaining activation of a word’s peripheral features) may appear to contradict prior evidence of RHD suppression deficit (prolonged activation for context-inappropriate meanings of words). However, the sentence contexts in this study were unbiased and thus did not provide an appropriate test of suppression function. Correlations between coarse coding and the discourse measures were small and nonsignificant. There were no differences in coarse coding between RHD comprehension subgroups on the high-level inferencing task. There was also no distinction in early coarse coding for subgroups based on comprehension of implied main ideas and details. But for these same subgroups, there was a difference in sustained coarse coding. Poorer RHD comprehenders of implied information from discourse were also poorer at maintaining activation for semantically distant features of concrete nouns. Conclusions This study provides evidence of a variant of the postulated link between coarse coding and discourse comprehension in RHD. Specifically, adults with RHD who were particularly poor at sustaining activation for peripheral semantic features of nouns were also relatively poor comprehenders of implied information from narratives. PMID:20037670

TOWARDS AN IMPROVED UNDERSTANDING OF SIMULATED AND OBSERVED CHANGES IN EXTREME PRECIPITATION

EPA Science Inventory

The evaluation of climate model precipitation is expected to reveal biases in simulated mean and extreme precipitation which may be a result of coarse model resolution or inefficiencies in the precipitation generating mechanisms in models. The analysis of future extreme precip...

Concrete pavement mixture design and analysis (MDA) : effect of aggregate systems on concrete mixture properties.

DOT National Transportation Integrated Search

2012-07-01

For years, specifications have focused on the water to cement ratio (w/cm) and strength of concrete, despite the majority of the volume : of a concrete mixture consisting of aggregate. An aggregate distribution of roughly 60% coarse aggregate and 40%...

OFF-GAS ANALYSIS RESULTS AND FINE PORE RETROFIT INFORMATION FOR GLASTONBURY, CONNECTICUT

EPA Science Inventory

In the summer of 1984, the Glastonbury, Connecticut Water Pollution Control Plant underwent a retrofit from a spiral roll coarse bubble to a spiral roll fine pore aeration system. Only diffuser replacement was performed in the aeration tanks. From November 1985 through Septembe...

OFF-GAS ANALYSIS RESULTS AND FINE PORE RETROFIT CASE HISTORY FOR HARTFORD, CONNECTICUT

EPA Science Inventory

In the summer of 1982, the Hartford Metropolitan District Commission, Hartford County, Connecticut, Water Pollution Control Facility underwent a retrofit form a spiral roll coarse bubble to a full floor coverage fine pore aeration system. Work performed included all new in-tank ...

GUIDELINES FOR THE APPLICATION OF SEM/EDX ANALYTICAL TECHNIQUES FOR FINE AND COARSE PM SAMPLES

EPA Science Inventory

Scanning Electron Microscopy (SEM) coupled with Energy-Dispersive X-ray analysis (EDX) is a powerful tool in the characterization and source apportionment of environmental particulate matter (PM), providing size, chemistry, and morphology of particles as small as a few tenths ...

In silico design of anti-atherogenic biomaterials.

PubMed

Lewis, Daniel R; Kholodovych, Vladyslav; Tomasini, Michael D; Abdelhamid, Dalia; Petersen, Latrisha K; Welsh, William J; Uhrich, Kathryn E; Moghe, Prabhas V

2013-10-01

Atherogenesis, the uncontrolled deposition of modified lipoproteins in inflamed arteries, serves as a focal trigger of cardiovascular disease (CVD). Polymeric biomaterials have been envisioned to counteract atherogenesis based on their ability to repress scavenger mediated uptake of oxidized lipoprotein (oxLDL) in macrophages. Following the conceptualization in our laboratories of a new library of amphiphilic macromolecules (AMs), assembled from sugar backbones, aliphatic chains and poly(ethylene glycol) tails, a more rational approach is necessary to parse the diverse features such as charge, hydrophobicity, sugar composition and stereochemistry. In this study, we advance a computational biomaterials design approach to screen and elucidate anti-atherogenic biomaterials with high efficacy. AMs were quantified in terms of not only 1D (molecular formula) and 2D (molecular connectivity) descriptors, but also new 3D (molecular geometry) descriptors of AMs modeled by coarse-grained molecular dynamics (MD) followed by all-atom MD simulations. Quantitative structure-activity relationship (QSAR) models for anti-atherogenic activity were then constructed by screening a total of 1164 descriptors against the corresponding, experimentally measured potency of AM inhibition of oxLDL uptake in human monocyte-derived macrophages. Five key descriptors were identified to provide a strong linear correlation between the predicted and observed anti-atherogenic activity values, and were then used to correctly forecast the efficacy of three newly designed AMs. Thus, a new ligand-based drug design framework was successfully adapted to computationally screen and design biomaterials with cardiovascular therapeutic properties. Copyright © 2013 Elsevier Ltd. All rights reserved.

Enrichment of Mineral Dust Storm Particles with Sea Salt Elements - Using bulk and Single Particle Analyses

NASA Astrophysics Data System (ADS)

Mamane, Y.; Perrino, C.; Yossef, O.

2009-12-01

Mineral aerosol emitted from African and Asian deserts plays an important role in the atmosphere. During their long-range transport, the physical and chemical properties of mineral dust particles change due to heterogeneous reactions with trace gases, coagulation with other particles, and in-cloud processing. These processes affect the optical and hygroscopic properties of dust particles, and in general influencing the physics and chemistry of the atmosphere. Four African and Arabian dust storm episodes affecting the East Mediterranean Coast in the spring of 2006 have been characterized, to determine if atmospheric natural dust particles are enriched with sea salt and anthropogenic pollution. Particle samplers included PM10 and manual dichotomous sampler that collected fine and coarse particles. Three sets of filters were used: Teflon filters for gravimetric, elemental and ionic analyses; Pre-fired Quartz-fiber filters for elemental and organic carbon; and Nuclepore filters for scanning electron microscopy analysis. Computer-controlled scanning electron microscopy (Philips XL 30 ESEM) was used to analyze single particle, for morphology, size and chemistry of selected filter samples. A detailed chemical and microscopical characterization has been performed for the particles collected during dust event days and during clear days. The Saharan and Arabian air masses increased significantly the daily mass concentrations of the coarse and the fine particle fractions. Carbonates, mostly as soil calcites mixed with dolomites, and silicates are the major components of the coarse fraction, followed by sea salt particles. In addition, the levels of anthropogenic heavy metals and sea salt elements registered during the dust episode were considerably higher than levels recorded during clear days. Sea salt elements contain Na and Cl, and smaller amounts of Mg, K, S and Br. Cl ranges from 300 to 5500 ng/m3 and Na from 100 to almost 2400 ng/m3. The Cl to Na ratio on dusty days in the coarse fraction is 2.94 versus 1.88 on clear days, quite different from the value of 1.8 found in sea water. It is rather clear that dust events are enriched with Cl. Those findings are to be investigated. The computer controlled SEM-EDX observations of the coarse fraction of PM10 confirmed the results obtained by XRF. The majority of the African dust particles are made up of mixed minerals, mostly carbonates and alumino - silicates. The EDX analysis coupled to CCSEM showed that minerals are mixed often with sea salt particles. Although some of it may be artifact (a sea salt particle is pile up on a mineral particle), it is believed that the results present reality: sea salt particles were often found on the surfaces of the aggregate minerals. Pollen and spores of diameters were not identified. Those results may have implication on the atmospheric chemistry. High concentrations of sulfates were also observed in the coarse fraction of dust episodes, and were not correlated with sea salt particles. They could be part of the soil matrix and may also form by the reaction of sulfur oxides with the natural aerosols. These reactions may be affected by the high concentration of coarse mineral particles during the Saharan and Arabian episodes.

A Cleaner Process for Selective Recovery of Valuable Metals from Electronic Waste of Complex Mixtures of End-of-Life Electronic Products.

PubMed

Sun, Zhi; Xiao, Y; Sietsma, J; Agterhuis, H; Yang, Y

2015-07-07

In recent years, recovery of metals from electronic waste within the European Union has become increasingly important due to potential supply risk of strategic raw material and environmental concerns. Electronic waste, especially a mixture of end-of-life electronic products from a variety of sources, is of inherently high complexity in composition, phase, and physiochemical properties. In this research, a closed-loop hydrometallurgical process was developed to recover valuable metals, i.e., copper and precious metals, from an industrially processed information and communication technology waste. A two-stage leaching design of this process was adopted in order to selectively extract copper and enrich precious metals. It was found that the recovery efficiency and extraction selectivity of copper both reached more than 95% by using ammonia-based leaching solutions. A new electrodeposition process has been proven feasible with 90% current efficiency during copper recovery, and the copper purity can reach 99.8 wt %. The residue from the first-stage leaching was screened into coarse and fine fractions. The coarse fraction was returned to be releached for further copper recovery. The fine fraction was treated in the second-stage leaching using sulfuric acid to further concentrate precious metals, which could achieve a 100% increase in their concentrations in the residue with negligible loss into the leaching solution. By a combination of different leaching steps and proper physical separation of light materials, this process can achieve closed-loop recycling of the waste with significant efficiency.

Effects of molecular model, ionic strength, divalent ions, and hydrophobic interaction on human neurofilament conformation

NASA Astrophysics Data System (ADS)

Lee, Joonseong; Kim, Seonghoon; Chang, Rakwoo; Jayanthi, Lakshmi; Gebremichael, Yeshitila

2013-01-01

The present study examines the effects of the model dependence, ionic strength, divalent ions, and hydrophobic interaction on the structural organization of the human neurofilament (NF) brush, using canonical ensemble Monte Carlo (MC) simulations of a coarse-grained model with the amino-acid resolution. The model simplifies the interactions between the NF core and the sidearm or between the sidearms by the sum of excluded volume, electrostatic, and hydrophobic interactions, where both monovalent salt ions and solvents are implicitly incorporated into the electrostatic interaction potential. Several important observations are made from the MC simulations of the coarse-grained model NF systems. First, the mean-field type description of monovalent salt ions works reasonably well in the NF system. Second, the manner by which the NF sidearms are arranged on the surface of the NF backbone core has little influence on the lateral extension of NF sidearms. Third, the lateral extension of the NF sidearms is highly affected by the ionic strength of the system: at low ionic strength, NF-M is most extended but at high ionic strength, NF-H is more stretched out because of the effective screening of the electrostatic interaction. Fourth, the presence of Ca2 + ions induces the attraction between negatively charged residues, which leads to the contraction of the overall NF extension. Finally, the introduction of hydrophobic interaction does not change the general structural organization of the NF sidearms except that the overall extension is contracted.

Combination of submicroemulsion and phospholipid complex for novel delivery of ursodeoxycholic acid.

PubMed

Ma, Yue-Qin; Li, Gang; Xu, Jiang-Hong; Zhang, Jing; Zhang, Zeng-Zhu; Xiao, Han-Yang; Li, Xian-Fei

2014-05-01

The objective of this study was to prepare and characterize ursodeoxycholic acid submicron emulsion (UA-SME) loaded with ursodeoxycholic acid phytosomes (UA-PS) and optimize the process variables. A screening experiment with response surface methodology with Box-Behnken design (BBD) was used to optimize the process parameters of UA-SME. The blood concentrations of UA after oral administration of UA-SME and UA coarse drug were assayed. The optimum process conditions were finally obtained by using a desirability function. It was found that stirring velocity, homogenization pressure and homogenization cycles were the most important variables that affected the particles size, polydispersity index and entrapment efficiency of UA-SME. Results showed that the optimum stirring velocity, homogenization pressure and cycles were 16 000 rpm, 60 MPa and 10 cycles, respectively. The mean diameter, polydispersity index and entrapment efficiency of UA-SME were 251.9 nm, 0.241 and 74.36%, respectively. Pharmacokinetic parameters of UA and UA-SME in rats were Tmax 2.215 and 1.489 h, Cmax 0.0364 and 0.1562 μg/mL, AUC0-∞ 3.682 and 13.756 μg h/mL, respectively. The bioavailability of UA in rats was significantly different (p < 0.05) after oral administration of UA-SME compared to those of UA coarse drug. This was due to improvement of the hydrophilicity and lipophilic property of UA-SME.

Predictors of coarse particulate matter and associated endotoxin concentrations in residential environments

NASA Astrophysics Data System (ADS)

Bari, Md. Aynul; MacNeill, Morgan; Kindzierski, Warren B.; Wallace, Lance; Héroux, Marie-Ève; Wheeler, Amanda J.

2014-08-01

Exposure to coarse particulate matter (PM), i.e., particles with an aerodynamic diameter between 2.5 and 10 μm (PM10-2.5), is of increasing interest due to the potential for health effects including asthma, allergy and respiratory symptoms. Limited information is available on indoor and outdoor coarse PM and associated endotoxin exposures. Seven consecutive 24-h samples of indoor and outdoor coarse PM were collected during winter and summer 2010 using Harvard Coarse Impactors in a total of 74 Edmonton homes where no reported smoking took place. Coarse PM filters were subsequently analyzed for endotoxin content. Data were also collected on indoor and outdoor temperature, relative humidity, air exchange rate, housing characteristics and occupants' activities. During winter, outdoor concentrations of coarse PM (median = 6.7 μg/m3, interquartile range, IQR = 3.4-12 μg/m3) were found to be higher than indoor concentrations (median 3.4 μg/m3, IQR = 1.6-5.7 μg/m3); while summer levels of indoor and outdoor concentrations were similar (median 4.5 μg/m3, IQR = 2.3-6.8 μg/m3, and median 4.7 μg/m3, IQR = 2.1-7.9 μg/m3, respectively). Similar predictors were identified for indoor coarse PM in both seasons and included corresponding outdoor coarse PM concentrations, whether vacuuming, sweeping or dusting was performed during the sampling period, and number of occupants in the home. Winter indoor coarse PM predictors also included the number of dogs and indoor endotoxin concentrations. Summer median endotoxin concentrations (indoor: 0.41 EU/m3, outdoor: 0.64 EU/m3) were 4-fold higher than winter concentrations (indoor: 0.12 EU/m3, outdoor: 0.16 EU/m3). Other than outdoor endotoxin concentrations, indoor endotoxin concentration predictors for both seasons were different. Winter endotoxin predictors also included presence of furry pets and whether the vacuum had a high efficiency particulate air (HEPA) filter. Summer endotoxin predictors were problems with mice in the previous 12 months and mean indoor relative humidity levels.

Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS

NASA Astrophysics Data System (ADS)

Fu, S.-P.; Peng, Z.; Yuan, H.; Kfoury, R.; Young, Y.-N.

2017-01-01

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiencies have been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 ∼ 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane, such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity Yuan et al. (2010). In this work we implement such an interaction potential in LAMMPS to simulate large-scale lipid systems such as a giant unilamellar vesicle (GUV) and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for RBC dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. To demonstrate that the proposed methods do capture the observed dynamics of vesicles and RBCs, we focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with enclosed volume; 2. RBC shape transitions with different enclosed volume. Finally utilizing the parallel computing capability in LAMMPS, we provide some timing results for parallel coarse-grained simulations to illustrate that it is possible to use LAMMPS to simulate large-scale realistic complex biological membranes for more than 1 ms.

Two- and three-dimensional natural and mixed convection simulation using modular zonal models

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

Wurtz, E.; Nataf, J.M.; Winkelmann, F.

We demonstrate the use of the zonal model approach, which is a simplified method for calculating natural and mixed convection in rooms. Zonal models use a coarse grid and use balance equations, state equations, hydrostatic pressure drop equations and power law equations of the form {ital m} = {ital C}{Delta}{sup {ital n}}. The advantage of the zonal approach and its modular implementation are discussed. The zonal model resolution of nonlinear equation systems is demonstrated for three cases: a 2-D room, a 3-D room and a pair of 3-D rooms separated by a partition with an opening. A sensitivity analysis withmore » respect to physical parameters and grid coarseness is presented. Results are compared to computational fluid dynamics (CFD) calculations and experimental data.« less

The Effects of Hydration on Protein of Azurin using Coarse-Grained Method and The Free-Energy Analysis

NASA Astrophysics Data System (ADS)

Fitrasari, Dian; Purqon, Acep

2017-07-01

Proteins play important roles in body metabolism. However, to reveal hydration effects, it is cost computing especially for all-atom calculation. Coarse-grained method is one of potential solution to reduce the calculation and computable in longer timescale. Furthermore, the protein of Azurin is interesting protein and potentially applicable to cancer medicine for the stability property reason. We investigate the effects of hydration on Azurin, the conformation and the stabilities. Furthermore, we analyze the free-energy of the conformation system to find the favorable structure using free energy perturbation (FEP) calculation. Our calculation results show that free energy value of azurin is -136.9 kJ/mol. It shows a good agreement with experimental results with relative error index remained at 0.07%.

Modelling soil properties in a crop field located in Croatia

NASA Astrophysics Data System (ADS)

Bogunovic, Igor; Pereira, Paulo; Millan, Mesic; Percin, Aleksandra; Zgorelec, Zeljka

2016-04-01

Development of tillage activities had negative effects on soil quality as destruction of soil horizons, compacting and aggregates destruction, increasing soil erosion and loss of organic matter. For a better management in order to mitigate the effects of intensive soil management in land degradation it is fundamental to map the spatial distribution of soil properties (Brevik et al., 2016). The understanding the distribution of the variables in space is very important for a sustainable management, in order to identify areas that need a potential intervention and decrease the economic losses (Galiati et al., 2016). The objective of this work is study the spatial distribution of some topsoil properties as clay, fine silt, coarse silt, fine sand, coarse sand, penetration resistance, moisture and organic matter in a crop field located in Croatia. A grid with 275x25 (625 m2) was designed and a total of 48 samples were collected. Previous to data modelling, data normality was checked using the Shapiro wilk-test. As in previous cases (Pereira et al., 2015), data did not followed the normal distribution, even after a logarithmic (Log), square-root, and box cox transformation. Thus, for modeling proposes, we used the log transformed data, since was the closest to the normality. In order to identify groups among the variables we applied a principal component analysis (PCA), based on the correlation matrix. On average clay content was 15.47% (±3.23), fine silt 24.24% (±4.08), coarse silt 35.34% (±3.12), fine sand 20.93% (±4.68), coarse sand 4.02% (±1.69), penetration resistance 0.66 MPa (±0.28), organic matter 1.51% (±0.25) and soil moisture 32.04% (±3.27). The results showed that the PCA identified three factors explained at least one of the variables. The first factor had high positive loadings in soil clay, fine silt and organic matter and a high negative loading in fine sand. The second factor had high positive loadings in coarse sand and moisture and a high negative loading in coarse silt. Finally, the factor 3 had a positive loading in penetration resistance. The loadings of these three factors were mapped using ordinary kriging method. The analysis of incremental spatial correlation identified that the highest spatial correlation in the factor 1 was identified at 41.87 m, in factor 2 at 75.61 m and factor 3 at 143.9 m. In the case of factor 2, the maximum peak of spatial autocorrelation was significant at a p<0.05. This showed that the variable has a random distribution, as confirmed with the Moran's I spatial correlation analysis. In relation to the other factors the maximum peaks were significantly clustered at a p<0.001. These results suggested that the each factor has a different spatial pattern and the studied soil properties explained by each factor had a different spatial distribution. References Breivik, E., Baumgarten, A., Calzolari, C., Miller, B., Pereira, P., Kabala, C., Jordán, A. Soil mapping, classification, and modelling: history and future directions. Geoderma, 264, Part B, 256-274. Galiati, A., Gristina, L., Crescimanno, Barone, E., Novara, A. (2016) Towards more efficient incentives for agri-environment measures in degraded and eroded vineyards. Land Degradation and Development, DOI: 10.1002/ldr.2389 Pereira, P., Cerdà, A., Úbeda, X., Mataix-Solera, J. Arcenegui, V., Zavala, L. (2015) Modelling the impacts of wildfire on ash thickness in a short-term period, Land Degradation and Development, 26, 180-192.

Mineralogical control of soil organic carbon persistence at the multidecadal time scale

NASA Astrophysics Data System (ADS)

Lutfalla, Suzanne; Barré, Pierre; Bernard, Sylvain; Le Guillou, Corentin; Chenu, Claire

2015-04-01

One of the current challenges in understanding the long term persistence of organic carbon in soils is to assess how mineral surfaces, especially at small scale, can stabilize soil organic carbon (SOC). The question we address in this work is whether different mineral species stabilize different types of SOC. Here we used the unique opportunity offered by long term bare fallows to study in situ C dynamics in several fine fractions of a silty loam soil. Indeed, with no vegetation i.e. no external input of fresh C, the plant-free soil of the Versailles 42 Plots (INRA, France) has been progressively enriched in persistent SOC during the 80 years of bare fallow. To separate mineral phases of the clay size fraction we performed a size fractionation on samples taken from 4 different plots at 5 different dates (0, 10, 22, 52, and 79 years after the beginning of the BF) and analyzed the SOC in the different fractions thus obtained. First, the clay fraction (< 2 µm) was isolated by wet sieving and centrifugation in water. Then, the clay fraction was further separated into 3 size fractions by centrifugation: fine clay (< 0.05 µm), intermediate clay (0.05 - 0.2 µm), and coarse clay (0.2 - 2 µm). X-ray diffraction was used to determine the mineralogy of the phases and we found that the coarse clay fraction on the one hand and fine and intermediate clay fractions on the other hand exhibited contrasted mineralogies. Fine and intermediate clay fractions contained almost exclusively smectite and mixed-layered illite/smectite minerals whereas coarse clays contained also discrete illite and kaolinite on top of smectite and illite/smectite. We carried out CHN elemental analysis to study the C and nitrogen dynamics with time in the different fractions. And synchrotron based spectroscopy and microscopy (NEXAFS bulk and STXM at the carbon K edge of 280 eV, CLS Saskatoon, Canada) was used to get information on the distribution and the chemical speciation of the SOC in fractions with contrasted mineralogies. Data analysis is still ongoing and full results will be presented at EGU. First results show that the dynamics and quality of the SOC differ in the different clay fractions. SOC decay was greater in coarse clays compared to intermediate clays, SOC in the coarse clay fraction displaying more diversity than in the other fractions. SOC persistence at the multidecadal timescale also seems to be mineral dependent: smectite being more efficient at protecting carbon compared to illite.

Are pretreatment 18F-FDG PET tumor textural features in non-small cell lung cancer associated with response and survival after chemoradiotherapy?

PubMed

Cook, Gary J R; Yip, Connie; Siddique, Muhammad; Goh, Vicky; Chicklore, Sugama; Roy, Arunabha; Marsden, Paul; Ahmad, Shahreen; Landau, David

2013-01-01

There is evidence in some solid tumors that textural features of tumoral uptake in (18)F-FDG PET images are associated with response to chemoradiotherapy and survival. We have investigated whether a similar relationship exists in non-small cell lung cancer (NSCLC). Fifty-three patients (mean age, 65.8 y; 31 men, 22 women) with NSCLC treated with chemoradiotherapy underwent pretreatment (18)F-FDG PET/CT scans. Response was assessed by CT Response Evaluation Criteria in Solid Tumors (RECIST) at 12 wk. Overall survival (OS), progression-free survival (PFS), and local PFS (LPFS) were recorded. Primary tumor texture was measured by the parameters coarseness, contrast, busyness, and complexity. The following parameters were also derived from the PET data: primary tumor standardized uptake values (SUVs) (mean SUV, maximum SUV, and peak SUV), metabolic tumor volume, and total lesion glycolysis. Compared with nonresponders, RECIST responders showed lower coarseness (mean, 0.012 vs. 0.027; P = 0.004) and higher contrast (mean, 0.11 vs. 0.044; P = 0.002) and busyness (mean, 0.76 vs. 0.37; P = 0.027). Neither complexity nor any of the SUV parameters predicted RECIST response. By Kaplan-Meier analysis, OS, PFS, and LPFS were lower in patients with high primary tumor coarseness (median, 21.1 mo vs. not reached, P = 0.003; 12.6 vs. 25.8 mo, P = 0.002; and 12.9 vs. 20.5 mo, P = 0.016, respectively). Tumor coarseness was an independent predictor of OS on multivariable analysis. Contrast and busyness did not show significant associations with OS (P = 0.075 and 0.059, respectively), but PFS and LPFS were longer in patients with high levels of each (for contrast: median of 20.5 vs. 12.6 mo, P = 0.015, and median not reached vs. 24 mo, P = 0.02; and for busyness: median of 20.5 vs. 12.6 mo, P = 0.01, and median not reached vs. 24 mo, P = 0.006). Neither complexity nor any of the SUV parameters showed significant associations with the survival parameters. In NSCLC, baseline (18)F-FDG PET scan uptake showing abnormal texture as measured by coarseness, contrast, and busyness is associated with nonresponse to chemoradiotherapy by RECIST and with poorer prognosis. Measurement of tumor metabolic heterogeneity with these parameters may provide indices that can be used to stratify patients in clinical trials for lung cancer chemoradiotherapy.

Root architecture impacts on root decomposition rates in switchgrass

NASA Astrophysics Data System (ADS)

de Graaff, M.; Schadt, C.; Garten, C. T.; Jastrow, J. D.; Phillips, J.; Wullschleger, S. D.

2010-12-01

Roots strongly contribute to soil organic carbon accrual, but the rate of soil carbon input via root litter decomposition is still uncertain. Root systems are built up of roots with a variety of different diameter size classes, ranging from very fine to very coarse roots. Since fine roots have low C:N ratios and coarse roots have high C:N ratios, root systems are heterogeneous in quality, spanning a range of different C:N ratios. Litter decomposition rates are generally well predicted by litter C:N ratios, thus decomposition of roots may be controlled by the relative abundance of fine versus coarse roots. With this study we asked how root architecture (i.e. the relative abundance of fine versus coarse roots) affects the decomposition of roots systems in the biofuels crop switchgrass (Panicum virgatum L.). To understand how root architecture affects root decomposition rates, we collected roots from eight switchgrass cultivars (Alamo, Kanlow, Carthage, Cave-in-Rock, Forestburg, Southlow, Sunburst, Blackwell), grown at FermiLab (IL), by taking 4.8-cm diameter soil cores from on top of the crown and directly next to the crown of individual plants. Roots were carefully excised from the cores by washing and analyzed for root diameter size class distribution using WinRhizo. Subsequently, root systems of each of the plants (4 replicates per cultivar) were separated in 'fine' (0-0.5 mm), 'medium' (0.5-1 mm) and 'coarse' roots (1-2.5 mm), dried, cut into 0.5 cm (medium and coarse roots) and 2 mm pieces (fine roots), and incubated for 90 days. For each of the cultivars we established five root-treatments: 20g of soil was amended with 0.2g of (1) fine roots, (2) medium roots, (3) coarse roots, (4) a 1:1:1 mixture of fine, medium and coarse roots, and (5) a mixture combining fine, medium and coarse roots in realistic proportions. We measured CO2 respiration at days 1, 3, 7, 15, 30, 60 and 90 during the experiment. The 13C signature of the soil was -26‰, and the 13C signature of plants was -12‰, enabling us to differentiate between root-derived C and native SOM-C respiration. We found that the relative abundance of fine, medium and coarse roots were significantly different among cultivars. Root systems of Alamo, Kanlow and Cave-in-Rock were characterized by a large abundance of coarse-, relative to fine roots, whereas Carthage, Forestburg and Blackwell had a large abundance of fine, relative to coarse roots. Fine roots had a 28% lower C:N ratio than medium and coarse roots. These differences led to different root decomposition rates. We conclude that root architecture should be taken into account when predicting root decomposition rates; enhanced understanding of the mechanisms of root decomposition will improve model predictions of C input to soil organic matter.

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...

Fine gravel controls hydrologic and erodibility responses to trampling disturbance for coarse-textured soils with weak cyanobacterial crusts.

USDA-ARS?s Scientific Manuscript database

We compared short-term effects of lug-soled boot trampling disturbance on water infiltration and soil erodibility on coarse-textured soils covered by a mixture of fine gravel and coarse sand over weak cyanobacterially-dominated biological soil crusts. Trampling significantly reduced final infiltrati...

Consumer clusters in Denmark based on coarse vegetable intake frequency, explained by hedonics, socio-demographic, health and food lifestyle factors. A cross-sectional national survey.

PubMed

Beck, Tove K; Jensen, Sidsel; Simmelsgaard, Sonni Hansen; Kjeldsen, Chris; Kidmose, Ulla

2015-08-01

Vegetable intake seems to play a protective role against major lifestyle diseases. Despite this, the Danish population usually eats far less than the recommended daily intake. The present study focused on the intake of 17 coarse vegetables and the potential barriers limiting their intake. The present study drew upon a large Danish survey (n = 1079) to study the intake of coarse vegetables among Danish consumers. Four population clusters were identified based on their intake of 17 different coarse vegetables, and profiled according to hedonics, socio-demographic, health, and food lifestyle factors. The four clusters were characterized by a very low intake frequency of coarse vegetables ('low frequency'), a low intake frequency of coarse vegetables; but high intake frequency of carrots ('carrot eaters'), a moderate coarse vegetable intake frequency and high intake frequency of beetroot ('beetroot eaters'), and a high intake frequency of all coarse vegetables ('high frequency'). There was a relationship between reported liking and reported intake frequency for all tested vegetables. Preference for foods with a sweet, salty or bitter taste, in general, was also identified to be decisive for the reported vegetable intake, as these differed across the clusters. Each cluster had distinct socio-demographic, health and food lifestyle profiles. 'Low frequency' was characterized by uninvolved consumers with lack of interest in food, 'carrot eaters' vegetable intake was driven by health aspects, 'beetroot eaters' were characterized as traditional food consumers, and 'high frequency' were individuals with a strong food engagement and high vegetable liking. 'Low frequency' identified more barriers than other consumer clusters and specifically regarded low availability of pre-cut/prepared coarse vegetables on the market as a barrier. Across all clusters a low culinary knowledge was identified as the main barrier. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effective connectivity in the neural network underlying coarse-to-fine categorization of visual scenes. A dynamic causal modeling study.

PubMed

Kauffmann, Louise; Chauvin, Alan; Pichat, Cédric; Peyrin, Carole

2015-10-01

According to current models of visual perception scenes are processed in terms of spatial frequencies following a predominantly coarse-to-fine processing sequence. Low spatial frequencies (LSF) reach high-order areas rapidly in order to activate plausible interpretations of the visual input. This triggers top-down facilitation that guides subsequent processing of high spatial frequencies (HSF) in lower-level areas such as the inferotemporal and occipital cortices. However, dynamic interactions underlying top-down influences on the occipital cortex have never been systematically investigated. The present fMRI study aimed to further explore the neural bases and effective connectivity underlying coarse-to-fine processing of scenes, particularly the role of the occipital cortex. We used sequences of six filtered scenes as stimuli depicting coarse-to-fine or fine-to-coarse processing of scenes. Participants performed a categorization task on these stimuli (indoor vs. outdoor). Firstly, we showed that coarse-to-fine (compared to fine-to-coarse) sequences elicited stronger activation in the inferior frontal gyrus (in the orbitofrontal cortex), the inferotemporal cortex (in the fusiform and parahippocampal gyri), and the occipital cortex (in the cuneus). Dynamic causal modeling (DCM) was then used to infer effective connectivity between these regions. DCM results revealed that coarse-to-fine processing resulted in increased connectivity from the occipital cortex to the inferior frontal gyrus and from the inferior frontal gyrus to the inferotemporal cortex. Critically, we also observed an increase in connectivity strength from the inferior frontal gyrus to the occipital cortex, suggesting that top-down influences from frontal areas may guide processing of incoming signals. The present results support current models of visual perception and refine them by emphasizing the role of the occipital cortex as a cortical site for feedback projections in the neural network underlying coarse-to-fine processing of scenes. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparative analysis of coarse surfacing aggregate using Micro-Deval, L.A. Abrasion and Sodium Sulfate Soundness Tests.

DOT National Transportation Integrated Search

2007-01-01

"Aggregates used in the construction of roads must be durable, abrasion resistant, and freeze-thaw resistant in : order to perform well in pavement or as base course. The objective of this study was to investigate whether the : Micro-Deval test will ...

Sampling interval analysis and CDF generation for grain-scale gravel bed topography

USDA-ARS?s Scientific Manuscript database

In river hydraulics, there is a continuing need for characterizing bed elevations to arrive at quantitative roughness measures that can be used in predicting flow depth and for improved prediction of fine-sediment transport over and through coarse beds. Recently published prediction methods require...

MICROARRAY ANALYSIS OF PM-INDUCED GENEEXPRESSION IN HUMAN BRONCHIAL EPITHELIAL CELLS

EPA Science Inventory

Ambient air particles (PM) are generally classified into 3 sizes; coarse (2.5, 10m), fine (0.1, 2.5m), and ultrafine (<0.lpm). Each particle size is evolved from different sources and transformation processes (e.g., combustion vs. mechanical abrasion, and atmospheric conversion ...

Current status of chestnut in eastern US forests

Treesearch

William H. McWiliams; Tonya W. Lister; Elizabeth B. LaPoint; Anita K. Rose; John S. Vissage

2006-01-01

The USDA Forest Service, Forest Inventory and Analysis (FIA) program provides the opportunity to assess the current distribution of American chestnut (Castanea dentata (Marsh.) Borkh) and prospective trends. Assessing chestnut using the FIA data was challenging because of the coarse nature of the FIA sample and chestnut's rarity in natural...

Representations of Scientists in Canadian High School and College Textbooks

ERIC Educational Resources Information Center

van Eijck, Michiel; Roth, Wolff-Michael

2008-01-01

This study investigated the representations of a select group of scientists (n = 10) in a sample of Canadian high school and college textbooks. Drawing on semiotic and cultural-historical activity theoretical frameworks, we conducted two analyses. A coarse-grained, quantitative analysis of the prevalence and structure of these representations…

The Ribosome Shape Directs mRNA Translocation through Entrance and Exit Dynamics

USDA-ARS?s Scientific Manuscript database

The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs (transfer ribonucleic acids) and mRNA (messenger ribonucleic acid); here the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal struc...

Analysis of North Atlantic Tropical Cyclone Intensify Change Using Data Mining

ERIC Educational Resources Information Center

Tang, Jiang

2010-01-01

Tropical cyclones (TC), especially when their intensity reaches hurricane scale, can become a costly natural hazard. Accurate prediction of tropical cyclone intensity is very difficult because of inadequate observations on TC structures, poor understanding of physical processes, coarse model resolution and inaccurate initial conditions, etc. This…

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

Dongil Chun; Dohyeon Kim; Kwangyong Eun

TiC-Ni-Mo cermet specimens were prepared by using a mixture of fine (1.5 [mu]m) and coarse (30 [mu]m) TiC powders. When the fraction of fine TiC particles was 80%, a (Ti,Mo,Ni)C complex carbide phase was observed deposited on the coarse TiC particles and resulted in a typical cored structure. As the fraction of fine TiC particles decreased, the coarse TiC particles exhibited a unique microstructural evolution with the development of a concave interface. This microstructural change of the coarse TiC grains can be explained in terms of the coherency strain energy.

Coarse Scale In Situ Albedo Observations over Heterogeneous Land Surfaces and Validation Strategy

NASA Astrophysics Data System (ADS)

Xiao, Q.; Wu, X.; Wen, J.; BAI, J., Sr.

2017-12-01

To evaluate and improve the quality of coarse-pixel land surface albedo products, validation with ground measurements of albedo is crucial over the spatially and temporally heterogeneous land surface. The performance of albedo validation depends on the quality of ground-based albedo measurements at a corresponding coarse-pixel scale, which can be conceptualized as the "truth" value of albedo at coarse-pixel scale. The wireless sensor network (WSN) technology provides access to continuously observe on the large pixel scale. Taking the albedo products as an example, this paper was dedicated to the validation of coarse-scale albedo products over heterogeneous surfaces based on the WSN observed data, which is aiming at narrowing down the uncertainty of results caused by the spatial scaling mismatch between satellite and ground measurements over heterogeneous surfaces. The reference value of albedo at coarse-pixel scale can be obtained through an upscaling transform function based on all of the observations for that pixel. We will devote to further improve and develop new method that that are better able to account for the spatio-temporal characteristic of surface albedo in the future. Additionally, how to use the widely distributed single site measurements over the heterogeneous surfaces is also a question to be answered. Keywords: Remote sensing; Albedo; Validation; Wireless sensor network (WSN); Upscaling; Heterogeneous land surface; Albedo truth at coarse-pixel scale

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

Satellite-Scale Snow Water Equivalent Assimilation into a High-Resolution Land Surface Model

NASA Technical Reports Server (NTRS)

De Lannoy, Gabrielle J.M.; Reichle, Rolf H.; Houser, Paul R.; Arsenault, Kristi R.; Verhoest, Niko E.C.; Paulwels, Valentijn R.N.

2009-01-01

An ensemble Kalman filter (EnKF) is used in a suite of synthetic experiments to assimilate coarse-scale (25 km) snow water equivalent (SWE) observations (typical of satellite retrievals) into fine-scale (1 km) model simulations. Coarse-scale observations are assimilated directly using an observation operator for mapping between the coarse and fine scales or, alternatively, after disaggregation (re-gridding) to the fine-scale model resolution prior to data assimilation. In either case observations are assimilated either simultaneously or independently for each location. Results indicate that assimilating disaggregated fine-scale observations independently (method 1D-F1) is less efficient than assimilating a collection of neighboring disaggregated observations (method 3D-Fm). Direct assimilation of coarse-scale observations is superior to a priori disaggregation. Independent assimilation of individual coarse-scale observations (method 3D-C1) can bring the overall mean analyzed field close to the truth, but does not necessarily improve estimates of the fine-scale structure. There is a clear benefit to simultaneously assimilating multiple coarse-scale observations (method 3D-Cm) even as the entire domain is observed, indicating that underlying spatial error correlations can be exploited to improve SWE estimates. Method 3D-Cm avoids artificial transitions at the coarse observation pixel boundaries and can reduce the RMSE by 60% when compared to the open loop in this study.

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.

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.

Wavelet processing techniques for digital mammography

NASA Astrophysics Data System (ADS)

Laine, Andrew F.; Song, Shuwu

1992-09-01

This paper introduces a novel approach for accomplishing mammographic feature analysis through multiresolution representations. We show that efficient (nonredundant) representations may be identified from digital mammography and used to enhance specific mammographic features within a continuum of scale space. The multiresolution decomposition of wavelet transforms provides a natural hierarchy in which to embed an interactive paradigm for accomplishing scale space feature analysis. Similar to traditional coarse to fine matching strategies, the radiologist may first choose to look for coarse features (e.g., dominant mass) within low frequency levels of a wavelet transform and later examine finer features (e.g., microcalcifications) at higher frequency levels. In addition, features may be extracted by applying geometric constraints within each level of the transform. Choosing wavelets (or analyzing functions) that are simultaneously localized in both space and frequency, results in a powerful methodology for image analysis. Multiresolution and orientation selectivity, known biological mechanisms in primate vision, are ingrained in wavelet representations and inspire the techniques presented in this paper. Our approach includes local analysis of complete multiscale representations. Mammograms are reconstructed from wavelet representations, enhanced by linear, exponential and constant weight functions through scale space. By improving the visualization of breast pathology we can improve the chances of early detection of breast cancers (improve quality) while requiring less time to evaluate mammograms for most patients (lower costs).

Analysis of the typical small watershed of warping dams in the sand properties

NASA Astrophysics Data System (ADS)

Li, Li; Yang, Ji Shan; Sun, Wei Ying; Shen, Sha Sha

2018-06-01

Coarse sediment with a particle size greater than 0.05mm is the main deposit of riverbed in the lower Yellow River, the Loess Plateau is one of the concentrated source of coarse sediment, warping dam is one of the important engineering measures for gully control. Jiuyuangou basin is a typical small basin in the first sub region of hilly-gullied loess region, twenty warping dams in Jiuyuangou basin was selected as research object, samples of sediment along the main line of dam from upper, middle to lower reaches of dam fields and samples of undisturbed soil in slope of dam control basin were taken to carry out particle gradation analysis, in the hope of clearing reducing capacity on coarse sediment of different types of warping dam through the experimental data. The results show that the undisturbed soil in slope of dam control basin has characteristics of standard loess, the particle size are mainly distributed in 0.025 0.05mm, and the 0.05mm particle size of Jiuyuangou basinof loess is an obvious boundary; Particle size of sediment in 15 warping dam of Jiuyuangou basin are mainly distributed in 0.031 0.05mm with the dam tail is greater than dam front in general. The separation effect of horizontal pipe drainage is better than shaft drainage for which particle size greater than 0.05mm, notch dam is for particle size between 0.025 0.1 mm, and fill dam is for particle size between 0.016 0.1 mm, they all have a certain function in the sediment sorting.

MAHLI at the Rocknest sand shadow: Science and science-enabling activities

NASA Astrophysics Data System (ADS)

Minitti, M. E.; Kah, L. C.; Yingst, R. A.; Edgett, K. S.; Anderson, R. C.; Beegle, L. W.; Carsten, J. L.; Deen, R. G.; Goetz, W.; Hardgrove, C.; Harker, D. E.; Herkenhoff, K. E.; Hurowitz, J. A.; Jandura, L.; Kennedy, M. R.; Kocurek, G.; Krezoski, G. M.; Kuhn, S. R.; Limonadi, D.; Lipkaman, L.; Madsen, M. B.; Olson, T. S.; Robinson, M. L.; Rowland, S. K.; Rubin, D. M.; Seybold, C.; Schieber, J.; Schmidt, M.; Sumner, D. Y.; Tompkins, V. V.; Van Beek, J. K.; Van Beek, T.

2013-11-01

Martian solar days 57-100, the Mars Science Laboratory Curiosity rover acquired and processed a solid (sediment) sample and analyzed its mineralogy and geochemistry with the Chemistry and Mineralogy and Sample Analysis at Mars instruments. An aeolian deposit—herein referred to as the Rocknest sand shadow—was inferred to represent a global average soil composition and selected for study to facilitate integration of analytical results with observations from earlier missions. During first-time activities, the Mars Hand Lens Imager (MAHLI) was used to support both science and engineering activities related to sample assessment, collection, and delivery. Here we report on MAHLI activities that directly supported sample analysis and provide MAHLI observations regarding the grain-scale characteristics of the Rocknest sand shadow. MAHLI imaging confirms that the Rocknest sand shadow is one of a family of bimodal aeolian accumulations on Mars—similar to the coarse-grained ripples interrogated by the Mars Exploration Rovers Spirit and Opportunity—in which a surface veneer of coarse-grained sediment stabilizes predominantly fine-grained sediment of the deposit interior. The similarity in grain size distribution of these geographically disparate deposits support the widespread occurrence of bimodal aeolian transport on Mars. We suggest that preservation of bimodal aeolian deposits may be characteristic of regions of active deflation, where winnowing of the fine-sediment fraction results in a relatively low sediment load and a preferential increase in the coarse-grained fraction of the sediment load. The compositional similarity of Martian aeolian deposits supports the potential for global redistribution of fine-grained components, combined with potential local contributions.

Thermomechanical Response of Self-Assembled Nanoparticle Membranes

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

Wang, Yifan; Chan, Henry; Narayanan, Badri

2017-07-21

Monolayers composed of colloidal nanoparticles, with a thickness of less than 10 nm, have remarkable mechanical moduli and can suspend over micrometer-sized holes to form free-standing membranes. In this paper, we discuss experiment's and coarse-grained molecular dynamics simulations characterizing the thermomechanical properties of these self-assembled nanoparticle membranes. These membranes remain strong and resilient up to temperatures much higher than previous simulation predictions and exhibit an unexpected hysteretic behavior during the first heating cooling cycle. We show this hysteretic behavior can be explained by an asymmetric ligand configuration from the self assembly process and can be controlled by changing the ligandmore » coverage or cross-linking the ligand molecules. Finally, we show the screening effect of water molecules on the ligand interactions can strongly affect the moduli and thermomechanical behavior.« less

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...

The Influence of Organic Material and Temperature on the Burial Tolerance of the Blue Mussel, Mytilus edulis: Considerations for the Management of Marine Aggregate Dredging

PubMed Central

Cottrell, Richard S.; Black, Kenny D.; Hutchison, Zoë L.; Last, Kim S.

2016-01-01

Rationale and Experimental Approach Aggregate dredging is a growing source of anthropogenic disturbance in coastal UK waters and has the potential to impact marine systems through the smothering of benthic fauna with organically loaded screening discards. This study investigates the tolerance of the blue mussel, Mytilus edulis to such episodic smothering events using a multi-factorial design, including organic matter concentration, temperature, sediment fraction size and duration of burial as important predictor variables. Results and Discussion Mussel mortality was significantly higher in organically loaded burials when compared to control sediments after just 2 days. Particularly, M. edulis specimens under burial in fine sediment with high (1%) concentrations of organic matter experienced a significantly higher mortality rate (p<0.01) than those under coarse control aggregates. Additionally, mussels exposed to the summer maximum temperature treatment (20°C) exhibited significantly increased mortality (p<0.01) compared to those in the ambient treatment group (15°C). Total Oxygen Uptake rates of experimental aggregates were greatest (112.7 mmol m-2 day-1) with 1% organic loadings in coarse sediment at 20°C. Elevated oxygen flux rates in porous coarse sediments are likely to be a function of increased vertical migration of anaerobically liberated sulphides to the sediment-water interface. However, survival of M. edulis under bacterial mats of Beggiatoa spp. indicates the species’ resilience to sulphides and so we propose that the presence of reactive organic matter within the burial medium may facilitate bacterial growth and increase mortality through pathogenic infection. This may be exacerbated under the stable interstitial conditions in fine sediment and increased bacterial metabolism under high temperatures. Furthermore, increased temperature may impose metabolic demands upon the mussel that cannot be met during burial-induced anaerobiosis. Summary Lack of consideration for the role of organic matter and temperature during sedimentation events may lead to an overestimation of the tolerance of benthic species to smothering from dredged material. PMID:26809153

Biology of the Coarse Aerosol Mode: Insights Into Urban Aerosol Ecology

NASA Astrophysics Data System (ADS)

Dueker, E.; O'Mullan, G. D.; Montero, A.

2015-12-01

Microbial aerosols have been understudied, despite implications for climate studies, public health, and biogeochemical cycling. Because viable bacterial aerosols are often associated with coarse aerosol particles, our limited understanding of the coarse aerosol mode further impedes our ability to develop models of viable bacterial aerosol production, transport, and fate in the outdoor environment, particularly in crowded urban centers. To address this knowledge gap, we studied aerosol particle biology and size distributions in a broad range of urban and rural settings. Our previously published findings suggest a link between microbial viability and local production of coarse aerosols from waterways, waste treatment facilities, and terrestrial systems in urban and rural environments. Both in coastal Maine and in New York Harbor, coarse aerosols and viable bacterial aerosols increased with increasing wind speeds above 4 m s-1, a dynamic that was observed over time scales ranging from minutes to hours. At a New York City superfund-designated waterway regularly contaminated with raw sewage, aeration remediation efforts resulted in significant increases of coarse aerosols and bacterial aerosols above that waterway. Our current research indicates that bacterial communities in aerosols at this superfund site have a greater similarity to bacterial communities in the contaminated waterway with wind speeds above 4 m s-1. Size-fractionated sampling of viable microbial aerosols along the urban waterfront has also revealed significant shifts in bacterial aerosols, and specifically bacteria associated with coarse aerosols, when wind direction changes from onshore to offshore. This research highlights the key connections between bacterial aerosol viability and the coarse aerosol fraction, which is important in assessments of production, transport, and fate of bacterial contamination in the urban environment.

Contribution of radioactive 137Cs discharge by suspended sediment, coarse organic matter, and dissolved fraction from a headwater catchment in Fukushima after the Fukushima Dai-ichi Nuclear Power Plant accident.

PubMed

Iwagami, Sho; Onda, Yuichi; Tsujimura, Maki; Abe, Yutaka

2017-01-01

Radiocesium ( 137 Cs) migration from headwaters in forested areas provides important information, as the output from forest streams subsequently enters various land-use areas and downstream rivers. Thus, it is important to determine the composition of 137 Cs fluxes (dissolved fraction, suspended sediment, or coarse organic matter) that migrate through a headwater stream. In this study, the 137 Cs discharge by suspended sediment and coarse organic matter from a forest headwater catchment was monitored. The 137 Cs concentrations in suspended sediment and coarse organic matter, such as leaves and branches, and the amounts of suspended sediment and coarse organic matter were measured at stream sites in three headwater catchments in Yamakiya District, located ∼35 km northwest of Fukushima Dai-ichi Nuclear Power Plant (FDNPP) from August 2012 to September 2013, following the earthquake and tsunami disaster. Suspended sediment and coarse organic matter were sampled at intervals of approximately 1-2 months. The 137 Cs concentrations of suspended sediment and coarse organic matter were 2.4-49 kBq/kg and 0.85-14 kBq/kg, respectively. The 137 Cs concentrations of the suspended sediment were closely correlated with the average deposition density of the catchment. The annual proportions of contribution of 137 Cs discharge by suspended sediment, coarse organic matter, and dissolved fraction were 96-99%, 0.0092-0.069%, and 0.73-3.7%, respectively. The total annual 137 Cs discharge from the catchment was 0.02-0.3% of the deposition. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mutually unbiased coarse-grained measurements of two or more phase-space variables

NASA Astrophysics Data System (ADS)

Paul, E. C.; Walborn, S. P.; Tasca, D. S.; Rudnicki, Łukasz

2018-05-01

Mutual unbiasedness of the eigenstates of phase-space operators—such as position and momentum, or their standard coarse-grained versions—exists only in the limiting case of infinite squeezing. In Phys. Rev. Lett. 120, 040403 (2018), 10.1103/PhysRevLett.120.040403, it was shown that mutual unbiasedness can be recovered for periodic coarse graining of these two operators. Here we investigate mutual unbiasedness of coarse-grained measurements for more than two phase-space variables. We show that mutual unbiasedness can be recovered between periodic coarse graining of any two nonparallel phase-space operators. We illustrate these results through optics experiments, using the fractional Fourier transform to prepare and measure mutually unbiased phase-space variables. The differences between two and three mutually unbiased measurements is discussed. Our results contribute to bridging the gap between continuous and discrete quantum mechanics, and they could be useful in quantum-information protocols.

Applying Reduced Generator Models in the Coarse Solver of Parareal in Time Parallel Power System Simulation

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

Duan, Nan; Dimitrovski, Aleksandar D; Simunovic, Srdjan

2016-01-01

The development of high-performance computing techniques and platforms has provided many opportunities for real-time or even faster-than-real-time implementation of power system simulations. One approach uses the Parareal in time framework. The Parareal algorithm has shown promising theoretical simulation speedups by temporal decomposing a simulation run into a coarse simulation on the entire simulation interval and fine simulations on sequential sub-intervals linked through the coarse simulation. However, it has been found that the time cost of the coarse solver needs to be reduced to fully exploit the potentials of the Parareal algorithm. This paper studies a Parareal implementation using reduced generatormore » models for the coarse solver and reports the testing results on the IEEE 39-bus system and a 327-generator 2383-bus Polish system model.« less

A Markov Chain Model for Changes in Users' Assessment of Search Results.

PubMed

Zhitomirsky-Geffet, Maayan; Bar-Ilan, Judit; Levene, Mark

2016-01-01

Previous research shows that users tend to change their assessment of search results over time. This is a first study that investigates the factors and reasons for these changes, and describes a stochastic model of user behaviour that may explain these changes. In particular, we hypothesise that most of the changes are local, i.e. between results with similar or close relevance to the query, and thus belong to the same"coarse" relevance category. According to the theory of coarse beliefs and categorical thinking, humans tend to divide the range of values under consideration into coarse categories, and are thus able to distinguish only between cross-category values but not within them. To test this hypothesis we conducted five experiments with about 120 subjects divided into 3 groups. Each student in every group was asked to rank and assign relevance scores to the same set of search results over two or three rounds, with a period of three to nine weeks between each round. The subjects of the last three-round experiment were then exposed to the differences in their judgements and were asked to explain them. We make use of a Markov chain model to measure change in users' judgments between the different rounds. The Markov chain demonstrates that the changes converge, and that a majority of the changes are local to a neighbouring relevance category. We found that most of the subjects were satisfied with their changes, and did not perceive them as mistakes but rather as a legitimate phenomenon, since they believe that time has influenced their relevance assessment. Both our quantitative analysis and user comments support the hypothesis of the existence of coarse relevance categories resulting from categorical thinking in the context of user evaluation of search results.

Seasonal characteristics of water-soluble inorganic ions and carbonaceous aerosols in total suspended particulate matter at a rural semi-arid site, Kadapa (India).

PubMed

Begam, G Reshma; Vachaspati, C Viswanatha; Ahammed, Y Nazeer; Kumar, K Raghavendra; Reddy, R R; Sharma, S K; Saxena, Mohit; Mandal, T K

2017-01-01

To better understand the sources as well as characterization of regional aerosols at a rural semi-arid region Kadapa (India), size-resolved composition of atmospheric particulate matter (PM) mass concentrations was sampled and analysed. This was carried out by using the Anderson low-pressure impactor for a period of 2 years during March 2013-February 2015. Also, the variations of organic carbon (OC), elemental carbon (EC) and water-soluble inorganic ion components (WSICs) present in total suspended particulate matter (TSPM) were studied over the measurement site. From the statistical analysis, the PM mass concentration showed a higher abundance of coarse mode particles than the fine mode during pre-monsoon season. In contrast, fine mode particles in the PM concentration showed dominance over coarse mode particle contribution during the winter. During the post-monsoon season, the percentage contributions of coarse and fine fractions were equal, whereas during the monsoon, coarse mode fraction was approximately 26 % higher than the fine mode. This distinct feature in the case of fine mode particles during the studied period is mainly attributed to large-scale anthropogenic activities and regional prevailing meteorological conditions. Further, the potential sources of PM have been identified qualitatively by using the ratios of certain ions. A high sulphate (SO 4 ) concentration at the measurement site was observed during the studied period which is caused by the nearby/surrounding mining activity. Carbon fractions (OC and EC) were also analysed from the TSPM, and the results indicated (OC/EC ratio of ~4.2) the formation of a secondary organic aerosol. At last, the cluster backward trajectory analyses were also performed at Kadapa for different seasons to reveal the origin of sources from long-range transport during the study period.

Real time coarse orientation detection in MR scans using multi-planar deep convolutional neural networks

NASA Astrophysics Data System (ADS)

Bhatia, Parmeet S.; Reda, Fitsum; Harder, Martin; Zhan, Yiqiang; Zhou, Xiang Sean

2017-02-01

Automatically detecting anatomy orientation is an important task in medical image analysis. Specifically, the ability to automatically detect coarse orientation of structures is useful to minimize the effort of fine/accurate orientation detection algorithms, to initialize non-rigid deformable registration algorithms or to align models to target structures in model-based segmentation algorithms. In this work, we present a deep convolution neural network (DCNN)-based method for fast and robust detection of the coarse structure orientation, i.e., the hemi-sphere where the principal axis of a structure lies. That is, our algorithm predicts whether the principal orientation of a structure is in the northern hemisphere or southern hemisphere, which we will refer to as UP and DOWN, respectively, in the remainder of this manuscript. The only assumption of our method is that the entire structure is located within the scan's field-of-view (FOV). To efficiently solve the problem in 3D space, we formulated it as a multi-planar 2D deep learning problem. In the training stage, a large number coronal-sagittal slice pairs are constructed as 2-channel images to train a DCNN to classify whether a scan is UP or DOWN. During testing, we randomly sample a small number of coronal-sagittal 2-channel images and pass them through our trained network. Finally, coarse structure orientation is determined using majority voting. We tested our method on 114 Elbow MR Scans. Experimental results suggest that only five 2-channel images are sufficient to achieve a high success rate of 97.39%. Our method is also extremely fast and takes approximately 50 milliseconds per 3D MR scan. Our method is insensitive to the location of the structure in the FOV.

Toward Automatic Georeferencing of Archival Aerial Photogrammetric Surveys

NASA Astrophysics Data System (ADS)

Giordano, S.; Le Bris, A.; Mallet, C.

2018-05-01

Images from archival aerial photogrammetric surveys are a unique and relatively unexplored means to chronicle 3D land-cover changes over the past 100 years. They provide a relatively dense temporal sampling of the territories with very high spatial resolution. Such time series image analysis is a mandatory baseline for a large variety of long-term environmental monitoring studies. The current bottleneck for accurate comparison between epochs is their fine georeferencing step. No fully automatic method has been proposed yet and existing studies are rather limited in terms of area and number of dates. State-of-the art shows that the major challenge is the identification of ground references: cartographic coordinates and their position in the archival images. This task is manually performed, and extremely time-consuming. This paper proposes to use a photogrammetric approach, and states that the 3D information that can be computed is the key to full automation. Its original idea lies in a 2-step approach: (i) the computation of a coarse absolute image orientation; (ii) the use of the coarse Digital Surface Model (DSM) information for automatic absolute image orientation. It only relies on a recent orthoimage+DSM, used as master reference for all epochs. The coarse orthoimage, compared with such a reference, allows the identification of dense ground references and the coarse DSM provides their position in the archival images. Results on two areas and 5 dates show that this method is compatible with long and dense archival aerial image series. Satisfactory planimetric and altimetric accuracies are reported, with variations depending on the ground sampling distance of the images and the location of the Ground Control Points.

Monitoring forest dynamics with multi-scale and time series imagery.

PubMed

Huang, Chunbo; Zhou, Zhixiang; Wang, Di; Dian, Yuanyong

2016-05-01

To learn the forest dynamics and evaluate the ecosystem services of forest effectively, a timely acquisition of spatial and quantitative information of forestland is very necessary. Here, a new method was proposed for mapping forest cover changes by combining multi-scale satellite remote-sensing imagery with time series data. Using time series Normalized Difference Vegetation Index products derived from the Moderate Resolution Imaging Spectroradiometer images (MODIS-NDVI) and Landsat Thematic Mapper/Enhanced Thematic Mapper Plus (TM/ETM+) images as data source, a hierarchy stepwise analysis from coarse scale to fine scale was developed for detecting the forest change area. At the coarse scale, MODIS-NDVI data with 1-km resolution were used to detect the changes in land cover types and a land cover change map was constructed using NDVI values at vegetation growing seasons. At the fine scale, based on the results at the coarse scale, Landsat TM/ETM+ data with 30-m resolution were used to precisely detect the forest change location and forest change trend by analyzing time series forest vegetation indices (IFZ). The method was tested using the data for Hubei Province, China. The MODIS-NDVI data from 2001 to 2012 were used to detect the land cover changes, and the overall accuracy was 94.02 % at the coarse scale. At the fine scale, the available TM/ETM+ images at vegetation growing seasons between 2001 and 2012 were used to locate and verify forest changes in the Three Gorges Reservoir Area, and the overall accuracy was 94.53 %. The accuracy of the two layer hierarchical monitoring results indicated that the multi-scale monitoring method is feasible and reliable.

Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

PubMed

Song, Bin; Molinero, Valeria

2013-08-07

Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

A Beta Oscillation Network in the Rat Olfactory System During a 2-Alternative Choice Odor Discrimination Task

PubMed Central

Beshel, Jennifer

2010-01-01

We previously showed that in a two-alternative choice (2AC) task, olfactory bulb (OB) gamma oscillations (∼70 Hz in rats) were enhanced during discrimination of structurally similar odorants (fine discrimination) versus discrimination of dissimilar odorants (coarse discrimination). In other studies (mostly employing go/no-go tasks) in multiple labs, beta oscillations (15–35 Hz) dominate the local field potential (LFP) signal in olfactory areas during odor sampling. Here we analyzed the beta frequency band power and pairwise coherence in the 2AC task. We show that in a task dominated by gamma in the OB, beta oscillations are also present in three interconnected olfactory areas (OB and anterior and posterior pyriform cortex). Only the beta band showed consistently elevated coherence during odor sniffing across all odor pairs, classes (alcohols and ketones), and discrimination types (fine and coarse), with stronger effects in first than in final criterion sessions (>70% correct). In the first sessions for fine discrimination odor pairs, beta power for incorrect trials was the same as that for correct trials for the other odor in the pair. This pattern was not repeated in coarse discrimination, in which beta power was elevated for correct relative to incorrect trials. This difference between fine and coarse odor discriminations may relate to different behavioral strategies for learning to differentiate similar versus dissimilar odors. Phase analysis showed that the OB led both pyriform areas in the beta frequency band during odor sniffing. We conclude that the beta band may be the means by which information is transmitted from the OB to higher order areas, even though task specifics modify dominance of one frequency band over another within the OB. PMID:20538778

Effects of Coarse Legacy Sediment on Rivers of the Ozark Plateaus and Implications for Native Mussel Fauna

NASA Astrophysics Data System (ADS)

Erwin, S. O.; Jacobson, R. B.; Eric, A. B.; Jones, J. C.; Anderson, B. W.

2015-12-01

Perturbations to sediment regimes due to anthropogenic activities may have long lasting effects, especially in systems dominated by coarse sediment where travel times are relatively long. Effectively evaluating management alternatives requires understanding the future trajectory of river response at both the river network and reach scales. The Ozark Plateaus physiographic province is a montane region in the interior US composed primarily of Paleozoic sedimentary rock. Historic land-use practices around the turn of the last century accelerated delivery of coarse sediment to river channels. Effects of this legacy sediment persist in two national parks, Ozark National Scenic Riverways, MO and Buffalo National River, AR, and are of special concern for management of native mussel fauna. These species require stable habitat, yet they occupy inherently dynamic environments: alluvial rivers. At the river-network scale, analysis of historical data reveals the signature of sediment waves moving through river networks in the Ozarks. Channel planform alternates between relatively stable, straight reaches, and wider, multithread reaches which have been more dynamic over the past several decades. These alternate planform configurations route and store sediment differently, and translate into different patterns of bed stability at the reach scale, which in turn affects the distribution and availability of habitat for native biota. Geomorphic mapping and hydrodynamic modeling reveal the complex relations between planform (in)stability, flow dynamics, bed mobility, and aquatic habitat in systems responding to increased sediment supply. Reaches that have a more dynamic planform may provide more hydraulic refugia and habitat heterogeneity compared to stable, homogeneous reaches. This research provides new insights that may inform management of sediment and mussel habitat in rivers subject to coarse legacy sediment.

Calibration of numerical models for small debris flows in Yosemite Valley, California, USA

USGS Publications Warehouse

Bertolo, P.; Wieczorek, G.F.

2005-01-01

This study compares documented debris flow runout distances with numerical simulations in the Yosemite Valley of California, USA, where about 15% of historical events of slope instability can be classified as debris flows and debris slides (Wieczorek and Snyder, 2004). To model debris flows in the Yosemite Valley, we selected six streams with evidence of historical debris flows; three of the debris flow deposits have single channels, and the other three split their pattern in the fan area into two or more channels. From field observations all of the debris flows involved coarse material, with only very small clay content. We applied the one dimensional DAN (Dynamic ANalysis) model (Hungr, 1995) and the two-dimensional FLO2D model (O'Brien et al., 1993) to predict and compare the runout distance and the velocity of the debris flows observed in the study area. As a first step, we calibrated the parameters for the two softwares through the back analysis of three debris- flows channels using a trial-and-error procedure starting with values suggested in the literature. In the second step we applied the selected values to the other channels, in order to evaluate their predictive capabilities. After parameter calibration using three debris flows we obtained results similar to field observations We also obtained a good agreement between the two models for velocities. Both models are strongly influenced by topography: we used the 30 m cell size DTM available for the study area, that is probably not accurate enough for a highly detailed analysis, but it can be sufficient for a first screening. European Geosciences Union ?? 2005 Author(s). This work is licensed under a Creative Commons License.

Analysis of DNA Sequences by an Optical Time-Integrating Correlator: Proof-of-Concept Experiments.

DTIC Science & Technology

1992-05-01

DNA ANALYSIS STRATEGY 4 2.1 Representation of DNA Bases 4 2.2 DNA Analysis Strategy 6 3.0 CUSTOM GENERATORS FOR DNA SEQUENCES 10 3.1 Hardware Design 10...of the DNA bases where each base is represented by a 7-bits long pseudorandom sequence. 5 Figure 4: Coarse analysis of a DNA sequence. 7 Figure 5: Fine...a 20-bases long database. 32 xiii LIST OF TABLES PAGE Table 1: Short representations of the DNA bases where each base is represented by 7-bits long

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...

Spatial and Temporal Variability of Outdoor Coarse Particulate Matter Mass Concentrations Measured with a New Coarse Particulate Sampler during the Detroit Exposure and Aerosol Research Study

EPA Science Inventory

The Detroit Exposure and Aerosol Research Study (DEARS) provided data to compare outdoor residential coarse particulate matter (PM_10-2.5) concentrations in six different areas of Detroit with data from a central monitoring site. Daily and seasonal influences on the spa...

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...

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

Jones, J E; Vassilevski, P S; Woodward, C S

This paper provides extensions of an element agglomeration AMG method to nonlinear elliptic problems discretized by the finite element method on general unstructured meshes. The method constructs coarse discretization spaces and corresponding coarse nonlinear operators as well as their Jacobians. We introduce both standard (fairly quasi-uniformly coarsened) and non-standard (coarsened away) coarse meshes and respective finite element spaces. We use both kind of spaces in FAS type coarse subspace correction (or Schwarz) algorithms. Their performance is illustrated on a number of model problems. The coarsened away spaces seem to perform better than the standard spaces for problems with nonlinearities inmore » the principal part of the elliptic operator.« less

Nonlinear evolution of coarse-grained quantum systems with generalized purity constraints

NASA Astrophysics Data System (ADS)

Burić, Nikola

2010-12-01

Constrained quantum dynamics is used to propose a nonlinear dynamical equation for pure states of a generalized coarse-grained system. The relevant constraint is given either by the generalized purity or by the generalized invariant fluctuation, and the coarse-grained pure states correspond to the generalized coherent, i.e. generalized nonentangled states. Open system model of the coarse-graining is discussed. It is shown that in this model and in the weak coupling limit the constrained dynamical equations coincide with an equation for pointer states, based on Hilbert-Schmidt distance, that was previously suggested in the context of the decoherence theory.

NONLINEAR MULTIGRID SOLVER EXPLOITING AMGe COARSE SPACES WITH APPROXIMATION PROPERTIES

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

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

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, ourmore » 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.« less

Bryophyte species associations with coarse woody debris and stand ages in Oregon

USGS Publications Warehouse

Rambo, T.; Muir, Patricia S.

1998-01-01

We quantified the relationships of 93 forest floor bryophyte species, including epiphytes from incorporated litterfall, to substrate and stand age in Pseudotsuga menziesii-Tsuga heterophylla stands at two sites in western Oregon. We used the method of Dufrêne and Legendre that combines a species' relative abundance and relative frequency, to calculate that species' importance in relation to environmental variables. The resulting "indicator value" describes a species' reliability for indicating the given environmental parameter. Thirty-nine species were indicative of either humus, a decay class of coarse woody debris, or stand age. Bryophyte community composition changed along the continuum of coarse woody debris decomposition from recently fallen trees with intact bark to forest floor humus. Richness of forest floor bryophytes will be enhanced when a full range of coarse woody debris decay classes is present. A suite of bryophytes indicated old-growth forest. These were mainly either epiphytes associated with older conifers or liverworts associated with coarse woody debris. Hardwood-associated epiphytes mainly indicated young stands. Mature conifers, hardwoods, and coarse woody debris are biological legacies that can be protected when thinning managed stands to foster habitat complexity and biodiversity, consistent with an ecosystem approach to forest management.

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.

Performance Comparison of Systematic Methods for Rigorous Definition of Coarse-Grained Sites of Large Biomolecules.

PubMed

Zhang, Yuwei; Cao, Zexing; Zhang, John Zenghui; Xia, Fei

2017-02-27

Construction of coarse-grained (CG) models for large biomolecules used for multiscale simulations demands a rigorous definition of CG sites for them. Several coarse-graining methods such as the simulated annealing and steepest descent (SASD) based on the essential dynamics coarse-graining (ED-CG) or the stepwise local iterative optimization (SLIO) based on the fluctuation maximization coarse-graining (FM-CG), were developed to do it. However, the practical applications of these methods such as SASD based on ED-CG are subject to limitations because they are too expensive. In this work, we extend the applicability of ED-CG by combining it with the SLIO algorithm. A comprehensive comparison of optimized results and accuracy of various algorithms based on ED-CG show that SLIO is the fastest as well as the most accurate algorithm among them. ED-CG combined with SLIO could give converged results as the number of CG sites increases, which demonstrates that it is another efficient method for coarse-graining large biomolecules. The construction of CG sites for Ras protein by using MD fluctuations demonstrates that the CG sites derived from FM-CG can reflect the fluctuation properties of secondary structures in Ras accurately.

Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

NASA Astrophysics Data System (ADS)

Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

2016-11-01

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiencies have been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume. This work is funded by NSF under Grant DMS-1222550.

Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

NASA Astrophysics Data System (ADS)

Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiency has been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume.

Hemodynamic, Autonomic, and Vascular Effects of Exposure to Coarse Particulate Matter Air Pollution from a Rural Location

PubMed Central

Bard, Robert L.; Morishita, Masako; Dvonch, J. Timothy; Wang, Lu; Yang, Hui-yu; Spino, Catherine; Mukherjee, Bhramar; Kaplan, Mariana J.; Yalavarthi, Srilakshmi; Oral, Elif A.; Ajluni, Nevin; Sun, Qinghua; Harkema, Jack; Rajagopalan, Sanjay

2014-01-01

Background: Fine particulate matter (PM) air pollution is associated with numerous adverse health effects, including increased blood pressure (BP) and vascular dysfunction. Coarse PM substantially contributes to global air pollution, yet differs in characteristics from fine particles and is currently not regulated. However, the cardiovascular (CV) impacts of coarse PM exposure remain largely unknown. Objectives: Our goal was to elucidate whether coarse PM, like fine PM, is itself capable of eliciting adverse CV responses. Methods: We performed a randomized double-blind crossover study in which 32 healthy adults (25.9 ± 6.6 years of age) were exposed to concentrated ambient coarse particles (CAP; 76.2 ± 51.5 μg/m3) in a rural location and filtered air (FA) for 2 hr. We measured CV outcomes during, immediately after, and 2 hr postexposures. Results: Both systolic (mean difference = 0.32 mmHg; 95% CI: 0.05, 0.58; p = 0.021) and diastolic BP (0.27 mmHg; 95% CI: 0.003, 0.53; p = 0.05) linearly increased per 10 min of exposure during the inhalation of coarse CAP when compared with changes during FA exposure. Heart rate was on average higher (4.1 bpm; 95% CI: 3.06, 5.12; p < 0.0001) and the ratio of low-to-high frequency heart rate variability increased (0.24; 95% CI: 0.07, 0.41; p = 0.007) during coarse particle versus FA exposure. Other outcomes (brachial flow-mediated dilatation, microvascular reactive hyperemia index, aortic hemodynamics, pulse wave velocity) were not differentially altered by the exposures. Conclusions: Inhalation of coarse PM from a rural location is associated with a rapid elevation in BP and heart rate during exposure, likely due to the triggering of autonomic imbalance. These findings add mechanistic evidence supporting the biological plausibility that coarse particles could contribute to the triggering of acute CV events. Citation: Brook RD, Bard RL, Morishita M, Dvonch JT, Wang L, Yang HY, Spino C, Mukherjee B, Kaplan MJ, Yalavarthi S, Oral EA, Ajluni N, Sun Q, Brook JR, Harkema J, Rajagopalan S. 2014. Hemodynamic, autonomic, and vascular effects of exposure to coarse particulate matter air pollution from a rural location. Environ Health Perspect 122:624–630; http://dx.doi.org/10.1289/ehp.1306595 PMID:24618231

A Configurational-Bias-Monte-Carlo Back-Mapping Algorithm for Efficient and Rapid Conversion of Coarse-Grained Water Structures Into Atomistic Models.

PubMed

Loeffler, Troy David; Chan, Henry; Narayanan, Badri; Cherukara, Mathew J; Gray, Stephen K; Sankaranarayanan, Subramanian K R S

2018-06-20

Coarse-grained molecular dynamics (MD) simulations represent a powerful approach to simulate longer time scale and larger length scale phenomena than those accessible to all-atom models. The gain in efficiency, however, comes at the cost of atomistic details. The reverse transformation, also known as back-mapping, of coarse grained beads into their atomistic constituents represents a major challenge. Most existing approaches are limited to specific molecules or specific force-fields and often rely on running a long time atomistic MD of the back-mapped configuration to arrive at an optimal solution. Such approaches are problematic when dealing with systems with high diffusion barriers. Here, we introduce a new extension of the configurational-bias-Monte-Carlo (CBMC) algorithm, which we term the crystalline-configurational-bias-Monte-Carlo (C-CBMC) algortihm, that allows rapid and efficient conversion of a coarse-grained model back into its atomistic representation. Although the method is generic, we use a coarse-grained water model as a representative example and demonstrate the back-mapping or reverse transformation for model systems ranging from the ice-liquid water interface to amorphous and crystalline ice configurations. A series of simulations using the TIP4P/Ice model are performed to compare the new CBMC method to several other standard Monte Carlo and Molecular Dynamics based back-mapping techniques. In all the cases, the C-CBMC algorithm is able to find optimal hydrogen bonded configuration many thousand evaluations/steps sooner than the other methods compared within this paper. For crystalline ice structures such as a hexagonal, cubic, and cubic-hexagonal stacking disorder structures, the C-CBMC was able to find structures that were between 0.05 and 0.1 eV/water molecule lower in energy than the ground state energies predicted by the other methods. Detailed analysis of the atomistic structures show a significantly better global hydrogen positioning when contrasted with the existing simpler back-mapping methods. Our results demonstrate the efficiency and efficacy of our new back-mapping approach, especially for crystalline systems where simple force-field based relaxations have a tendency to get trapped in local minima.

Testing and Calibration of Phase Plates for JWST Optical Simulator

NASA Technical Reports Server (NTRS)

Gong, Qian; Chu, Jenny; Tournois, Severine; Eichhorn, William; Kubalak, David

2011-01-01

Three phase plates were designed to simulate the JWST segmented primary mirror wavefront at three on-orbit alignment stages: coarse phasing, intermediate phasing, and fine phasing. The purpose is to verify JWST's on-orbit wavefront sensing capability. Amongst the three stages, coarse alignment is defined to have piston error between adjacent segments being 30 m to 300 m, intermediate being 0.4 m to 10 m, and fine is below 0.4 m. The phase plates were made of fused silica, and were assembled in JWST Optical Simulator (OSIM). The piston difference was realized by the thickness difference of two adjacent segments. The two important parameters to phase plates are piston and wavefront errors. Dispersed Fringe Sensor (DFS) method was used for initial coarse piston evaluation, which is the emphasis of this paper. Point Diffraction Interferometer (PDI) is used for fine piston and wavefront error. In order to remove piston's 2 pi uncertainty with PDI, three laser wavelengths, 640nm, 660nm, and 780nm, are used for the measurement. The DHS test setup, analysis algorithm and results are presented. The phase plate design concept and its application (i.e. verifying the JWST on-orbit alignment algorithm) are described. The layout of JWST OSIM and the function of phase plates in OSIM are also addressed briefly.

Lethal pallister-killian syndrome: Phenotypic similarity with fryns syndrome

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

Ignacio Rodriquez, J.; Garcia, I.; Alvarez, J.

1994-11-01

The Pallister-Killian syndrome is a sporadic multiple congenital anomaly syndrome characterized by {open_quotes}coarse{close_quotes} face, profound mental retardation, and epilepsy. Chromosomes of peripheral lymphocytes are usually normal, but tissue cultures show varying degrees of mosaicism for isochromosome 12p. In babies who die neonatally of severe malformations, including diaphragmatic hernia, and who also have a {open_quotes}coarse{close_quotes} face, acral hypoplasia, and other internal anomalies, Fryns syndrome is more likely to be suspected than Pallister-Killian syndrome, especially if karyotyping is unavailable or if peripheral lumphocytes have a normal chromosome constitution. An initial diagnosis of Fryns syndrome had to be modified in 3 successive newbornmore » infants since chromosome analysis or in situ hybridization with a chromosome 12 probe on kidney tissue demonstrated the mosaic aneuploidy characteristic of Pallister-Killian syndrome. These 3 patients confirm that a similar pattern of malformations can be present in both conditions at birth. It consists of {open_quotes}coarse{close_quotes} face, acral hypoplasia, diaphragmatic hernia, and other defects. Newborn infants who present this phenotype, but lack a conclusively normal chromosome test, may not have Fryns syndrome. A diagnosis of Fryns syndrome should be made carefully to avoid the risk of inappropriate genetic counseling. 31 refs., 10 figs., 1 tab.« less

Crystallographic Analysis of Fatigue Crack Initiation Behavior in Coarse-Grained Magnesium Alloy Under Tension-Tension Loading Cycles

NASA Astrophysics Data System (ADS)

Tamada, Kazuhiro; Kakiuchi, Toshifumi; Uematsu, Yoshihiko

2017-07-01

Plane bending fatigue tests are conducted to investigate fatigue crack initiation mechanisms in coarse-grained magnesium alloy, AZ31, under the stress ratios R = -1 and 0.1. The initial crystallographic structures are analyzed by an electron backscatter diffraction method. The slip or twin operation during fatigue tests is identified from the line angle analyses based on Euler angles of the grains. Under the stress ratio R = -1, relatively thick tension twin bands are formed in coarse grains. Subsequently, compression twin or secondary pyramidal slip operates within the tension twin band, resulting in the fatigue crack initiation. On the other hand, under R = 0.1 with tension-tension loading cycles, twin bands are formed on the specimen surface, but the angles of those bands do not correspond to tension twins. Misorientation analyses of c-axes in the matrix grain and twin band reveal that double twins are activated. Under R = 0.1, fatigue crack initiates along the double twin boundaries. The different manners of fatigue crack initiation at R = -1 and 0.1 are related to the asymmetricity of twining under tension and compression loadings. The fatigue strengths under different stress ratios cannot be estimated by the modified Goodman diagram due to the effect of stress ratio on crack initiation mechanisms.

Weak Galilean invariance as a selection principle for coarse-grained diffusive models.

PubMed

Cairoli, Andrea; Klages, Rainer; Baule, Adrian

2018-05-29

How does the mathematical description of a system change in different reference frames? Galilei first addressed this fundamental question by formulating the famous principle of Galilean invariance. It prescribes that the equations of motion of closed systems remain the same in different inertial frames related by Galilean transformations, thus imposing strong constraints on the dynamical rules. However, real world systems are often described by coarse-grained models integrating complex internal and external interactions indistinguishably as friction and stochastic forces. Since Galilean invariance is then violated, there is seemingly no alternative principle to assess a priori the physical consistency of a given stochastic model in different inertial frames. Here, starting from the Kac-Zwanzig Hamiltonian model generating Brownian motion, we show how Galilean invariance is broken during the coarse-graining procedure when deriving stochastic equations. Our analysis leads to a set of rules characterizing systems in different inertial frames that have to be satisfied by general stochastic models, which we call "weak Galilean invariance." Several well-known stochastic processes are invariant in these terms, except the continuous-time random walk for which we derive the correct invariant description. Our results are particularly relevant for the modeling of biological systems, as they provide a theoretical principle to select physically consistent stochastic models before a validation against experimental data.

Comparison of fiber length analyzers

Treesearch

Don Guay; Nancy Ross Sutherland; Walter Rantanen; Nicole Malandri; Aimee Stephens; Kathleen Mattingly; Matt Schneider

2005-01-01

In recent years, several fiber new fiber length analyzers have been developed and brought to market. The new instruments provide faster measurements and the capability of both laboratory and on-line analysis. Do the various fiber analyzers provide the same length, coarseness, width, and fines measurements for a given fiber sample? This paper provides a comparison of...

Using Forest Health Monitoring to assess aspen forest cover change in the southern Rockies ecoregion

Treesearch

Paul Rogers

2002-01-01

Long-term qualitative observations suggest a marked decline in quaking aspen (Populus tremuloides Michx.) primarily due to advancing succession and fire suppression. This study presents an ecoregional coarse-grid analysis of the current aspen situation using Forest Health Monitoring (FHM) data from Idaho, Wyoming, and Colorado. A...

Dynamics of essential collective motions in proteins: Theory

NASA Astrophysics Data System (ADS)

Stepanova, Maria

2007-11-01

A general theoretical background is introduced for characterization of conformational motions in protein molecules, and for building reduced coarse-grained models of proteins, based on the statistical analysis of their phase trajectories. Using the projection operator technique, a system of coupled generalized Langevin equations is derived for essential collective coordinates, which are generated by principal component analysis of molecular dynamic trajectories. The number of essential degrees of freedom is not limited in the theory. An explicit analytic relation is established between the generalized Langevin equation for essential collective coordinates and that for the all-atom phase trajectory projected onto the subspace of essential collective degrees of freedom. The theory introduced is applied to identify correlated dynamic domains in a macromolecule and to construct coarse-grained models representing the conformational motions in a protein through a few interacting domains embedded in a dissipative medium. A rigorous theoretical background is provided for identification of dynamic correlated domains in a macromolecule. Examples of domain identification in protein G are given and employed to interpret NMR experiments. Challenges and potential outcomes of the theory are discussed.

Principal component analysis for protein folding dynamics.

PubMed

Maisuradze, Gia G; Liwo, Adam; Scheraga, Harold A

2009-01-09

Protein folding is considered here by studying the dynamics of the folding of the triple beta-strand WW domain from the Formin-binding protein 28. Starting from the unfolded state and ending either in the native or nonnative conformational states, trajectories are generated with the coarse-grained united residue (UNRES) force field. The effectiveness of principal components analysis (PCA), an already established mathematical technique for finding global, correlated motions in atomic simulations of proteins, is evaluated here for coarse-grained trajectories. The problems related to PCA and their solutions are discussed. The folding and nonfolding of proteins are examined with free-energy landscapes. Detailed analyses of many folding and nonfolding trajectories at different temperatures show that PCA is very efficient for characterizing the general folding and nonfolding features of proteins. It is shown that the first principal component captures and describes in detail the dynamics of a system. Anomalous diffusion in the folding/nonfolding dynamics is examined by the mean-square displacement (MSD) and the fractional diffusion and fractional kinetic equations. The collisionless (or ballistic) behavior of a polypeptide undergoing Brownian motion along the first few principal components is accounted for.

Interpretation of sedimentological processes of coarse-grained deposits applying a novel combined cluster and discriminant analysis

NASA Astrophysics Data System (ADS)

Farics, Éva; Farics, Dávid; Kovács, József; Haas, János

2017-10-01

The main aim of this paper is to determine the depositional environments of an Upper-Eocene coarse-grained clastic succession in the Buda Hills, Hungary. First of all, we measured some commonly used parameters of samples (size, amount, roundness and sphericity) in a much more objective overall and faster way than with traditional measurement approaches, using the newly developed Rock Analyst application. For the multivariate data obtained, we applied Combined Cluster and Discriminant Analysis (CCDA) in order to determine homogeneous groups of the sampling locations based on the quantitative composition of the conglomerate as well as the shape parameters (roundness and sphericity). The result is the spatial pattern of these groups, which assists with the interpretation of the depositional processes. According to our concept, those sampling sites which belong to the same homogeneous groups were likely formed under similar geological circumstances and by similar geological processes. In the Buda Hills, we were able to distinguish various sedimentological environments within the area based on the results: fan, intermittent stream or marine.

[Design of plant leaf bionic camouflage materials based on spectral analysis].

PubMed

Yang, Yu-Jie; Liu, Zhi-Ming; Hu, Bi-Ru; Wu, Wen-Jian

2011-06-01

The influence of structure parameters and contents of plant leaves on their reflectance spectra was analyzed using the PROSPECT model. The result showed that the bionic camouflage materials should be provided with coarse surface and spongy inner structure, the refractive index of main content must be close to that of plant leaves, the contents of materials should contain chlorophyll and water, and the content of C-H bond must be strictly controlled. Based on the analysis above, a novel camouflage material, which was constituted by coarse transparent waterproof surface, chlorophyll, water and spongy material, was designed. The result of verifiable experiment showed that the reflectance spectra of camouflage material exhibited the same characteristics as those of plant leaves. The similarity coefficient of reflectance spectrum of the camouflage material and camphor leaves was 0.988 1, and the characteristics of camouflage material did not change after sunlight treatment for three months. The bionic camouflage material, who exhibited a high spectral similarity with plant leaves and a good weather resistance, will be an available method for reconnaissance of hyperspectral imaging hopefully.

Origin and production process of eolian dust emitted from the Tarim Basin and their evolution through the Plio-Pleostocene based on ESR signal intensity and crystallinity of quartz

NASA Astrophysics Data System (ADS)

Tada, R.; Isozaki, Y.; Zheng, H.; Sun, Y.; Toyoda, S.; Hasegawa, H.; Yoshida, T.

2010-12-01

Tarim Basin (or Taklimakan Desert) is regarded as one of the major source area of eolian dust in the northern hemisphere. Although a previous study hypothesized that the detrital materials in the Tarim Basin were produced by glacial activity in the surrounding mountains, delivered by rivers, and homogenized by wind within the basin, not enough evidence has been presented to support this hypothesis. Here, we conducted provenance study of eolian dust in the Tarim Basin by examining fine silt fraction (< 20 μm) of the sediments collected from all over the Tarim Basin. We focused on quartz and measured its electron spin resonance [ESR] signal intensity and Crystallinity Index [CI] in the fine (<16μm) and coarse (> 64μm) fractions of various types of sediments including river sediments derived from the Kunlun and Tian Shan Mountains, dry lake sediments in the eastern part of the basin, and mountain loess on the northern slope of the Kunlun Mountains, to examine the process to produce eolian dust within the Tarim Basin. The result revealed that the coarse fractions of river sediments were derived from bedrocks exposed in the drainage area of each river, and that quartz in coarse fraction of the river sediment has ESR signal intensity and CI values unique to each river. ESR signal intensity and CI of quartz in fine fractions of river sediments discharged from the Tian Shan Mountains, which are located windward of the basin, and those discharged from mountainous rivers show values similar to the values for coarse fractions, suggesting that their sources are the same as those for the coarse fractions. On the other hand, ESR signal intensity and CI of quartz in fine fractions of river sediments discharged from the Kunlun Mountains show values different from those for the coarse fractions, and converged to the values close to the average values for the fine fractions of river sediments in the basin and also for the mountain loess, the latter represents the eolian dust emitted from the Tarim Basin. The converged values are considered as resulted from homogenization by the repeated recycling process within the basin. Analysis of the Quaternary mountain loess and Plio-Pleistocene loess-like siltstone intercalated in the alluvial sediments delivered from the Kunlun Mountains revealed that eolian dust source and production process essentially the same as the present has been established at ca. 3.5 Ma.

Influence of canopy closure and shrub coverage on travel along coarse woody debris by Eastern chipmunks (Tamias striatus)

Treesearch

Patrick A. Zollner; Kevin J. Crane

2003-01-01

We investigated relationships between canopy closure, shrub cover and the use of coarse woody debris as a travel path by eastern chipmunks (Tamias striatus) in the north central United States. Fine scale movements of chipmunks were followed with tracking spools and the percentage of each movement path directly along coarse woody debris was recorded...

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...

Climatic regions as an indicator of forest coarse and fine woody debris carbon stocks in the United States

Treesearch

Christopher W. Woodall; Greg C. Liknes

2008-01-01

Coarse and fine woody debris are substantial forest ecosystem carbon stocks; however, there is a lack of understanding how these detrital carbon stocks vary across forested landscapes. Because forest woody detritus production and decay rates may partially depend on climatic conditions, the accumulation of coarse and fine woody debris carbon stocks in forests may be...

Unsupervised segmentation of lungs from chest radiographs

NASA Astrophysics Data System (ADS)

Ghosh, Payel; Antani, Sameer K.; Long, L. Rodney; Thoma, George R.

2012-03-01

This paper describes our preliminary investigations for deriving and characterizing coarse-level textural regions present in the lung field on chest radiographs using unsupervised grow-cut (UGC), a cellular automaton based unsupervised segmentation technique. The segmentation has been performed on a publicly available data set of chest radiographs. The algorithm is useful for this application because it automatically converges to a natural segmentation of the image from random seed points using low-level image features such as pixel intensity values and texture features. Our goal is to develop a portable screening system for early detection of lung diseases for use in remote areas in developing countries. This involves developing automated algorithms for screening x-rays as normal/abnormal with a high degree of sensitivity, and identifying lung disease patterns on chest x-rays. Automatically deriving and quantitatively characterizing abnormal regions present in the lung field is the first step toward this goal. Therefore, region-based features such as geometrical and pixel-value measurements were derived from the segmented lung fields. In the future, feature selection and classification will be performed to identify pathological conditions such as pulmonary tuberculosis on chest radiographs. Shape-based features will also be incorporated to account for occlusions of the lung field and by other anatomical structures such as the heart and diaphragm.

Interactive high-resolution isosurface ray casting on multicore processors.

PubMed

Wang, Qin; JaJa, Joseph

2008-01-01

We present a new method for the interactive rendering of isosurfaces using ray casting on multi-core processors. This method consists of a combination of an object-order traversal that coarsely identifies possible candidate 3D data blocks for each small set of contiguous pixels, and an isosurface ray casting strategy tailored for the resulting limited-size lists of candidate 3D data blocks. While static screen partitioning is widely used in the literature, our scheme performs dynamic allocation of groups of ray casting tasks to ensure almost equal loads among the different threads running on multi-cores while maintaining spatial locality. We also make careful use of memory management environment commonly present in multi-core processors. We test our system on a two-processor Clovertown platform, each consisting of a Quad-Core 1.86-GHz Intel Xeon Processor, for a number of widely different benchmarks. The detailed experimental results show that our system is efficient and scalable, and achieves high cache performance and excellent load balancing, resulting in an overall performance that is superior to any of the previous algorithms. In fact, we achieve an interactive isosurface rendering on a 1024(2) screen for all the datasets tested up to the maximum size of the main memory of our platform.

Variability of Mediterranean aerosols properties at three regional background sites in the western Mediterranean Basin

NASA Astrophysics Data System (ADS)

Sicard, Michaël.; Totems, Julien; Barragan, Rubén.; Dulac, François; Mallet, Marc; Comerón, Adolfo; Alados-Arboledas, Lucas; Augustin, Patrick; Chazette, Patrick; Léon, Jean-François; Olmo-Reyes, Francisco José; Renard, Jean-Baptiste; Rocadenbosch, Francesc

2014-10-01

In the framework of the project ChArMEx (the Chemistry-Aerosol Mediterranean Experiment, http://charmex.lsce.ipsl.fr/), the variability of aerosol optical, microphysical and radiative properties is examined in three regional background sites on a southwest - northeast (SW-NE) straight line in the middle of the western Mediterranean Basin (WMB). The three sites are on the northward transport pathway of African dust: - Ersa, Corsica Island, France (43.00ºN, 9.36ºW, 80 m a.s.l), - Palma de Mallorca, Mallorca Island, Spain (39.55ºN, 2.62ºE, 10 m a.s.l) and - Alborán, Alboran Island, Spain (35.94ºN, 3.04ºW, 15 m a.s.l). AERONET (AErosol RObotic NETwork) sun-photometer products are mainly used. A preliminary analysis shows that at Ersa and Palma sites the annual aerosol optical depth (AOD) has a similar trend with a peak around 0.2 in July. The winter/spring AOD is lower in Palma than in Ersa, while it is reverse in summer/autumn. The aerosol particle size distribution (and the coarse mode fraction) shows clearly the SW-NE gradient with a decreasing coarse mode peak (and a decreasing coarse mode fraction from 0.5 - 0.35 - 0.2 in July) along the axis Alborán - Palma de Mallorca - Ersa. In addition to the seasonal and annual variability analysis, the analysis of AERONET products is completed with a large variety of ground-based and sounding balloons remote sensing and in situ instruments during the Special Observation Period (SOP) of the ADRIMED campaign in June 2013. The second part of the presentation will focus on the comparison of the observations at Palma de Mallorca and Ersa of the same long-range transported airmasses. The observations include lidar vertical profiles, balloon borne OPC (Optical Particle Counter) and MSG/SEVIRI AOD, among others.

Development of Test Rig for Robotization of Mining Technological Processes - Oversized Rock Breaking Process Case

NASA Astrophysics Data System (ADS)

Pawel, Stefaniak; Jacek, Wodecki; Jakubiak, Janusz; Zimroz, Radoslaw

2017-12-01

Production chain (PCh) in underground copper ore mine consists of several subprocesses. From our perspective implementation of so called ZEPA approach (Zero Entry Production Area) might be very interesting [16]. In practice, it leads to automation/robotization of subprocesses in production area. In this paper was investigated a specific part of PCh i.e. a place when cyclic transport by LHDs is replaced with continuous transport by conveying system. Such place is called dumping point. The objective of dumping points with screen is primary classification of the material (into coarse and fine material) and breaking oversized rocks with hydraulic hammer. Current challenges for the underground mining include e.g. safety improvement as well as production optimization related to bottlenecks, stoppages and operational efficiency of the machines. As a first step, remote control of the hydraulic hammer has been introduced, which not only transferred the operator to safe workplace, but also allowed for more comfortable work environment and control over multiple technical objects by a single person. Today literature analysis shows that current mining industry around the world is oriented to automation and robotization of mining processes and reveals technological readiness for 4th industrial revolution. The paper is focused on preliminary analysis of possibilities for the use of the robotic system to rock-breaking process. Prototype test rig has been proposed and experimental works have been carried out. Automatic algorithms for detection of oversized rocks, crushing them as well as sweeping and loosening of material have been formulated. Obviously many simplifications have been assumed. Some near future works have been proposed.

Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

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

Vögele, Martin; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt a. M.; Holm, Christian

2015-12-28

We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models aremore » able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.« less

A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

NASA Astrophysics Data System (ADS)

Kawaguchi, Kazutomo; Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer.

Centrifugal Sieve for Gravity-Level-Independent Size Segregation of Granular Materials

NASA Technical Reports Server (NTRS)

Walton, Otis R.; Dreyer, Christopher; Riedel, Edward

2013-01-01

Conventional size segregation or screening in batch mode, using stacked vibrated screens, is often a time-consuming process. Utilization of centrifugal force instead of gravity as the primary body force can significantly shorten the time to segregate feedstock into a set of different-sized fractions. Likewise, under reduced gravity or microgravity, a centrifugal sieve system would function as well as it does terrestrially. When vibratory and mechanical blade sieving screens designed for terrestrial conditions were tested under lunar gravity conditions, they did not function well. The centrifugal sieving design of this technology overcomes the issues that prevented sieves designed for terrestrial conditions from functioning under reduced gravity. These sieves feature a rotating outer (cylindrical or conical) screen wall, rotating fast enough for the centrifugal forces near the wall to hold granular material against the rotating screen. Conventional centrifugal sieves have a stationary screen and rapidly rotating blades that shear the granular solid near the stationary screen, and effect the sieving process assisted by the airflow inside the unit. The centrifugal sieves of this new design may (or may not) have an inner blade or blades, moving relative to the rotating wall screen. Some continuous flow embodiments would have no inner auger or blades, but achieve axial motion through vibration. In all cases, the shearing action is gentler than conventional centrifugal sieves, which have very high velocity differences between the stationary outer screen and the rapidly rotating blades. The new design does not depend on airflow in the sieving unit, so it will function just as well in vacuum as in air. One advantage of the innovation for batch sieving is that a batch-mode centrifugal sieve may accomplish the same sieving operation in much less time than a conventional stacked set of vibrated screens (which utilize gravity as the primary driving force for size separation). In continuous mode, the centrifugal sieves can provide steady streams of fine and coarse material separated from a mixed feedstock flow stream. The centrifugal sieves can be scaled to any desired size and/or mass flow rate. Thus, they could be made in sizes suitable for small robotic exploratory missions, or for semi-permanent processing of regolith for extraction of volatiles of minerals. An advantage of the continuous-mode system is that it can be made with absolutely no gravity flow components for feeding material into, or for extracting the separated size streams from, the centrifugal sieve. Thus, the system is capable of functioning in a true microgravity environment. Another advantage of the continuous-mode system is that some embodiments of the innovation have no internal blades or vanes, and thus, can be designed to handle a very wide range of feedstock sizes, including occasional very large oversized pieces, without jamming or seizing up.

Relationship of coarse woody debris to arthropod availability for red-cockaded woodpeckers and other bark-foraging birds on loblolly pine boles

Treesearch

Scott Horn; James L. Hanula

2008-01-01

This study determined if short-term removal of coarse woody debris would reduce prey available to red-cockaded woodpeckers (Picoides borealis Vieillot) and other bark-foraging 1 birds at the Savannah River Site in Aiken and Barnwell counties, SC. All coarse woody debris was removed from four 9-ha plots of mature loblolly pine (Pinus taeda...

Horizontal Residual Mean Circulation: Evaluation of Spatial Correlations in Coarse Resolution Ocean Models

NASA Astrophysics Data System (ADS)

Li, Y.; McDougall, T. J.

2016-02-01

Coarse resolution ocean models lack knowledge of spatial correlations between variables on scales smaller than the grid scale. Some researchers have shown that these spatial correlations play a role in the poleward heat flux. In order to evaluate the poleward transport induced by the spatial correlations at a fixed horizontal position, an equation is obtained to calculate the approximate transport from velocity gradients. The equation involves two terms that can be added to the quasi-Stokes streamfunction (based on temporal correlations) to incorporate the contribution of spatial correlations. Moreover, these new terms do not need to be parameterized and is ready to be evaluated by using model data directly. In this study, data from a high resolution ocean model have been used to estimate the accuracy of this HRM approach for improving the horizontal property fluxes in coarse-resolution ocean models. A coarse grid is formed by sub-sampling and box-car averaging the fine grid scale. The transport calculated on the coarse grid is then compared to the transport on original high resolution grid scale accumulated over a corresponding number of grid boxes. The preliminary results have shown that the estimate on coarse resolution grids roughly match the corresponding transports on high resolution grids.

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.

High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites.

PubMed

Haxton, Thomas K

2015-03-10

We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are accurately approximated by their average values, while retaining soft degrees of freedom (unconstrained dihedral angles) mostly responsible for conformational variability. We demonstrate that our scheme retains nearly atomistic resolution by mapping all experimental protein configurations in the Protein Data Bank onto coarse-grained configurations and then analytically backmapping those configurations back to all-atom configurations. This roundtrip mapping throws away all information associated with the eliminated (stiff) degrees of freedom except for their average values, which we use to construct optimal backmapping functions. Despite the 4:1 reduction in the number of degrees of freedom, we find that heavy atoms move only 0.051 Å on average during the roundtrip mapping, while hydrogens move 0.179 Å on average, an unprecedented combination of efficiency and accuracy among coarse-grained protein models. We discuss the advantages of such a high-resolution model for parametrizing effective interactions and accurately calculating observables through direct or multiscale simulations.

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

A new hypothesis and exploratory model for the formation of large-scale inner-shelf sediment sorting and ``rippled scour depressions''

NASA Astrophysics Data System (ADS)

Murray, A. Brad; Thieler, E. Robert

2004-02-01

Recent observations of inner continental shelves in many regions show numerous collections of relatively coarse sediment, which extend kilometers in the cross-shore direction and are on the order of 100 m wide. These "rippled scour depressions" have been interpreted to indicate concentrated cross-shelf currents. However, recent observations strongly suggest that they are associated with sediment transport along-shore rather than cross-shore. A new hypothesis for the origin of these features involves the large wave-generated ripples that form in the coarse material. Wave motions interacting with these large roughness elements generate near-bed turbulence that is greatly enhanced relative to that in other areas. This enhances entrainment and inhibits settling of fine material in an area dominated by coarse sediment. The fine sediment is then carried by mean currents past the coarse accumulations, and deposited where the bed is finer. We hypothesize that these interactions constitute a feedback tending to produce accumulations of fine material separated by self-perpetuating patches of coarse sediments. As with many types of self-organized bedforms, small features would interact as they migrate, leading to a better-organized, larger-scale pattern. As an initial test of this hypothesis, we use a numerical model treating the transport of coarse and fine sediment fractions, treated as functions of the local bed composition—a proxy for the presence of large roughness elements in coarse areas. Large-scale sorted patterns exhibiting the main characteristics of the natural features result robustly in the model, indicating that this new hypothesis offers a plausible explanation for the phenomena.

Multidetector CT features of pulmonary focal ground-glass opacity: differences between benign and malignant

PubMed Central

Fan, L; Liu, S-Y; Li, Q-C; Yu, H; Xiao, X-S

2012-01-01

Objective To evaluate different features between benign and malignant pulmonary focal ground-glass opacity (fGGO) on multidetector CT (MDCT). Methods 82 pathologically or clinically confirmed fGGOs were retrospectively analysed with regard to demographic data, lesion size and location, attenuation value and MDCT features including shape, margin, interface, internal characteristics and adjacent structure. Differences between benign and malignant fGGOs were analysed using a χ2 test, Fisher's exact test or Mann–Whitney U-test. Morphological characteristics were analysed by binary logistic regression analysis to estimate the likelihood of malignancy. Results There were 21 benign and 61 malignant lesions. No statistical differences were found between benign and malignant fGGOs in terms of demographic data, size, location and attenuation value. The frequency of lobulation (p=0.000), spiculation (p=0.008), spine-like process (p=0.004), well-defined but coarse interface (p=0.000), bronchus cut-off (p=0.003), other air-containing space (p=0.000), pleural indentation (p=0.000) and vascular convergence (p=0.006) was significantly higher in malignant fGGOs than that in benign fGGOs. Binary logistic regression analysis showed that lobulation, interface and pleural indentation were important indicators for malignant diagnosis of fGGO, with the corresponding odds ratios of 8.122, 3.139 and 9.076, respectively. In addition, a well-defined but coarse interface was the most important indicator of malignancy among all interface types. With all three important indicators considered, the diagnostic sensitivity, specificity and accuracy were 93.4%, 66.7% and 86.6%, respectively. Conclusion An fGGO with lobulation, a well-defined but coarse interface and pleural indentation gives a greater than average likelihood of being malignant. PMID:22128130

Electrolytes in a nanometer slab-confinement: Ion-specific structure and solvation forces

NASA Astrophysics Data System (ADS)

Kalcher, Immanuel; Schulz, Julius C. F.; Dzubiella, Joachim

2010-10-01

We study the liquid structure and solvation forces of dense monovalent electrolytes (LiCl, NaCl, CsCl, and NaI) in a nanometer slab-confinement by explicit-water molecular dynamics (MD) simulations, implicit-water Monte Carlo (MC) simulations, and modified Poisson-Boltzmann (PB) theories. In order to consistently coarse-grain and to account for specific hydration effects in the implicit methods, realistic ion-ion and ion-surface pair potentials have been derived from infinite-dilution MD simulations. The electrolyte structure calculated from MC simulations is in good agreement with the corresponding MD simulations, thereby validating the coarse-graining approach. The agreement improves if a realistic, MD-derived dielectric constant is employed, which partially corrects for (water-mediated) many-body effects. Further analysis of the ionic structure and solvation pressure demonstrates that nonlocal extensions to PB (NPB) perform well for a wide parameter range when compared to MC simulations, whereas all local extensions mostly fail. A Barker-Henderson mapping of the ions onto a charged, asymmetric, and nonadditive binary hard-sphere mixture shows that the strength of structural correlations is strongly related to the magnitude and sign of the salt-specific nonadditivity. Furthermore, a grand canonical NPB analysis shows that the Donnan effect is dominated by steric correlations, whereas solvation forces and overcharging effects are mainly governed by ion-surface interactions. However, steric corrections to solvation forces are strongly repulsive for high concentrations and low surface charges, while overcharging can also be triggered by steric interactions in strongly correlated systems. Generally, we find that ion-surface and ion-ion correlations are strongly coupled and that coarse-grained methods should include both, the latter nonlocally and nonadditive (as given by our specific ionic diameters), when studying electrolytes in highly inhomogeneous situations.

Spectral variations in rocks and soils containing ferric iron hydroxide and(or) sulfate minerals as seen by AVIRIS and laboratory spectroscopy

USGS Publications Warehouse

Rockwell, Barnaby W.

2004-01-01

Analysis of Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data covering the Big Rock Candy Mountain area of the Marysvale volcanic field, west-central Utah, identified abundant rocks and soils bearing jarosite, goethite, and chlorite associated with volcanic rocks altered to propylitic grade during the Miocene (2321 Ma). Propylitically-altered rocks rich in pyrite associated with the relict feeder zones of convecting, shallow hydrothermal systems are currently undergoing supergene oxidation to natrojarosite, kaolinite, and gypsum. Goethite coatings are forming at the expense of jarosite where most pyrite has been consumed through oxidation in alluvium derived from pyrite-bearing zones. Spectral variations in the goethite-bearing rocks that resemble variations found in reference library samples of goethites of varying grain size were observed in the AVIRIS data. Rocks outside of the feeder zones have relatively low pyrite content and are characterized by chlorite, epidote, and calcite, with local copper-bearing quartz-calcite veins. Iron-bearing minerals in these rocks are weathering directly to goethite. Laboratory spectral analyses were applied to samples of iron-bearing rock outcrops and alluvium collected from the area to determine the accuracy of the AVIRIS-based mineral identification. The accuracy of the iron mineral identification results obtained by analysis of the AVIRIS data was confirmed. In general, the AVIRIS analysis results were accurate in identifying medium-grained goethite, coarse-grained goethite, medium- to coarse-grained goethite with trace jarosite, and mixtures of goethite and jarosite. However, rock fragments from alluvial areas identified as thin coatings of goethite with the AVIRIS data were found to consist mainly of medium- to coarse-grained goethite based on spectral characteristics in the visible and near-infrared. To determine if goethite abundance contributed to the spectral variations observed in goethite-bearing rocks with AVIRIS data, a laboratory experiment was performed in which spectra were acquired of a goethite-bearing rock while progressively decreasing the areal abundance of the rock with respect to a background of white, fine-grained quartz sand. This experiment found that, with decreasing material abundance, the crystal field absorption feature of goethite near 1.0 micron decreases in depth and narrows more from the long wavelength side of the feature than from the short wavelength side, as is the case in goethite reference spectra as grain size decreases from coarse to fine. In the Marysvale study area, goethite-bearing alluvium downgradient from source outcrops tends to be identified as finer-grained or thin coatings of goethite due to the minerals presence in lesser abundance. The goethite-bearing alluvium is a closer match to reference spectra of thin coatings of goethite even though the actual grain size of the contained goethite fragments is medium to coarse grained, the same on average as that from the source outcrops. Coarser-grained goethite most likely will be correctly identified in areas of greater goethite abundance proximal to jarosite-bearing source rock where the surface is relatively free of goethite-free soil components and vegetation that corrupt the goethite spectral response. When analysis of imaging spectroscopy data is performed using reference spectra of iron minerals of varying grain sizes and mixed compositions, the results are useful not only for purposes of mineral identification, but also for distinguishing goethite-bearing outcrop from alluvial surfaces with similar mineralogy, providing valuable information for geologic, geomorphologic, mineral exploration, and environmental assessment studies.

Why is particulate matter produced by wildfires toxic to lung macrophages?

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

Franzi, Lisa M.; Bratt, Jennifer M.; Williams, Keisha M.

The mechanistic basis of the high toxicity to lung macrophages of coarse PM from the California wildfires of 2008 was examined in cell culture experiments with mouse macrophages. Wildfire PM directly killed macrophages very rapidly in cell culture at relatively low doses. The wildfire coarse PM is about four times more toxic to macrophages on an equal weight basis than the same sized PM collected from normal ambient air (no wildfires) from the same region and season. There was a good correlation between the extent of cytotoxicity and the amount of oxidative stress observed at a given dose of wildfiremore » PM in vitro. Our data implicate NF-{kappa}B signaling in the response of macrophages to wildfire PM, and suggest that most, if not all, of the cytotoxicity of wildfire PM to lung macrophages is the result of oxidative stress. The relative ratio of toxicity and of expression of biomarkers of oxidant stress between wildfire PM and 'normal' PM collected from ambient air is consistent with our previous results in mice in vivo, also suggesting that most, if not all, of the cytotoxicity of wildfire PM to lung macrophages is the result of oxidative stress. Our findings from this and earlier studies suggest that the active components of coarse PM from the wildfire are heat-labile organic compounds. While we cannot rule out a minor role for endotoxin in coarse PM preparations from the collected wildfire PM in our observed results both in vitro and in vivo, based on experiments using the inhibitor Polymyxin B most of the oxidant stress and pro-inflammatory activity observed was not due to endotoxin. -- Highlights: Black-Right-Pointing-Pointer Wildfire coarse PM kills macrophages at lower doses than coarse. Black-Right-Pointing-Pointer Wildfire coarse PM activates the NF-kB pathway at lower doses than ambient. Black-Right-Pointing-Pointer Wildfire coarse PM in vitro and in vivo kill macrophages by oxidative stress.« less

Effects of rumen-escape starch and coarseness of ingredients in pelleted concentrates on performance and rumen wall characteristics of rosé veal calves.

PubMed

Vestergaard, M; Jarltoft, T C; Kristensen, N B; Børsting, C F

2013-08-01

The objective was to study the effect of rumen-escape starch and coarseness of ingredients in pelleted concentrates on performance, carcass quality and rumen wall characteristics in rosé veal calf production. Two alternative concentrates (Coarse and Slow) were compared with a traditional (Control) concentrate. Control was based on finely ground ingredients, whereas in Coarse, the same ingredients were coarsely ground resulting in a mean particle size before pelleting of 1.5 in Coarse and 0.6 mm in Control. Slow compared with Control and Coarse contained finely ground sorghum and corn instead of barley and wheat which increased the amount of rumen-escape starch to 59 compared with 22 g/kg in Control and Coarse. All concentrates had the same total starch (362 g/kg), NDF (168 g/kg), CP (154 g/kg) and DE (15.5 MJ/kg DM) content and a pellet diameter of 3.5 to 4 mm. Use of an 'indicator of starch digestibility' method gave a value of 98.6% for Control and Coarse and 91.1% for Slow (P < 0.001). A total of 57 Holstein bull calves (n = 19 per treatment) were offered one of the three concentrates ad libitum from weaning (2½ months of age) to slaughter (<10 months of age). Concentrate intake was recorded individually. Barley straw was available ad libitum but intake was not recorded. Average daily gain (1.43 kg/day), concentrate conversion efficiency (3.7 kg DM concentrate/kg gain), LW at slaughter (386 kg), carcass weight (194 kg) and EUROP conformation (3.9) were not affected by type of concentrate (P > 0.05). Papillae length and shape evaluated in atrium ruminis and the cranial part of the ventral rumen sac at slaughter were not affected by type of concentrate (P > 0.05). Rumen wall characteristics showed degrees of plaque formation (i.e., papillary aggregation), hyperaemia and necrotic areas in all treatment groups, but with no general difference between type of concentrate (P > 0.05). Incidence of liver abscesses (LAs, 16%) was not affected by type of concentrate (P > 0.05). There were no differences in performance or rumen wall characteristics between liver-abscessed and non-abscessed calves. The results show a high level of production performance with the three types of pelleted concentrates and indicates that neither the more coarse ingredients nor the additional rumen-escape starch tested, when fed ad libitum, could improve rumen wall characteristics or reduce LAs of rosé veal calves.

Optimal graph based segmentation using flow lines with application to airway wall segmentation.

PubMed

Petersen, Jens; Nielsen, Mads; Lo, Pechin; Saghir, Zaigham; Dirksen, Asger; de Bruijne, Marleen

2011-01-01

This paper introduces a novel optimal graph construction method that is applicable to multi-dimensional, multi-surface segmentation problems. Such problems are often solved by refining an initial coarse surface within the space given by graph columns. Conventional columns are not well suited for surfaces with high curvature or complex shapes but the proposed columns, based on properly generated flow lines, which are non-intersecting, guarantee solutions that do not self-intersect and are better able to handle such surfaces. The method is applied to segment human airway walls in computed tomography images. Comparison with manual annotations on 649 cross-sectional images from 15 different subjects shows significantly smaller contour distances and larger area of overlap than are obtained with recently published graph based methods. Airway abnormality measurements obtained with the method on 480 scan pairs from a lung cancer screening trial are reproducible and correlate significantly with lung function.

Temporally coherent 4D video segmentation for teleconferencing

NASA Astrophysics Data System (ADS)

Ehmann, Jana; Guleryuz, Onur G.

2013-09-01

We develop an algorithm for 4-D (RGB+Depth) video segmentation targeting immersive teleconferencing ap- plications on emerging mobile devices. Our algorithm extracts users from their environments and places them onto virtual backgrounds similar to green-screening. The virtual backgrounds increase immersion and interac- tivity, relieving the users of the system from distractions caused by disparate environments. Commodity depth sensors, while providing useful information for segmentation, result in noisy depth maps with a large number of missing depth values. By combining depth and RGB information, our work signi¯cantly improves the other- wise very coarse segmentation. Further imposing temporal coherence yields compositions where the foregrounds seamlessly blend with the virtual backgrounds with minimal °icker and other artifacts. We achieve said improve- ments by correcting the missing information in depth maps before fast RGB-based segmentation, which operates in conjunction with temporal coherence. Simulation results indicate the e±cacy of the proposed system in video conferencing scenarios.

Improved segmentation of abnormal cervical nuclei using a graph-search based approach

NASA Astrophysics Data System (ADS)

Zhang, Ling; Liu, Shaoxiong; Wang, Tianfu; Chen, Siping; Sonka, Milan

2015-03-01

Reliable segmentation of abnormal nuclei in cervical cytology is of paramount importance in automation-assisted screening techniques. This paper presents a general method for improving the segmentation of abnormal nuclei using a graph-search based approach. More specifically, the proposed method focuses on the improvement of coarse (initial) segmentation. The improvement relies on a transform that maps round-like border in the Cartesian coordinate system into lines in the polar coordinate system. The costs consisting of nucleus-specific edge and region information are assigned to the nodes. The globally optimal path in the constructed graph is then identified by dynamic programming. We have tested the proposed method on abnormal nuclei from two cervical cell image datasets, Herlev and H and E stained liquid-based cytology (HELBC), and the comparative experiments with recent state-of-the-art approaches demonstrate the superior performance of the proposed method.

Comminution and sizing processes of concrete block waste as recycled aggregates.

PubMed

Gomes, P C C; Ulsen, C; Pereira, F A; Quattrone, M; Angulo, S C

2015-11-01

Due to the environmental impact of construction and demolition waste (CDW), recycling is mandatory. It is also important that recycled concrete aggregates (RCA) are used in concrete to meet market demands. In the literature, the influence of RCAs on concrete has been investigated, but very limited studies have been conducted on how the origin of concrete waste and comminution processes influence RCA characteristics. This paper aims to investigate the influence of three different comminution and sizing processes (simple screening, crushing and grinding) on the composition, shape and porosity characteristics of RCA obtained from concrete block waste. Crushing and grinding implies a reduction of RCA porosity. However, due to the presence of coarse quartz rounded river pebbles in the original concrete block mixtures, the shape characteristics deteriorated. A large amount of powder (<0.15 mm) without detectable anhydrous cement was also generated. Copyright © 2015 Elsevier Ltd. All rights reserved.

Siblings with fucosidosis

PubMed Central

Muthusamy, Karthik; Thomas, Maya Mary; George, Renu Elizabeth; Alexander, Mathew; Mani, Sunithi; Benjamin, Rohit N

2014-01-01

Fucosidosis is a rare lysosomal storage disorder due to deficiency of fucosidase enzyme, with around 100 cases reported worldwide. Here, we describe the clinical and imaging features in two siblings with fucosidosis. An 8-year-old girl presented with global developmental delay, followed by regression of acquired milestones from 3 years of age with bipyramidal, extrapyramidal involvement, coarse facies, telangiectatic lesions, dysostosis multiplex, characteristic magnetic resonance imaging finding along with undetectable levels of the fucosidase activity, which confirmed the diagnosis. Younger sibling has mild developmental delay with autistic traits with no neuroregression until now. He also has undetectable level of fucosidase enzyme activity and is being considered for stem cell transplantation. New case reports would expand the clinical spectrum, early diagnosis and help formulating appropriate therapy. Early diagnosis is crucial and hence sibling screening can be done, and those in the presymptomatic stage can undergo hematopoietic stem cell transplantation, which is potentially curable. PMID:25250075

[Analysis of washing efficiency and change in lead speciation in lead-contaminated soil of a battery factory].

PubMed

Ren, Bei; Huang, Jin-lou; Miao, Ming-sheng

2013-09-01

Lead-contaminated soil with different pollution load in a lead battery factory in the southwest of China was chosen as the research object, the lead content and speciation were analyzed, and different washing agents were screened. The lead washing efficiency and lead speciation were analyzed under different pH conditions, and the soil of different particle size was washed using different duration to determine the best washing time. The results showed that the soil of sites A and B in the factory was severely contaminated, the lead concentration reaching 15,703.22 mg x kg(-1) and 1747.78 mg x kg(-1), respectively, and the proportion of the active-state lead was relatively high, while the residue state accounted for only 17.32%, 11.64%, 14.6% and 10.2%. EDTA and hydrochloric acid showed the best extraction effect in the 5 washing agents tested, which included EDTA, hydrochloric acid, citric acid, rhamnolipid and SDS. Cleaning under acidic conditions could not only effectively extract the total amount of lead but also effectively reduce the environmental risk of active-state lead. pH 4-7 was suggested as the most appropriate condition. The cleaning effect of coarse sand and fine sand was good, while for washing powder clay, it is better to improve the process, with the optimal washing time determined as 240 min.

An interactive web-based application for Comprehensive Analysis of RNAi-screen Data.

PubMed

Dutta, Bhaskar; Azhir, Alaleh; Merino, Louis-Henri; Guo, Yongjian; Revanur, Swetha; Madhamshettiwar, Piyush B; Germain, Ronald N; Smith, Jennifer A; Simpson, Kaylene J; Martin, Scott E; Buehler, Eugen; Beuhler, Eugen; Fraser, Iain D C

2016-02-23

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment.

An interactive web-based application for Comprehensive Analysis of RNAi-screen Data

PubMed Central

Dutta, Bhaskar; Azhir, Alaleh; Merino, Louis-Henri; Guo, Yongjian; Revanur, Swetha; Madhamshettiwar, Piyush B.; Germain, Ronald N.; Smith, Jennifer A.; Simpson, Kaylene J.; Martin, Scott E.; Beuhler, Eugen; Fraser, Iain D. C.

2016-01-01

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment. PMID:26902267

Systematic NMR Analysis of Stable Isotope Labeled Metabolite Mixtures in Plant and Animal Systems: Coarse Grained Views of Metabolic Pathways

PubMed Central

Chikayama, Eisuke; Suto, Michitaka; Nishihara, Takashi; Shinozaki, Kazuo; Hirayama, Takashi; Kikuchi, Jun

2008-01-01

Background Metabolic phenotyping has become an important ‘bird's-eye-view’ technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of ‘top-down’ chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems. Methodology/Principal Findings The analysis method includes a stable isotope labeling technique for use in living organisms; a systematic method for simultaneously identifying a large number of metabolites by using a newly developed HSQC-based metabolite chemical shift database combined with heteronuclear multidimensional NMR spectroscopy; Principal Components Analysis; and a visualization method using a coarse-grained overview of the metabolic system. The database contains more than 1000 1H and 13C chemical shifts corresponding to 142 metabolites measured under identical physicochemical conditions. Using the stable isotope labeling technique in Arabidopsis T87 cultured cells and Bombyx mori, we systematically detected >450 HSQC peaks in each 13C-HSQC spectrum derived from model plant, Arabidopsis T87 cultured cells and the invertebrate animal model Bombyx mori. Furthermore, for the first time, efficient 13C labeling has allowed reliable signal assignment using analytical separation techniques such as 3D HCCH-COSY spectra in higher organism extracts. Conclusions/Significance Overall physiological changes could be detected and categorized in relation to a critical developmental phase change in B. mori by coarse-grained representations in which the organization of metabolic pathways related to a specific developmental phase was visualized on the basis of constituent changes of 56 identified metabolites. Based on the observed intensities of 13C atoms of given metabolites on development-dependent changes in the 56 identified 13C-HSQC signals, we have determined the changes in metabolic networks that are associated with energy and nitrogen metabolism. PMID:19030231

Demonstration of a Balloon Borne Arc-second Pointer Design

NASA Astrophysics Data System (ADS)

Deweese, K.; Ward, P.

Many designs for utilizing stratospheric balloons as low-cost platforms on which to conduct space science experiments have been proposed throughout the years A major hurdle in extending the range of experiments for which these vehicles are useful has been the imposition of the gondola dynamics on the accuracy with which an instrument can be kept pointed at a celestial target A significant number of scientists have sought the ability to point their instruments with jitter in the arc-second range This paper presents the design and analysis of a stratospheric balloon borne pointing system that is able to meet this requirement The test results of a demonstration prototype of the design with similar ability are also presented Discussion of a high fidelity controller simulation for design analysis is presented The flexibility of the flight train is represented through generalized modal analysis A multiple controller scheme is utilized for coarse and fine pointing Coarse azimuth pointing is accomplished by an established pointing system with extensive flight history residing above the gondola structure A pitch-yaw gimbal mount is used for fine pointing providing orthogonal axes when nominally on target Fine pointing actuation is from direct drive dc motors eliminating backlash problems An analysis of friction nonlinearities and a demonstration of the necessity in eliminating static friction are provided A unique bearing hub design is introduced that eliminates static friction from the system dynamics A control scheme involving linear

Molecular Simulation Studies of Covalently and Ionically Grafted Nanoparticles

NASA Astrophysics Data System (ADS)

Hong, Bingbing

Solvent-free covalently- or ionically-grafted nanoparticles (CGNs and IGNs) are a new class of organic-inorganic hybrid composite materials exhibiting fluid-like behaviors around room temperature. With similar structures to prior systems, e.g. nanocomposites, neutral or charged colloids, ionic liquids, etc, CGNs and IGNs inherit the functionality of inorganic nanopariticles, the facile processibility of polymers, as well as conductivity and nonvolatility from their constituent materials. In spite of the extensive prior experimental research having covered synthesis and measurements of thermal and dynamic properties, little progress in understanding of these new materials at the molecular level has been achieved, because of the lack of simulation work in this new area. Atomistic and coarse-grained molecular dynamics simulations have been performed in this thesis to investigate the thermodynamics, structure, and dynamics of these systems and to seek predictive methods predictable for their properties. Starting from poly(ethylene oxide) oligomers (PEO) melts, we established atomistic models based on united-atom representations of methylene. The Green-Kubo and Einstein-Helfand formulas were used to calculate the transport properties. The simulations generate densities, viscosities, diffusivities, in good agreement with experimental data. The chain-length dependence of the transport properties suggests that neither Rouse nor reptation models are applicable in the short-chain regime investigated. Coupled with thermodynamic integration methods, the models give good predictions of pressure-composition-density relations for CO 2 + PEO oligomers. Water effects on the Henry's constant of CO 2 in PEO have also been investigated. The dependence of the calculated Henry's constants on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. CGNs are modeled by the inclusion of solid-sphere nanoparticles into the atomistic oligomers. The calculated viscosities from Green-Kubo relationships and temperature extrapolation are of the same order of magnitude as experimental values, but show a smaller activation energy relative to real CGNs systems. Grafted systems have higher viscosities, smaller diffusion coefficients, and slower chain dynamics than the ungrafted counterparts - nanocomposites - at high temperatures. At lower temperatures, grafted systems exhibit faster dynamics for both nanoparticles and chains relative to ungrafted systems, because of lower aggregation of nanoparticles and enhanced correlations between nanoparticles and chains. This agrees with the experimental observation that the new materials have liquid-like behavior in the absence of a solvent. To lower the simulated temperatures into the experimental range, we established a coarse-grained CGNs model by matching structural distribution functions to atomistic simulation data. In contrast with linear polymer systems, for which coarse-graining always accelerate dynamics, coarse-graining of grafted nanoparticles can either accelerate or slowdown the core motions, depending on the length of the grafted chains. This can be qualitatively predicted by a simple transition-state theory. Similar atomistic models to CGNs were developed for IGNs, with ammonium counterions described by an explicit-hydrogen way; these were in turn compared with "generic" coarse-grained IGNs. The elimination of chemical details in the coarse-grained models does not bring in qualitative changes to the radial distribution functions and diffusion of atomistic IGNs, but saves considerable simulation resources and make simulations near room temperatures affordable. The chain counterions in both atomistic and coarse-grained models are mobile, moving from site to site and from nanoparticle to nanoparticle. At the same temperature and the same core volume fractions, the nanoparticle diffusivities in coarse-grained IGNs are slower by a factor ten than the cores of CGNs. The coarse-grained IGNs models are later used to investigate the system dynamics through analysis of the dependence on temperature and structural parameters of the transport properties (self-diffusion coefficients, viscosities and conductivities). Further, migration kinetics of oligomeric counterions is analyzed in a manner analogous to unimer exchange between micellar aggregates. The counterion migrations follow the "double-core" mechanism and are kinetically controlled by neighboring-core collisions. (Abstract shortened by UMI.)

Refined generalized multiscale entropy analysis for physiological signals

NASA Astrophysics Data System (ADS)

Liu, Yunxiao; Lin, Youfang; Wang, Jing; Shang, Pengjian

2018-01-01

Multiscale entropy analysis has become a prevalent complexity measurement and been successfully applied in various fields. However, it only takes into account the information of mean values (first moment) in coarse-graining procedure. Then generalized multiscale entropy (MSEn) considering higher moments to coarse-grain a time series was proposed and MSEσ2 has been implemented. However, the MSEσ2 sometimes may yield an imprecise estimation of entropy or undefined entropy, and reduce statistical reliability of sample entropy estimation as scale factor increases. For this purpose, we developed the refined model, RMSEσ2, to improve MSEσ2. Simulations on both white noise and 1 / f noise show that RMSEσ2 provides higher entropy reliability and reduces the occurrence of undefined entropy, especially suitable for short time series. Besides, we discuss the effect on RMSEσ2 analysis from outliers, data loss and other concepts in signal processing. We apply the proposed model to evaluate the complexity of heartbeat interval time series derived from healthy young and elderly subjects, patients with congestive heart failure and patients with atrial fibrillation respectively, compared to several popular complexity metrics. The results demonstrate that RMSEσ2 measured complexity (a) decreases with aging and diseases, and (b) gives significant discrimination between different physiological/pathological states, which may facilitate clinical application.

KOSMOS: a universal morph server for nucleic acids, proteins and their complexes.

PubMed

Seo, Sangjae; Kim, Moon Ki

2012-07-01

KOSMOS is the first online morph server to be able to address the structural dynamics of DNA/RNA, proteins and even their complexes, such as ribosomes. The key functions of KOSMOS are the harmonic and anharmonic analyses of macromolecules. In the harmonic analysis, normal mode analysis (NMA) based on an elastic network model (ENM) is performed, yielding vibrational modes and B-factor calculations, which provide insight into the potential biological functions of macromolecules based on their structural features. Anharmonic analysis involving elastic network interpolation (ENI) is used to generate plausible transition pathways between two given conformations by optimizing a topology-oriented cost function that guarantees a smooth transition without steric clashes. The quality of the computed pathways is evaluated based on their various facets, including topology, energy cost and compatibility with the NMA results. There are also two unique features of KOSMOS that distinguish it from other morph servers: (i) the versatility in the coarse-graining methods and (ii) the various connection rules in the ENM. The models enable us to analyze macromolecular dynamics with the maximum degrees of freedom by combining a variety of ENMs from full-atom to coarse-grained, backbone and hybrid models with one connection rule, such as distance-cutoff, number-cutoff or chemical-cutoff. KOSMOS is available at http://bioengineering.skku.ac.kr/kosmos.

Inverse Coarse-Graining: A New Tool for Molecular Design

DTIC Science & Technology

2010-12-16

simulations. When compared with the more general multiscale coarse-graining (MS-CG) method, the EF-CG method retains the transferable part of the CG...Y.; Yan, T.; Voth, G. A., A Multiscale coarse-graining study of liquid/vacuum interface of room-temperature ionic liquids with alkyl substituents of...Energetic Room Temperature Ionic Liquid 1-Hydroxyethyl-4Amino-1, 2, 4-Triazolium Nitrate (HEATN). J. Phys. Chem. B 2008, 112, 3121-3131. 6. Liu, P

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.

Preparation of Entangled Polymer Melts of Various Architecture for Coarse-Grained Models

DTIC Science & Technology

2011-09-01

Simulator ( LAMMPS ). This report presents a theory overview and a manual how to use the method. 15. SUBJECT TERMS Ammunition, coarse-grained model...polymer builder, LAMMPS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF PAGES 26 19a. NAME OF RESPONSIBLE PERSON...scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ). Gel is an in house written C program of coarse- grained polymer builder, and LAMMPS is

SIZE DISTRIBUTION OF AMBIENT AND INDOOR PARTICLES: DOES THE OVERLAP OF FINE AND COARSE PARTICLES CAUSE PROBLEMS IN THE INTERPRETATION OF RESEARCH RESULTS?

EPA Science Inventory

Measurement of the mass and composition of particulate matter (PM) as a function of size is important for research studies for chemical mass balance, factor analysis, air quality model evaluation, epidemiology, and risk assessment. Such measurements are also important in underst...

Shark: Fast Data Analysis Using Coarse-grained Distributed Memory

DTIC Science & Technology

2013-05-01

Schemes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 7.1.1 Java Objects...often MySQL or Derby) with a namespace for tables, table metadata, and par- tition information. Table data is stored in an HDFS directory, while a...saving time and space for large data sets. This is achieved with support for custom SerDe (serialization/deserialization) java interface implementations

Evaluation of Learning Unit Design with Use of Page Flip Information Analysis

ERIC Educational Resources Information Center

Horikoshi, Izumi; Noguchi, Masato; Tamura, Yasuhisa

2016-01-01

In this paper, the authors attempted to evaluate design of leaning units with use of Learning Analytics technique on page flip information. Traditional formative assessment has been carried out by giving assignments and evaluating their results. However, the information that teacher can get from the evaluation is limited and coarse-grained. The…

Summary of mortality statistics and forest health monitoring results for the Northeastern United States

Treesearch

William H. McWilliams; Stanford L. Arner; Charles J. Barnett

1997-01-01

The USDA Forest Service's Forest Inventory and Analysis (FIA) program and the Forest Health Monitoring (FHM) program maintain networks of sample locations providing coarse-scale information that characterize general indicators of forest health. Tree mortality is the primary FIA variable for analyzing forest health. Recent FIA inventories of New York, Pennsylvania...

A structural analysis of an ocean going patrol boat subjected to planning loads

NASA Technical Reports Server (NTRS)

Clark, James H.; Lafreniere, Robert; Stoodt, Robert; Wiedenheft, John

1987-01-01

A static structural analysis of an ocean going patrol vessel subjected to hydrodynamic planning loads is discussed. The analysis required the development of a detailed model that included hull plating, five structural bulkheads, longitudinal and transverse stiffners, and a coarse representation of the superstructure. The finite element model was developed from fabrication drawings using the Navy computer aided design system. Various stress and displacement contours are shown for the entire hull. Because several critical areas appeared to be overstressed, these areas were remeshed for detail and are presented for completeness.

Compact cell-centered discretization stencils at fine-coarse block structured grid interfaces

NASA Astrophysics Data System (ADS)

Pletzer, Alexander; Jamroz, Ben; Crockett, Robert; Sides, Scott

2014-03-01

Different strategies for coupling fine-coarse grid patches are explored in the context of the adaptive mesh refinement (AMR) method. We show that applying linear interpolation to fill in the fine grid ghost values can produce a finite volume stencil of comparable accuracy to quadratic interpolation provided the cell volumes are adjusted. The volume of fine cells expands whereas the volume of neighboring coarse cells contracts. The amount by which the cells contract/expand depends on whether the interface is a face, an edge, or a corner. It is shown that quadratic or better interpolation is required when the conductivity is spatially varying, anisotropic, the refinement ratio is other than two, or when the fine-coarse interface is concave.

Structure et caractérisation des matériaux utilisés dans la construction d'une mosaı̈que romaine de la cité de Volubilis (Maroc)

NASA Astrophysics Data System (ADS)

Dekayir, Abdelilah; Amouric, Marc; Olives, Juan; Parron, Claude; Nadiri, Abdelilah; Chergui, Abdelkader; El Hajraoui, M. Abdeljalil

2004-09-01

In Volubilis, Roman mosaics are very beautiful and reveal, from the bottom to the surface, three layers: ( i) 'hedgehog' layer, ( ii) coarse grain mortar layer (rudus + nucleus) and ( iii) tesselatum. Mineralogical analysis of coarse grain mortar sampled in Flavius Germanus mosaic shows that it consisted of quartz and calcite, with some feldspar and probably mica and dolomite. Fine-grained mortar in tesselatum is made from a mixture of calcite and quartz only. Limestone tesserae (white, pink and brown) show petrographic facies that change from micritic to oolithic limestone. Conversely, black and brick red tesserae are respectively made of marble, red sandstone and from fire clay. Other colours as yellow, blue, green and grey are obtained from artificial glass with different chemical compositions. To cite this article: A. Dekayir et al., C. R. Geoscience 336 (2004).

Dasymetric high resolution population distribution estimates for improved decision making, with a case study of sea-level rise vulnerability in Boca Raton, Florida

NASA Astrophysics Data System (ADS)

Ziegler, Hannes Moritz

Planners and managers often rely on coarse population distribution data from the census for addressing various social, economic, and environmental problems. In the analysis of physical vulnerabilities to sea-level rise, census units such as blocks or block groups are coarse relative to the required decision-making application. This study explores the benefits offered from integrating image classification and dasymetric mapping at the household level to provide detailed small area population estimates at the scale of residential buildings. In a case study of Boca Raton, FL, a sea-level rise inundation grid based on mapping methods by NOAA is overlaid on the highly detailed population distribution data to identify vulnerable residences and estimate population displacement. The enhanced spatial detail offered through this method has the potential to better guide targeted strategies for future development, mitigation, and adaptation efforts.

Physicochemical hair conformation of patients with Sanfilippo disease type IIIA.

PubMed

Charan, R K; Nauer, G; Wagner, U; Klabuschnig, A; Lubec, G

1986-01-01

Sanfilippo disease type IIIA is an inborn error of metabolism with a deficiency in the heparan sulfamidase. Besides severe psychomotor retardation hair changes are obligatory. Hair is found to be coarse like a brush. We applied X-ray diffraction and infrared spectroscopy to characterize the conformation of hair samples of Sanfilippo patients. In healthy subjects as well as in the affected hair samples we found the wave numbers of structural relevance 1450, 1500, 1630, 1730, the pair 2337 and 2362, the quadruplet 2850, 2870, 2917, 2930 and 3080 cm-1. Also on X-ray diffraction analysis no differences could be detected. Though morphological-macroscopically and microscopically-changes were described for Sanfilippo hair samples, we could not find any change in supramolecular structure. The physical properties of coarseness of those hair specimen seems to be due to differences in the structural assembly of hair fibres and storage of heparan sulfate.

Structure and dynamics of Ebola virus matrix protein VP40 by a coarse-grained Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Pandey, Ras; Farmer, Barry

Ebola virus matrix protein VP40 (consisting of 326 residues) plays a critical role in viral assembly and its functions such as regulation of viral transcription, packaging, and budding of mature virions into the plasma membrane of infected cells. How does the protein VP40 go through structural evolution during the viral life cycle remains an open question? Using a coarse-grained Monte Carlo simulation we investigate the structural evolution of VP40 as a function of temperature with the input of a knowledge-based residue-residue interaction. A number local and global physical quantities (e.g. mobility profile, contact map, radius of gyration, structure factor) are analyzed with our large-scale simulations. Our preliminary data show that the structure of the protein evolves through different state with well-defined morphologies which can be identified and quantified via a detailed analysis of structure factor.

Advanced Interrogation of Fiber-Optic Bragg Grating and Fabry-Perot Sensors with KLT Analysis

PubMed Central

Tosi, Daniele

2015-01-01

The Karhunen-Loeve Transform (KLT) is applied to accurate detection of optical fiber sensors in the spectral domain. By processing an optical spectrum, although coarsely sampled, through the KLT, and subsequently processing the obtained eigenvalues, it is possible to decode a plurality of optical sensor results. The KLT returns higher accuracy than other demodulation techniques, despite coarse sampling, and exhibits higher resilience to noise. Three case studies of KLT-based processing are presented, representing most of the current challenges in optical fiber sensing: (1) demodulation of individual sensors, such as Fiber Bragg Gratings (FBGs) and Fabry-Perot Interferometers (FPIs); (2) demodulation of dual (FBG/FPI) sensors; (3) application of reverse KLT to isolate different sensors operating on the same spectrum. A simulative outline is provided to demonstrate the KLT operation and estimate performance; a brief experimental section is also provided to validate accurate FBG and FPI decoding. PMID:26528975

Advanced Interrogation of Fiber-Optic Bragg Grating and Fabry-Perot Sensors with KLT Analysis.

PubMed

Tosi, Daniele

2015-10-29

The Karhunen-Loeve Transform (KLT) is applied to accurate detection of optical fiber sensors in the spectral domain. By processing an optical spectrum, although coarsely sampled, through the KLT, and subsequently processing the obtained eigenvalues, it is possible to decode a plurality of optical sensor results. The KLT returns higher accuracy than other demodulation techniques, despite coarse sampling, and exhibits higher resilience to noise. Three case studies of KLT-based processing are presented, representing most of the current challenges in optical fiber sensing: (1) demodulation of individual sensors, such as Fiber Bragg Gratings (FBGs) and Fabry-Perot Interferometers (FPIs); (2) demodulation of dual (FBG/FPI) sensors; (3) application of reverse KLT to isolate different sensors operating on the same spectrum. A simulative outline is provided to demonstrate the KLT operation and estimate performance; a brief experimental section is also provided to validate accurate FBG and FPI decoding.

Enhanced oral bioavailability of glycyrrhetinic acid via nanocrystal formulation.

PubMed

Lei, Yaya; Kong, Yindi; Sui, Hong; Feng, Jun; Zhu, Rongyue; Wang, Wenping

2016-10-01

The purpose of this study was to prepare solid nanocrystals of glycyrrhetinic acid (GA) for improved oral bioavailability. The anti-solvent precipitation-ultrasonication method followed by freeze-drying was adopted for the preparation of GA nanocrystals. The physicochemical properties, drug dissolution and pharmacokinetic of the obtained nanocrystals were investigated. GA nanocrystals showed a mean particle size of 220 nm and shaped like short rods. The analysis results from differential scanning calorimetry and X-ray powder diffraction indicated that GA remained in crystalline state despite a huge size reduction. The equilibrium solubility and dissolution rate of GA nanocrystal were significantly improved in comparison with those of the coarse GA or the physical mixture. The bioavailability of GA nanocrystals in rats was 4.3-fold higher than that of the coarse GA after oral administration. With its rapid dissolution and absorption performance, the solid nanocrystal might be a more preferable formulation for oral administration of poorly soluble GA.

Weighted least squares phase unwrapping based on the wavelet transform

NASA Astrophysics Data System (ADS)

Chen, Jiafeng; Chen, Haiqin; Yang, Zhengang; Ren, Haixia

2007-01-01

The weighted least squares phase unwrapping algorithm is a robust and accurate method to solve phase unwrapping problem. This method usually leads to a large sparse linear equation system. Gauss-Seidel relaxation iterative method is usually used to solve this large linear equation. However, this method is not practical due to its extremely slow convergence. The multigrid method is an efficient algorithm to improve convergence rate. However, this method needs an additional weight restriction operator which is very complicated. For this reason, the multiresolution analysis method based on the wavelet transform is proposed. By applying the wavelet transform, the original system is decomposed into its coarse and fine resolution levels and an equivalent equation system with better convergence condition can be obtained. Fast convergence in separate coarse resolution levels speeds up the overall system convergence rate. The simulated experiment shows that the proposed method converges faster and provides better result than the multigrid method.

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

PubMed Central

Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

2013-01-01

We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems. PMID:23665897

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.

Multiple groups of orientation-selective visual mechanisms underlying rapid orientated-line detection.

PubMed Central

Foster, D H; Westland, S

1998-01-01

Visual search for an edge or line element differing in orientation from a background of other edge or line elements can be performed rapidly and effortlessly. In this study, based on psychophysical measurements with ten human observers, threshold values of the angle between a target and background line elements were obtained as functions of background-element orientation, in brief masked displays. A repeated-loess analysis of the threshold functions suggested the existence of several groups of orientation-selective mechanisms contributing to rapid orientated-line detection; specifically, coarse, intermediate and fine mechanisms with preferred orientations spaced at angles of approximately 90 degrees, 35 degrees, and 10 degrees-25 degrees, respectively. The preferred orientations of coarse and some intermediate mechanisms coincided with the vertical or horizontal of the frontoparallel plane, but the preferred orientations of fine mechanisms varied randomly from observer to observer, possibly reflecting individual variations in neuronal sampling characteristics. PMID:9753784

Screening Efficiency Analysis of Vibrosieves with the Circular Vibrations

NASA Astrophysics Data System (ADS)

Djoković, Jelena M.; Tanikić, Dejan I.; Nikolić, Ružica R.; Kalinović, Saša M.

2017-06-01

The analysis of influence of factors that depend on construction characteristics of the vibrosieves with circular vibrations on screening efficiency is presented in this paper. The dependence of the screening efficiency on the aperture size, length and inclination of the screen, as well as on vibration amplitude, is considered. Based on obtained results, one can see that the screening efficiency increases with vibration amplitude and the screen length increase. Further, increases of the screen inclination and aperture size are causing an initial increase of the screening efficiency, which is later decreasing.

Print news coverage of cancer: what prevention messages are conveyed when screening is newsworthy?

PubMed

Smith, Katherine Clegg; Kromm, Elizabeth Edsall; Klassen, Ann Carroll

2010-08-01

Americans are generally favorable towards cancer screening, but fatalistic about cancer prevention. News coverage shapes perceptions of cancer control in meaningful ways, but there is little consensus as to the impact of news on our understanding of and engagement in cancer screening practices. Our analysis of cancer screening-related print news coverage during a four month period in 2005 suggests that the newsworthiness of new screening technologies may undermine public confidence in currently available and effective secondary prevention programs, while promoting tests whose effectiveness is debated or not yet established. We conducted a structured text analysis of 517 cancer-related news articles from 15 leading daily newspapers and a subsequent qualitative analysis of the 79 screening news articles. Screening articles were analyzed for content related to criteria for screening effectiveness. Content patterns for each type of screening and cancer were also noted. News coverage consistently conveyed screening as important and highlighted the need to protect and expand access to screening. At the same time, to the extent that story content was framed by the newsworthiness of new tests and technologies this often indirectly called into question effective and established protocols and programs without providing any actionable alternative. This analysis revealed unexpected messages about screening that are potentially problematic for cancer control. The cancer control community should continue efforts to understand and shape news coverage of screening in order to promote balanced and action-oriented content. Research has shown that Americans hold conflicting views regarding cancer-having a favorable opinion of screening while simultaneously feeling fatalistic about prevention. Our analysis of print news stories on cancer screening suggests that the determination of screening's "newsworthiness" is related to newly developed tests and protocols, which may create demand for new tests whose effectiveness is unknown and undermine confidence in established and effective screening programs.

Observations of fine and coarse particle nitrate at several rural locations in the United States

NASA Astrophysics Data System (ADS)

Lee, Taehyoung; Yu, Xiao-Ying; Ayres, Benjamin; Kreidenweis, Sonia M.; Malm, William C.; Collett, Jeffrey L.

Nitrate comprises an important part of aerosol mass at many non-urban locations during some times of the year. Little is known, however, about the chemical form and size distribution of particulate nitrate in these environments. While submicron ammonium nitrate is often assumed to be the dominant species, this assumption is rarely tested. Properties of aerosol nitrate were characterized at several IMPROVE monitoring sites during a series of field studies. Study sites included Bondville, Illinois (February 2003), San Gorgonio Wilderness Area, California (April and July 2003), Grand Canyon National Park, Arizona (May 2003), Brigantine National Wildlife Refuge, New Jersey (November 2003), and Great Smoky Mountains National Park, Tennessee (July/August 2004). Nitrate was found predominantly in submicron ammonium nitrate particles during the Bondville and San Gorgonio (April) campaigns. Coarse mode nitrate particles, resulting from reactions of nitric acid or its precursors with sea salt or soil dust, were more important at Grand Canyon and Great Smoky Mountains. Both fine and coarse mode nitrate were important during the studies at Brigantine and San Gorgonio (July). These results, which complement earlier findings about the importance of coarse particle nitrate at Yosemite and Big Bend National Parks, suggest a need to more closely examine common assumptions regarding the importance of ammonium nitrate at non-urban sites, to include pathways for coarse mode nitrate formation in regional models, and to consider impacts of coarse particle nitrate on visibility. Because coarse particle nitrate modes often extend well below 2.5 μm aerodynamic diameter, measurements of PM 2.5 nitrate in these environments should not automatically be assumed to contain only ammonium nitrate.

Optical properties of aerosols at Grand Canyon National Park

NASA Astrophysics Data System (ADS)

Malm, William C.; Day, Derek E.

Visibility in the United States is expected to improve over the next few decades because of reduced emissions, especially sulfur dioxide. In the eastern United States, sulfates make up about 60-70% of aerosol extinction, while in the inner mountain west that fraction is only about 30%. In the inner mountain west, carbon aerosols make up about 35% of extinction, while coarse mass contributes between 15 and 25% depending on how absorption is estimated. Although sulfur dioxide emissions are projected to decrease, carbon emissions due to prescribed fire activity will increase by factors of 5-10, and while optical properties of sulfates have been extensively studied, similar properties of carbon and coarse particles are less well understood. The inability to conclusively apportion about 50% of the extinction budget motivated a study to examine aerosol physio-chemical-optical properties at Grand Canyon, Arizona during the months of July and August. Coarse particle mass has usually been assumed to consist primarily of wind-blown dust, with a mass-scattering efficiency between about 0.4 and 0.6 m 2 g -1. Although there were episodes where crustal material made up most of the coarse mass, on the average, organics and crustal material mass were about equal. Furthermore, about one-half of the sampling periods had coarse-mass-scattering efficiencies greater than 0.6 m 2 g -1 and at times coarse-mass-scattering efficiencies were near 1.0 m 2 g -1. It was shown that absorption by coarse- and fine-particle absorption were about equal and that both fine organic and sulfate mass-scattering efficiencies were substantially less than the nominal values of 4.0 and 3.0 m 2 g -1 that have typically been used.

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale.

PubMed

McCarty, J; Clark, A J; Copperman, J; Guenza, M G

2014-05-28

Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.

A new hypothesis and exploratory model for the formation of large-scale inner-shelf sediment sorting and "rippled scour depressions"

USGS Publications Warehouse

Murray, A.B.; Thieler, E.R.

2004-01-01

Recent observations of inner continental shelves in many regions show numerous collections of relatively coarse sediment, which extend kilometers in the cross-shore direction and are on the order of 100m wide. These "rippled scour depressions" have been interpreted to indicate concentrated cross-shelf currents. However, recent observations strongly suggest that they are associated with sediment transport along-shore rather than cross-shore. A new hypothesis for the origin of these features involves the large wave-generated ripples that form in the coarse material. Wave motions interacting with these large roughness elements generate near-bed turbulence that is greatly enhanced relative to that in other areas. This enhances entrainment and inhibits settling of fine material in an area dominated by coarse sediment. The fine sediment is then carried by mean currents past the coarse accumulations, and deposited where the bed is finer. We hypothesize that these interactions constitute a feedback tending to produce accumulations of fine material separated by self-perpetuating patches of coarse sediments. As with many types of self-organized bedforms, small features would interact as they migrate, leading to a better-organized, larger-scale pattern. As an initial test of this hypothesis, we use a numerical model treating the transport of coarse and fine sediment fractions, treated as functions of the local bed composition - a proxy for the presence of large roughness elements in coarse areas. Large-scale sorted patterns exhibiting the main characteristics of the natural features result robustly in the model, indicating that this new hypothesis offers a plausible explanation for the phenomena. ?? 2003 Elsevier Ltd. All rights reserved.

Cost-effectiveness of breast cancer screening policies using simulation.

PubMed

Gocgun, Y; Banjevic, D; Taghipour, S; Montgomery, N; Harvey, B J; Jardine, A K S; Miller, A B

2015-08-01

In this paper, we study breast cancer screening policies using computer simulation. We developed a multi-state Markov model for breast cancer progression, considering both the screening and treatment stages of breast cancer. The parameters of our model were estimated through data from the Canadian National Breast Cancer Screening Study as well as data in the relevant literature. Using computer simulation, we evaluated various screening policies to study the impact of mammography screening for age-based subpopulations in Canada. We also performed sensitivity analysis to examine the impact of certain parameters on number of deaths and total costs. The analysis comparing screening policies reveals that a policy in which women belonging to the 40-49 age group are not screened, whereas those belonging to the 50-59 and 60-69 age groups are screened once every 5 years, outperforms others with respect to cost per life saved. Our analysis also indicates that increasing the screening frequencies for the 50-59 and 60-69 age groups decrease mortality, and that the average number of deaths generally decreases with an increase in screening frequency. We found that screening annually for all age groups is associated with the highest costs per life saved. Our analysis thus reveals that cost per life saved increases with an increase in screening frequency. Copyright © 2015 Elsevier Ltd. All rights reserved.

Contextual Constraint Treatment for coarse coding deficit in adults with right hemisphere brain damage: Generalization to narrative discourse comprehension

PubMed Central

Blake, Margaret Lehman; Tompkins, Connie A.; Scharp, Victoria L.; Meigh, Kimberly M.; Wambaugh, Julie

2014-01-01

Coarse coding is the activation of broad semantic fields that can include multiple word meanings and a variety of features, including those peripheral to a word’s core meaning. It is a partially domain-general process related to general discourse comprehension and contributes to both literal and non-literal language processing. Adults with damage to the right cerebral hemisphere (RHD) and a coarse coding deficit are particularly slow to activate features of words that are relatively distant or peripheral. This manuscript reports a pre-efficacy study of Contextual Constraint Treatment (CCT), a novel, implicit treatment designed to increase the efficiency of coarse coding with the goal of improving narrative comprehension and other language performance that relies on coarse coding. Participants were four adults with RHD. The study used a single-subject controlled experimental design across subjects and behaviors. The treatment involves pre-stimulation, using a hierarchy of strong- and moderately-biased contexts, to prime the intended distantly-related features of critical stimulus words. Three of the four participants exhibited gains in auditory narrative discourse comprehension, the primary outcome measure. All participants exhibited generalization to untreated items. No strong generalization to processing nonliteral language was evident. The results indicate that CCT yields both improved efficiency of the coarse coding process and generalization to narrative comprehension. PMID:24983133

A two-level approach to large mixed-integer programs with application to cogeneration in energy-efficient buildings

DOE PAGES

Lin, Fu; Leyffer, Sven; Munson, Todd

2016-04-12

We study a two-stage mixed-integer linear program (MILP) with more than 1 million binary variables in the second stage. We develop a two-level approach by constructing a semi-coarse model that coarsens with respect to variables and a coarse model that coarsens with respect to both variables and constraints. We coarsen binary variables by selecting a small number of prespecified on/off profiles. We aggregate constraints by partitioning them into groups and taking convex combination over each group. With an appropriate choice of coarsened profiles, the semi-coarse model is guaranteed to find a feasible solution of the original problem and hence providesmore » an upper bound on the optimal solution. We show that solving a sequence of coarse models converges to the same upper bound with proven finite steps. This is achieved by adding violated constraints to coarse models until all constraints in the semi-coarse model are satisfied. We demonstrate the effectiveness of our approach in cogeneration for buildings. Here, the coarsened models allow us to obtain good approximate solutions at a fraction of the time required by solving the original problem. Extensive numerical experiments show that the two-level approach scales to large problems that are beyond the capacity of state-of-the-art commercial MILP solvers.« less

A two-level approach to large mixed-integer programs with application to cogeneration in energy-efficient buildings

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

Lin, Fu; Leyffer, Sven; Munson, Todd

We study a two-stage mixed-integer linear program (MILP) with more than 1 million binary variables in the second stage. We develop a two-level approach by constructing a semi-coarse model that coarsens with respect to variables and a coarse model that coarsens with respect to both variables and constraints. We coarsen binary variables by selecting a small number of prespecified on/off profiles. We aggregate constraints by partitioning them into groups and taking convex combination over each group. With an appropriate choice of coarsened profiles, the semi-coarse model is guaranteed to find a feasible solution of the original problem and hence providesmore » an upper bound on the optimal solution. We show that solving a sequence of coarse models converges to the same upper bound with proven finite steps. This is achieved by adding violated constraints to coarse models until all constraints in the semi-coarse model are satisfied. We demonstrate the effectiveness of our approach in cogeneration for buildings. Here, the coarsened models allow us to obtain good approximate solutions at a fraction of the time required by solving the original problem. Extensive numerical experiments show that the two-level approach scales to large problems that are beyond the capacity of state-of-the-art commercial MILP solvers.« less

Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM)

NASA Astrophysics Data System (ADS)

Sinitskiy, Anton V.; Voth, Gregory A.

2018-01-01

Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

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

Probing Sub-atomistic Free-Volume Imperfections in Dry-Milled Nanoarsenicals with PAL Spectroscopy.

PubMed

Shpotyuk, Oleh; Ingram, Adam; Bujňáková, Zdenka; Baláž, Peter; Shpotyuk, Yaroslav

2016-12-01

Structural transformations caused by coarse-grained powdering and fine-grained mechanochemical milling in a dry mode were probed in high-temperature modification of tetra-arsenic tetra-sulfide known as β-As4S4. In respect to X-ray diffraction analysis, the characteristic sizes of β-As4S4 crystallites in these coarse- and fine-grained powdered pellets were 90 and 40 nm, respectively. Positron annihilation lifetime spectroscopy was employed to characterize transformations occurred in free-volume structure of these nanoarsenicals. Experimentally measured positron lifetime spectra were parameterized in respect to three- or two-term fitting procedures and respectively compared with those accumulated for single crystalline realgar α-As4S4 polymorph. The effect of coarse-grained powdering was found to result in generation of large amount of positron and positronium Ps trapping sites inside arsenicals in addition to existing ones. In fine-grained powdered β-As4S4 pellets, the positron trapping sites with characteristic free volumes close to bi- and tri-atomic vacancies were evidently dominated. These defects were supposed to originate from grain boundary regions and interfacial free volumes near aggregated β-As4S4 crystallites. Thus, the cumulative production of different positron traps with lifetimes close to defect-related lifetimes in realgar α-As4S4 polymorph was detected in fine-grained milled samples.

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.

Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM).

PubMed

Sinitskiy, Anton V; Voth, Gregory A

2018-01-07

Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

Cortical feedback signals generalise across different spatial frequencies of feedforward inputs.

PubMed

Revina, Yulia; Petro, Lucy S; Muckli, Lars

2017-09-22

Visual processing in cortex relies on feedback projections contextualising feedforward information flow. Primary visual cortex (V1) has small receptive fields and processes feedforward information at a fine-grained spatial scale, whereas higher visual areas have larger, spatially invariant receptive fields. Therefore, feedback could provide coarse information about the global scene structure or alternatively recover fine-grained structure by targeting small receptive fields in V1. We tested if feedback signals generalise across different spatial frequencies of feedforward inputs, or if they are tuned to the spatial scale of the visual scene. Using a partial occlusion paradigm, functional magnetic resonance imaging (fMRI) and multivoxel pattern analysis (MVPA) we investigated whether feedback to V1 contains coarse or fine-grained information by manipulating the spatial frequency of the scene surround outside an occluded image portion. We show that feedback transmits both coarse and fine-grained information as it carries information about both low (LSF) and high spatial frequencies (HSF). Further, feedback signals containing LSF information are similar to feedback signals containing HSF information, even without a large overlap in spatial frequency bands of the HSF and LSF scenes. Lastly, we found that feedback carries similar information about the spatial frequency band across different scenes. We conclude that cortical feedback signals contain information which generalises across different spatial frequencies of feedforward inputs. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Iris Image Classification Based on Hierarchical Visual Codebook.

PubMed

Zhenan Sun; Hui Zhang; Tieniu Tan; Jianyu Wang

2014-06-01

Iris recognition as a reliable method for personal identification has been well-studied with the objective to assign the class label of each iris image to a unique subject. In contrast, iris image classification aims to classify an iris image to an application specific category, e.g., iris liveness detection (classification of genuine and fake iris images), race classification (e.g., classification of iris images of Asian and non-Asian subjects), coarse-to-fine iris identification (classification of all iris images in the central database into multiple categories). This paper proposes a general framework for iris image classification based on texture analysis. A novel texture pattern representation method called Hierarchical Visual Codebook (HVC) is proposed to encode the texture primitives of iris images. The proposed HVC method is an integration of two existing Bag-of-Words models, namely Vocabulary Tree (VT), and Locality-constrained Linear Coding (LLC). The HVC adopts a coarse-to-fine visual coding strategy and takes advantages of both VT and LLC for accurate and sparse representation of iris texture. Extensive experimental results demonstrate that the proposed iris image classification method achieves state-of-the-art performance for iris liveness detection, race classification, and coarse-to-fine iris identification. A comprehensive fake iris image database simulating four types of iris spoof attacks is developed as the benchmark for research of iris liveness detection.

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.

Barley processing, forage:concentrate, and forage length effects on chewing and digesta passage in lactating cows.

PubMed

Yang, W Z; Beauchemin, K A; Rode, L M

2001-12-01

Dietary factors that alter fermentability, NDF content, or particle size of the diet were evaluated for their effects on chewing behavior and distribution and passage of feed particles in the digestive tract of dairy cows. A double 4 x 4 quasi-Latin square design with a 2(3) factorial arrangement of treatments was used. The dietary factors were: extent of barley grain processing, coarse (1.60 mm) or flat (1.36 mm); forage-to-concentrate ratio (F:C), low (35:65) or high (55:45) (dry matter basis); and forage particle length, long (7.59 mm) or short (6.08 mm). Eight lactating cows with ruminal and duodenal cannulas were offered ad libitum access to total mixed diets. Chewing time, expressed as minutes per day or per kilogram of dry matter or neutral detergent fiber (NDF), was increased with high F:C diets due to increased eating and ruminating times but was decreased when expressed per kilogram of NDF intake from forage. The influence of forage particle length or grain processing on chewing activity was less pronounced than F:C ratio. Chewing activity was positively correlated to proportion of long forage particles in the diet but not to particle length of the diets. Influence of feed particle size on particle size distribution in different sites of the digestive tract was minimal. Particle size distributions of duodenal digesta and feces differed; the proportion of particles retained on the 3.35- or 1.18-mm screens was higher, but proportion of particles that passed through the 1.18-mm screen was lower in duodenal digesta than in feces. Relationships between chewing activities and ruminal pH or fractional passage rate of rumen contents were not significant. These results indicate that particle size of barley-based diets was not a reliable indicator of chewing activity. Forage particle size and NDF content of the diets were more reliable indicators of chewing activity than was the NDF content of forage. Fecal particle size was not an appropriate means of estimating the size of particles exiting the reticulorumen, at least for barley-based diets. Breakdown of coarse particles was necessary, but not a rate-limiting step for particles exiting the rumen. Passage rate of the rumen contents was affected by numerous factors including chewing activity.

Estimation of the contributions of long range transported aerosol in East Asia to carbonaceous aerosol and PM concentrations in Seoul, Korea using highly time resolved measurements: a PSCF model approach.

PubMed

Jeong, Ukkyo; Kim, Jhoon; Lee, Hanlim; Jung, Jinsang; Kim, Young J; Song, Chul H; Koo, Ja-Ho

2011-07-01

The contributions of long range transported aerosol in East Asia to carbonaceous aerosol and particulate matter (PM) concentrations in Seoul, Korea were estimated with potential source contribution function (PSCF) calculations. Carbonaceous aerosol (organic carbon (OC) and elemental carbon (EC)), PM(2.5), and PM(10) concentrations were measured from April 2007 to March 2008 in Seoul, Korea. The PSCF and concentration weighted trajectory (CWT) receptor models were used to identify the spatial source distributions of OC, EC, PM(2.5), and coarse particles. Heavily industrialized areas in Northeast China such as Harbin and Changchun and East China including the Pearl River Delta region, the Yangtze River Delta region, and the Beijing-Tianjin region were identified as high OC, EC and PM(2.5) source areas. The conditional PSCF analysis was introduced so as to distinguish the influence of aerosol transported from heavily polluted source areas on a receptor site from that transported from relatively clean areas. The source contributions estimated using the conditional PSCF analysis account for not only the aerosol concentrations of long range transported aerosols but also the number of transport days effective on the measurement site. Based on the proposed algorithm, the condition of airmass pathways was classified into two types: one condition where airmass passed over the source region (PS) and another condition where airmass did not pass over the source region (NPS). For most of the seasons during the measurement period, 249.5-366.2% higher OC, EC, PM(2.5), and coarse particle concentrations were observed at the measurement site under PS conditions than under NPS conditions. Seasonal variations in the concentrations of OC, EC, PM(2.5), and coarse particles under PS, NPS, and background aerosol conditions were quantified. The contributions of long range transported aerosols on the OC, EC, PM(2.5), and coarse particle concentrations during several Asian dust events were also estimated. We also investigated the performance of the PSCF results obtained from combining highly time resolved measurement data and backward trajectory calculations via comparison with those from data in low resolutions. Reduced tailing effects and the larger coverage over the area of interest were observed in the PSCF results obtained from using the highly time resolved data and trajectories.

Coarse mesh and one-cell block inversion based diffusion synthetic acceleration

NASA Astrophysics Data System (ADS)

Kim, Kang-Seog

DSA (Diffusion Synthetic Acceleration) has been developed to accelerate the SN transport iteration. We have developed solution techniques for the diffusion equations of FLBLD (Fully Lumped Bilinear Discontinuous), SCB (Simple Comer Balance) and UCB (Upstream Corner Balance) modified 4-step DSA in x-y geometry. Our first multi-level method includes a block Gauss-Seidel iteration for the discontinuous diffusion equation, uses the continuous diffusion equation derived from the asymptotic analysis, and avoids void cell calculation. We implemented this multi-level procedure and performed model problem calculations. The results showed that the FLBLD, SCB and UCB modified 4-step DSA schemes with this multi-level technique are unconditionally stable and rapidly convergent. We suggested a simplified multi-level technique for FLBLD, SCB and UCB modified 4-step DSA. This new procedure does not include iterations on the diffusion calculation or the residual calculation. Fourier analysis results showed that this new procedure was as rapidly convergent as conventional modified 4-step DSA. We developed new DSA procedures coupled with 1-CI (Cell Block Inversion) transport which can be easily parallelized. We showed that 1-CI based DSA schemes preceded by SI (Source Iteration) are efficient and rapidly convergent for LD (Linear Discontinuous) and LLD (Lumped Linear Discontinuous) in slab geometry and for BLD (Bilinear Discontinuous) and FLBLD in x-y geometry. For 1-CI based DSA without SI in slab geometry, the results showed that this procedure is very efficient and effective for all cases. We also showed that 1-CI based DSA in x-y geometry was not effective for thin mesh spacings, but is effective and rapidly convergent for intermediate and thick mesh spacings. We demonstrated that the diffusion equation discretized on a coarse mesh could be employed to accelerate the transport equation. Our results showed that coarse mesh DSA is unconditionally stable and is as rapidly convergent as fine mesh DSA in slab geometry. For x-y geometry our coarse mesh DSA is very effective for thin and intermediate mesh spacings independent of the scattering ratio, but is not effective for purely scattering problems and high aspect ratio zoning. However, if the scattering ratio is less than about 0.95, this procedure is very effective for all mesh spacing.

Particulate matter air pollution and respiratory symptoms in individuals having either asthma or chronic obstructive pulmonary disease: a European multicentre panel study.

PubMed

Karakatsani, Anna; Analitis, Antonis; Perifanou, Dimitra; Ayres, Jon G; Harrison, Roy M; Kotronarou, Anastasia; Kavouras, Ilias G; Pekkanen, Juha; Hämeri, Kaarle; Kos, Gerard Pa; de Hartog, Jeroen J; Hoek, Gerard; Katsouyanni, Klea

2012-10-05

Particulate matter air pollution has been associated with adverse health effects. The fraction of ambient particles that are mainly responsible for the observed health effects is still a matter of controversy. Better characterization of the health relevant particle fraction will have major implications for air quality policy since it will determine which sources should be controlled.The RUPIOH study, an EU-funded multicentre study, was designed to examine the distribution of various ambient particle metrics in four European cities (Amsterdam, Athens, Birmingham, Helsinki) and assess their health effects in participants with asthma or COPD, based on a detailed exposure assessment. In this paper the association of central site measurements with respiratory symptoms and restriction of activities is examined. At each centre a panel of participants with either asthma or COPD recorded respiratory symptoms and restriction of activities in a diary for six months. Exposure assessment included simultaneous measurements of coarse, fine and ultrafine particles at a central site. Data on gaseous pollutants were also collected. The associations of the 24-hour average concentrations of air pollution indices with the health outcomes were assessed in a hierarchical modelling approach. A city specific analysis controlling for potential confounders was followed by a meta-analysis to provide overall effect estimates. A 10 μg/m3 increase in previous day coarse particles concentrations was positively associated with most symptoms (an increase of 0.6 to 0.7% in average) and limitation in walking (OR= 1.076, 95% CI: 1.026-1.128). Same day, previous day and previous two days ozone concentrations were positively associated with cough (OR= 1.061, 95% CI: 1.013-1.111; OR= 1.049, 95% CI: 1.016-1.083 and OR= 1.059, 95% CI: 1.027-1.091, respectively). No consistent associations were observed between fine particle concentrations, nitrogen dioxide and respiratory health effects. As for particle number concentrations negative association (mostly non-significant at the nominal level) was observed with most symptoms whilst the positive association with limitation of activities did not reach the nominal level of significance. The observed associations with coarse particles are in agreement with the findings of toxicological studies. Together they suggest it is prudent to regulate also coarse particles in addition to fine particles.

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.

Novel Sample-handling Approach for XRD Analysis with Minimal Sample Preparation

NASA Technical Reports Server (NTRS)

Sarrazin, P.; Chipera, S.; Bish, D.; Blake, D.; Feldman, S.; Vaniman, D.; Bryson, C.

2004-01-01

Sample preparation and sample handling are among the most critical operations associated with X-ray diffraction (XRD) analysis. These operations require attention in a laboratory environment, but they become a major constraint in the deployment of XRD instruments for robotic planetary exploration. We are developing a novel sample handling system that dramatically relaxes the constraints on sample preparation by allowing characterization of coarse-grained material that would normally be impossible to analyze with conventional powder-XRD techniques.

Analysis of DNA Sequences by an Optical ime-Integrating Correlator: Proposal

DTIC Science & Technology

1991-11-01

CURRENT TECHNOLOGY 2 3.0 TIME-INTEGRATING CORRELATOR 2 4.0 REPRESENTATIONS OF THE DNA BASES 8 5.0 DNA ANALYSIS STRATEGY 8 6.0 STRATEGY FOR COARSE...1)-correlation peak formed by the AxB term and (2)-pedestal formed by the A + B terms. 7 Figure 4: Short representations of the DNA bases where each...linear scale. 15 x LIST OF TABLES PAGE Table 1: Short representations of the DNA bases where each base is represented by 7-bits long pseudorandom

The stability of the three transmembrane and the four transmembrane human vitamin K epoxide reductase models

NASA Astrophysics Data System (ADS)

Wu, Sangwook

2016-04-01

The three transmembrane and the four transmembrane helix models are suggested for human vitamin K epoxide reductase (VKOR). In this study, we investigate the stability of the human three transmembrane/four transmembrane VKOR models by employing a coarse-grained normal mode analysis and molecular dynamics simulation. Based on the analysis of the mobility of each transmembrane domain, we suggest that the three transmembrane human VKOR model is more stable than the four transmembrane human VKOR model.

A Scalable Analysis Toolkit

NASA Technical Reports Server (NTRS)

Aiken, Alexander

2001-01-01

The Scalable Analysis Toolkit (SAT) project aimed to demonstrate that it is feasible and useful to statically detect software bugs in very large systems. The technical focus of the project was on a relatively new class of constraint-based techniques for analysis software, where the desired facts about programs (e.g., the presence of a particular bug) are phrased as constraint problems to be solved. At the beginning of this project, the most successful forms of formal software analysis were limited forms of automatic theorem proving (as exemplified by the analyses used in language type systems and optimizing compilers), semi-automatic theorem proving for full verification, and model checking. With a few notable exceptions these approaches had not been demonstrated to scale to software systems of even 50,000 lines of code. Realistic approaches to large-scale software analysis cannot hope to make every conceivable formal method scale. Thus, the SAT approach is to mix different methods in one application by using coarse and fast but still adequate methods at the largest scales, and reserving the use of more precise but also more expensive methods at smaller scales for critical aspects (that is, aspects critical to the analysis problem under consideration) of a software system. The principled method proposed for combining a heterogeneous collection of formal systems with different scalability characteristics is mixed constraints. This idea had been used previously in small-scale applications with encouraging results: using mostly coarse methods and narrowly targeted precise methods, useful information (meaning the discovery of bugs in real programs) was obtained with excellent scalability.

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-resolved particles followed these patterns: fine particles > coarse particles > ultrafine particles for spring samples and ultrafine particles > fine particles > coarse particles for winter samples. Cell-free DCFH assay results conclusively showed that all of the measured particle suspensions displayed a higher oxidative potential than the negative control. The correlation coefficient (R2) between free radical intensity and fluorescent intensity generated by the size-resolved particles was 0.535 and 0.507 for the spring and winter seasons, respectively, implying that ambient air particles in the Xuanwei atmosphere have the ability to generate free radicals, and fine and ultrafine particles could be hazardous to local residents.

Determining in-situ thermal conductivity of coarse textured materials through numerical analysis of thermal

NASA Astrophysics Data System (ADS)

Saito, H.; Hamamoto, S.; Moldrup, P.; Komatsu, T.

2013-12-01

Ground source heat pump (GSHP) systems use ground or groundwater as a heat/cooling source, typically by circulating anti-freezing solution inside a vertically installed closed-loop tube known as a U-tube to transfer heat to/from the ground. Since GSHP systems are based on renewable energy and can achieve much higher coefficient of performance (COP) than conventional air source heat pump systems, use of GSHP systems has been rapidly increasing worldwide. However, environmental impacts by GSHP systems including thermal effects on subsurface physical-chemical and microbiological properties have not been fully investigated. To rigorously assess GSHP impact on the subsurface environment, ground thermal properties including thermal conductivity and heat capacity need to be accurately characterized. Ground thermal properties were investigated at two experimental sites at Tokyo University of Agriculture and Technology (TAT) and Saitama University (SA), both located in the Kanto area of Japan. Thermal properties were evaluated both by thermal probe measurements on boring core samples and by performing in-situ Thermal Response Tests (TRT) in 50-80 m deep U-tubes. At both TAT and SU sites, heat-pulse probe measurements gave unrealistic low thermal conductivities for coarse textured materials (dominated by particles > 75 micrometers). Such underestimation can be partly due to poor contact between probe and porous material and partly to markedly decreasing sample water content during drilling, carrying, and storing sandy/gravelly samples. A more reliable approach for estimating in-situ thermal conductivity of coarse textured materials is therefore needed, and may be based on the commonly used TRT test. However, analyses of TRT data is typically based on Kelvin's line source model and provides an average (effective) thermal property for the whole soil profile around the U-tube but not for each geological layer. The main objective of this study was therefore to develop a method for estimating thermal conductivity values of coarse textured layers by numerically analyzing TRT data. A numerical technique combining three-dimensional conductive heat transport and one-dimensional convective heat transport to simulate heat exchange processes between the U-tube and the ground was used. In the numerical simulations, the thermal conductivities for the fine textured layers were kept at the probe-measured values, while the thermal conductivity for the coarse textured layers (constituting around half of the profile depth at both sites) was calibrated. The numerically-based method yielded more reasonable thermal conductivity values for the coarse-textured materials at both TAT and SU sites as compared to the heat pulse probe measurements, while the temperature changes of the heat carry fluid inside the U-tubes were also well simulated.

Molecular Modeling of Thermosetting Polymers: Effects of Degree of Curing and Chain Length on Thermo-Mechanical Properties

DTIC Science & Technology

2012-08-01

paper, we will first briefly discuss our recent results, using coarse-grained bead - spring model , on the dependence of failure stress and failure...length of the resin strands. In the coarse-grained model used here the polymer network is treated as a bead - spring system. To create highly cross...simulations of Thermosets We have used a coarse-grained bead - spring model to study the dependence of the mechanical properties of thermosets on chain

Relative entropy as a universal metric for multiscale errors

NASA Astrophysics Data System (ADS)

Chaimovich, Aviel; Shell, M. Scott

2010-06-01

We show that the relative entropy, Srel , suggests a fundamental indicator of the success of multiscale studies, in which coarse-grained (CG) models are linked to first-principles (FP) ones. We demonstrate that Srel inherently measures fluctuations in the differences between CG and FP potential energy landscapes, and develop a theory that tightly and generally links it to errors associated with coarse graining. We consider two simple case studies substantiating these results, and suggest that Srel has important ramifications for evaluating and designing coarse-grained models.

Relative entropy as a universal metric for multiscale errors.

PubMed

Chaimovich, Aviel; Shell, M Scott

2010-06-01

We show that the relative entropy, Srel, suggests a fundamental indicator of the success of multiscale studies, in which coarse-grained (CG) models are linked to first-principles (FP) ones. We demonstrate that Srel inherently measures fluctuations in the differences between CG and FP potential energy landscapes, and develop a theory that tightly and generally links it to errors associated with coarse graining. We consider two simple case studies substantiating these results, and suggest that Srel has important ramifications for evaluating and designing coarse-grained models.

Nuclear fuel element with axially aligned fuel pellets and fuel microspheres therein

DOEpatents

Sease, J.D.; Harrington, F.E.

1973-12-11

Elongated single- and multi-region fuel elements are prepared by replacing within a cladding container a coarse fraction of fuel material which includes plutonium and uranium in the appropriate regions of the fuel element and then infiltrating with vibration a fine-sized fraction of uranium-containing microspheres throughout all interstices in the coarse material in a single loading. The fine, rigid material defines a thin annular layer between the coarse fraction and the cladding to reduce adverse mechanical and chemical interactions. (Official Gazette)

Understanding Puberty (For Parents)

MedlinePlus

... his voice is changing and will become deeper. Dark, coarse, curly hair will also sprout just above ... in texture over the next year or two. Dark, coarse, curly hair will appear on her labia ( ...

Global measurements of coarse-mode aerosol size distributions - first results from the Atmospheric Tomography Mission (ATom)

NASA Astrophysics Data System (ADS)

Weinzierl, B.; Dollner, M.; Schuh, H.; Brock, C. A.; Bui, T. V.; Gasteiger, J.; Froyd, K. D.; Schwarz, J. P.; Spanu, A.; Murphy, D. M.; Katich, J. M.; Kupc, A.; Williamson, C.

2016-12-01

Although coarse-mode aerosol (>1 µm diameter), composed mainly of mineral dust and sea-salt, is highly abundant over large regions of the world, these particles form a particularly poorly understood and characterized subset of atmospheric aerosol constituents. The NASA-sponsored Atmospheric Tomography Mission (ATom) is an unprecedented field program that investigates how human emissions affect air quality and climate change. ATom provides a singular opportunity to characterize the global coarse-mode size distribution by continuously profiling between 0.2 and 13 km with the NASA DC-8 research aircraft while traveling from the high Arctic down south the middle of the Pacific Ocean, to the Southern Ocean and back north over the Atlantic Ocean basin in four seasons. For ATom, the DC-8 aircraft has been equipped with multiple instruments to observe the composition of the air. The coarse mode and cloud particle size distribution is measured in-situ with a Cloud, Aerosol, and Precipitation Spectrometer (CAPS) mounted under the wing of the DC-8 research aircraft. The CAPS consists of an optical spectrometer providing size distributions in the size range between 0.5 and 50 µm and an imager detecting number concentration, size and shape of particles between 15 and 930 µm diameter. Early ATom flights indicated complicated vertical layering: over the sea, we regularly observed sea salt aerosol which extended from the ground up to 0.6-1 km altitude. In addition - depending on the location of the measurements - we frequently found layers with coarse mode aerosol originating from deserts and biomass burning aerosol aloft. In this study, we will present first results of coarse mode aerosol observations from the entire first ATom deployment in summer 2016. We will show vertical profiles of coarse mode aerosol number concentration, discuss their interhemispheric differences, and look into the question how frequently coarse-mode aerosol is externally mixed with submicron black carbon and other anthropogenic aerosol components. Furthermore, we will compare sequences with mineral dust observations made during ATom with results from the Saharan Aerosol Long-range Transport and Aerosol Cloud Interaction Experiment (SALTRACE) that took place around the tropical and northern Atlantic basin in 2013.

Coarse muscovite veins and alteration deep in the Yerington batholith, Nevada: insights into fluid exsolution in the roots of porphyry copper systems

NASA Astrophysics Data System (ADS)

Runyon, Simone E.; Steele-MacInnis, Matthew; Seedorff, Eric; Lecumberri-Sanchez, Pilar; Mazdab, Frank K.

2017-04-01

Veins and pervasive wall-rock alteration composed of coarse muscovite±quartz±pyrite are documented for the first time in a porphyritic granite at Luhr Hill in the Yerington District, Nevada. Coarse muscovite at Luhr Hill occurs at paleodepths of 6-7 km in the roots of a porphyry copper system and crops out on the scale of tens to hundreds of meters, surrounded by rock that is unaltered or variably altered to sodic-calcic assemblages. Coarse muscovite veins exhibit a consistent orientation, subvertical and N-S striking, which structurally restores to subhorizontal at the time of formation. Along strike, coarse muscovite veins swell from distal, millimeter-thick muscovite-only veinlets to proximal, centimeter-thick quartz-sulfide-bearing muscovite veins. Crosscutting relationships between coarse muscovite veins, pegmatite dikes, and sodic-calcic veins indicate that muscovite veins are late-stage magmatic-hydrothermal features predating final solidification of the Luhr Hill porphyritic granite. Fluid inclusions in the muscovite-quartz veins are high-density aqueous inclusions of 3-9 wt% NaCl eq. and <1 mol% CO2 that homogenize between 150 and 200 °C, similar to fluid inclusions from greisen veins in Sn-W-Mo vein systems. Our results indicate that muscovite-forming fluids at Luhr Hill were mildly acidic, of low to moderate salinity and sulfur content and low CO2 content, and that muscovite in deep veins and alteration differs in texture, composition, and process of formation from sericite at shallower levels of the hydrothermal system. Although the definition of greisen is controversial, we suggest that coarse muscovite alteration is more similar to alteration in greisen-type Sn-W-Mo districts worldwide than to sericitic alteration at higher levels of porphyry copper systems. The fluids that form coarse muscovite veins and alteration in the roots of porphyry copper systems are distinct from fluids that formed copper ore or widespread, shallower, acidic alteration. We propose that this style of veins and alteration at Luhr Hill represents degassing of moderate volumes of overpressured hydrothermal fluid during late crystallization of deep levels of the Yerington batholith.

Molecular Engineering for Mechanically Resilient and Stretchable Electronic Polymers and Composites

DTIC Science & Technology

2016-06-08

conjugated polymers and composites by analysis of the structural determinants of the mechanical properties. We developed coarse-grained molecular...dynamics simulations that predicted the mechanical properties of conjugated polymers and polymer -fullerene composites. We elucidated the mechanical...We also determined the effect of cyclic stretching on the microstructure and mechanical properties of conjugated polymers . We used many of

Temporal carbon dynamics of forests in Washington, US: implications for ecological theory and carbon management

Treesearch

Crystal L. Raymond; Donald McKenzie

2014-01-01

We quantified carbon (C) dynamics of forests in Washington, US using theoretical models of C dynamics as a function of forest age. We fit empirical models to chronosequences of forest inventory data at two scales: a coarse-scale ecosystem classification (ecosections) and forest types (potential vegetation) within ecosections. We hypothesized that analysis at the finer...

Wood-inhabiting fungi in southern Italy forest stands: morphogroups, vegetation types and decay classes.

PubMed

Granito, Vito Mario; Lunghini, Dario; Maggi, Oriana; Persiani, Anna Maria

2015-01-01

The authors conducted an ecological study of forests subjected to varying management. The aim of the study was to extend and integrate, within a multivariate context, knowledge of how saproxylic fungal communities behave along altitudinal/vegetational gradients in response to the varying features and quality of coarse woody debris (CWD). The intra-annual seasonal monitoring of saproxylic fungi, based on sporocarp inventories, was used to investigate saproxylic fungi in relation to vegetation types and management categories. We analyzed fungal species occurrence, recorded according to the presence/absence and frequency of sporocarps, on the basis of the harvest season, of coarse woody debris decay classes as well as other environmental and ecological variables. Two-way cluster analysis, DCA and Spearman's rank correlations, for indirect gradient analysis, were performed to identify any patterns of seasonality and decay. Most of the species were found on CWD in an intermediate decay stage. The first DCA axis revealed the vegetational/microclimate gradient as the main driver of fungal community composition, while the second axis corresponded to a strong gradient of CWD decay classes. © 2015 by The Mycological Society of America.

Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis.

PubMed

Demerdash, Omar N A; Mitchell, Julie C

2012-07-01

Normal mode analysis has emerged as a useful technique for investigating protein motions on long time scales. This is largely due to the advent of coarse-graining techniques, particularly Hooke's Law-based potentials and the rotational-translational blocking (RTB) method for reducing the size of the force-constant matrix, the Hessian. Here we present a new method for domain decomposition for use in RTB that is based on hierarchical clustering of atomic density gradients, which we call Density-Cluster RTB (DCRTB). The method reduces the number of degrees of freedom by 85-90% compared with the standard blocking approaches. We compared the normal modes from DCRTB against standard RTB using 1-4 residues in sequence in a single block, with good agreement between the two methods. We also show that Density-Cluster RTB and standard RTB perform well in capturing the experimentally determined direction of conformational change. Significantly, we report superior correlation of DCRTB with B-factors compared with 1-4 residue per block RTB. Finally, we show significant reduction in computational cost for Density-Cluster RTB that is nearly 100-fold for many examples. Copyright © 2012 Wiley Periodicals, Inc.

Otoacoustic Emissions in Rural Nicaragua: Cost Analysis and Implications for Newborn Hearing Screening.

PubMed

Wong, Lye-Yeng; Espinoza, Francisca; Alvarez, Karen Mojica; Molter, Dave; Saunders, James E

2017-05-01

Objective (1) Determine the incidence and risk factors for congenital hearing loss. (2) Perform cost analysis of screening programs. Study Design Proportionally distributed cross-sectional survey. Setting Jinotega, Nicaragua. Subjects and Methods Otoacoustic emissions (OAEs) were used to screen 640 infants <6 months of age from neonatal intensive care unit, institutional, and home birth settings. Data on 15 risk factors were analyzed. Cost of 4 implementation strategies was studied: universal screening, screening at the regional health center (RHC), targeted screening, and screening at the RHC plus targeted screening. Cost-effectiveness analysis over 10 years was based on disability-adjusted life year estimates, with the World Health Organization standard of cost-effectiveness ratio (CER) / gross domestic product (GDP) <3, with GDP set at $4884.15. Results Thirty-eight infants failed the initial OAE (5.94%). In terms of births, 325 (50.8%) were in the RHC, 69 (10.8%) in the neonatal intensive care unit, and 29 (4.5%) at home. Family history and birth defect were significant in univariate analysis; birth defect was significant in multivariate analysis. Cost-effectiveness analysis demonstrated that OAE screening is cost-effective without treatment (CER/GDP = 0.06-2.00) and with treatment (CER/GDP = 0.58-2.52). Conclusions Our rate of OAE failures was comparable to those of developed countries and lower than hearing loss rates noted among Nicaraguan schoolchildren, suggesting acquired or progressive etiology in the latter. Birth defects and familial hearing loss correlated with OAE failure. OAE screening of infants is feasible and cost-effective in rural Nicaragua, although highly influenced by estimated hearing loss severity in identified infants and the high travel costs incurred in a targeted screening strategy.

Electrical resisitivity of mechancially stablized earth wall backfill

NASA Astrophysics Data System (ADS)

Snapp, Michael; Tucker-Kulesza, Stacey; Koehn, Weston

2017-06-01

Mechanically stabilized earth (MSE) retaining walls utilized in transportation projects are typically backfilled with coarse aggregate. One of the current testing procedures to select backfill material for construction of MSE walls is the American Association of State Highway and Transportation Officials standard T 288: ;Standard Method of Test for Determining Minimum Laboratory Soil Resistivity.; T 288 is designed to test a soil sample's electrical resistivity which correlates to its corrosive potential. The test is run on soil material passing the No. 10 sieve and believed to be inappropriate for coarse aggregate. Therefore, researchers have proposed new methods to measure the electrical resistivity of coarse aggregate samples in the laboratory. There is a need to verify that the proposed methods yield results representative of the in situ conditions; however, no in situ measurement of the electrical resistivity of MSE wall backfill is established. Electrical resistivity tomography (ERT) provides a two-dimensional (2D) profile of the bulk resistivity of backfill material in situ. The objective of this study was to characterize bulk resistivity of in-place MSE wall backfill aggregate using ERT. Five MSE walls were tested via ERT to determine the bulk resistivity of the backfill. Three of the walls were reinforced with polymeric geogrid, one wall was reinforced with metallic strips, and one wall was a gravity retaining wall with no reinforcement. Variability of the measured resistivity distribution within the backfill may be a result of non-uniform particle sizes, thoroughness of compaction, and the presence of water. A quantitative post processing algorithm was developed to calculate mean bulk resistivity of in-situ backfill. Recommendations of the study were that the ERT data be used to verify proposed testing methods for coarse aggregate that are designed to yield data representative of in situ conditions. A preliminary analysis suggests that ERT may be utilized as construction quality assurance for thoroughness of compaction in MSE construction; however more data are needed at this time.

Lower Badenian coarse-grained Gilbert deltas in the southern margin of the Western Carpathian Foredeep basin

NASA Astrophysics Data System (ADS)

Nehyba, Slavomír

2018-02-01

Two coarse-grained Gilbert-type deltas in the Lower Badenian deposits along the southern margin of the Western Carpathian Foredeep (peripheral foreland basin) were newly interpreted. Facies characterizing a range of depositional processes are assigned to four facies associations — topset, foreset, bottomset and offshore marine pelagic deposits. The evidence of Gilbert deltas within open marine deposits reflects the formation of a basin with relatively steep margins connected with a relative sea level fall, erosion and incision. Formation, progradation and aggradation of the thick coarse-grained Gilbert delta piles generally indicate a dramatic increase of sediment supply from the hinterland, followed by both relatively continuous sediment delivery and an increase in accommodation space. Deltaic deposition is terminated by relatively rapid and extended drowning and is explained as a transgressive event. The lower Gilbert delta was significantly larger, more areally extended and reveals a more complicated stratigraphic architecture than the upper one. Its basal surface represents a sequence boundary and occurs around the Karpatian/Badenian stratigraphic limit. Two coeval deltaic branches were recognized in the lower delta with partly different stratigraphic arrangements. This different stratigraphic architecture is mostly explained by variations in the sediment delivery and /or predisposed paleotopography and paleobathymetry of the basin floor. The upper delta was recognized only in a restricted area. Its basal surface represents a sequence boundary probably reflecting a higher order cycle of a relative sea level rise and fall within the Lower Badenian. Evidence of two laterally and stratigraphically separated coarse-grained Gilbert deltas indicates two regional/basin wide transgressive/regressive cycles, but not necessarily of the same order. Provenance analysis reveals similar sources of both deltas. Several partial source areas were identified (Mesozoic carbonates of the Northern Calcareous Alps and the Western Carpathians, crystalline rocks of the eastern margin of the Bohemian Massif, older sedimentary infill of the Carpathian Foredeep and/or the North Alpine Foreland Basin, sedimentary rocks of the Western Carpathian/Alpine Flysch Zone).

Hyper-Resolution Groundwater Modeling using MODFLOW 6

NASA Astrophysics Data System (ADS)

Hughes, J. D.; Langevin, C.

2017-12-01

MODFLOW 6 is the latest version of the U.S. Geological Survey's modular hydrologic model. MODFLOW 6 was developed to synthesize many of the recent versions of MODFLOW into a single program, improve the way different process models are coupled, and to provide an object-oriented framework for adding new types of models and packages. The object-oriented framework and underlying numerical solver make it possible to tightly couple any number of hyper-resolution models within coarser regional models. The hyper-resolution models can be used to evaluate local-scale groundwater issues that may be affected by regional-scale forcings. In MODFLOW 6, hyper-resolution meshes can be maintained as separate model datasets, similar to MODFLOW-LGR, which simplifies the development of a coarse regional model with imbedded hyper-resolution models from a coarse regional model. For example, the South Atlantic Coastal Plain regional water availability model was converted from a MODFLOW-2000 model to a MODFLOW 6 model. The horizontal discretization of the original model is approximately 3,218 m x 3,218 m. Hyper-resolution models of the Aiken and Sumter County water budget areas in South Carolina with a horizontal discretization of approximately 322 m x 322 m were developed and were tightly coupled to a modified version of the original coarse regional model that excluded these areas. Hydraulic property and aquifer geometry data from the coarse model were mapped to the hyper-resolution models. The discretization of the hyper-resolution models is fine enough to make detailed analyses of the effect that changes in groundwater withdrawals in the production aquifers have on the water table and surface-water/groundwater interactions. The approach used in this analysis could be applied to other regional water availability models that have been developed by the U.S. Geological Survey to evaluate local scale groundwater issues.

Ecology of coarse wood decomposition by the saprotrophic fungus Fomes fomentarius.

PubMed

Větrovský, Tomáš; Voříšková, Jana; Snajdr, Jaroslav; Gabriel, Jiří; Baldrian, Petr

2011-07-01

Saprotrophic wood-inhabiting basidiomycetes are the most important decomposers of lignin and cellulose in dead wood and as such they attracted considerable attention. The aims of this work were to quantify the activity and spatial distribution of extracellular enzymes in coarse wood colonised by the white-rot basidiomycete Fomes fomentarius and in adjacent fruitbodies of the fungus and to analyse the diversity of the fungal and bacterial community in a fungus-colonised wood and its potential effect on enzyme production by F. fomentarius. Fungus-colonised wood and fruitbodies were collected in low management intensity forests in the Czech Republic. There were significant differences in enzyme production by F. fomentarius between Betula pendula and Fagus sylvatica wood, the activity of cellulose and xylan-degrading enzymes was significantly higher in beech wood than in birch wood. Spatial analysis of a sample B. pendula log segment proved that F. fomentarius was the single fungal representative found in the log. There was a high level of spatial variability in the amount of fungal biomass detected, but no effects on enzyme activities were observed. Samples from the fruiting body showed high β-glucosidase and chitinase activities compared to wood samples. Significantly higher levels of xylanase and cellobiohydrolase were found in samples located near the fruitbody (proximal), and higher laccase and Mn-peroxidase activities were found in the distal ones. The microbial community in wood was dominated by the fungus (fungal to bacterial DNA ratio of 62-111). Bacterial abundance composition was lower in proximal than distal parts of wood by a factor of 24. These results show a significant level of spatial heterogeneity in coarse wood. One of the explanations may be the successive colonization of wood by the fungus: due to differential enzyme production, the rates of biodegradation of coarse wood are also spatially inhomogeneous.

Coformer screening using thermal analysis based on binary phase diagrams.

PubMed

Yamashita, Hiroyuki; Hirakura, Yutaka; Yuda, Masamichi; Terada, Katsuhide

2014-08-01

The advent of cocrystals has demonstrated a growing need for efficient and comprehensive coformer screening in search of better development forms, including salt forms. Here, we investigated a coformer screening system for salts and cocrystals based on binary phase diagrams using thermal analysis and examined the effectiveness of the method. Indomethacin and tenoxicam were used as models of active pharmaceutical ingredients (APIs). Physical mixtures of an API and 42 kinds of coformers were analyzed using Differential Scanning Calorimetry (DSC) and X-ray DSC. We also conducted coformer screening using a conventional slurry method and compared these results with those from the thermal analysis method and previous studies. Compared with the slurry method, the thermal analysis method was a high-performance screening system, particularly for APIs with low solubility and/or propensity to form solvates. However, this method faced hurdles for screening coformers combined with an API in the presence of kinetic hindrance for salt or cocrystal formation during heating or if there is degradation near the metastable eutectic temperature. The thermal analysis and slurry methods are considered complementary to each other for coformer screening. Feasibility of the thermal analysis method in drug discovery practice is ensured given its small scale and high throughput.

Separation and collection of coarse aggregate from waste concrete by electric pulsed power

NASA Astrophysics Data System (ADS)

Shigeishi, Mitsuhiro

2017-09-01

Waste concrete accounts for a substantial fraction of construction waste, and the recycling of waste concrete as concrete aggregate for construction is an important challenge associated with the rapid increase in the amount of waste concrete and the tight supply of natural aggregate. In this study, we propose a technique based on the use of high-voltage pulsed electric discharge into concrete underwater for separating and collecting aggregate from waste concrete with minimal deterioration of quality. By using this technique, the quality of the coarse aggregate separated and collected from concrete test specimens is comparable to that of coarse aggregate recycled by heating and grinding methods, thus satisfying the criteria in Japan Industrial Standard (JIS) A 5021 for the oven-dry density and the water absorption of coarse aggregate by advanced recycling.

Spatial downscaling of soil prediction models based on weighted generalized additive models in smallholder farm settings.

PubMed

Xu, Yiming; Smith, Scot E; Grunwald, Sabine; Abd-Elrahman, Amr; Wani, Suhas P; Nair, Vimala D

2017-09-11

Digital soil mapping (DSM) is gaining momentum as a technique to help smallholder farmers secure soil security and food security in developing regions. However, communications of the digital soil mapping information between diverse audiences become problematic due to the inconsistent scale of DSM information. Spatial downscaling can make use of accessible soil information at relatively coarse spatial resolution to provide valuable soil information at relatively fine spatial resolution. The objective of this research was to disaggregate the coarse spatial resolution soil exchangeable potassium (K ex ) and soil total nitrogen (TN) base map into fine spatial resolution soil downscaled map using weighted generalized additive models (GAMs) in two smallholder villages in South India. By incorporating fine spatial resolution spectral indices in the downscaling process, the soil downscaled maps not only conserve the spatial information of coarse spatial resolution soil maps but also depict the spatial details of soil properties at fine spatial resolution. The results of this study demonstrated difference between the fine spatial resolution downscaled maps and fine spatial resolution base maps is smaller than the difference between coarse spatial resolution base maps and fine spatial resolution base maps. The appropriate and economical strategy to promote the DSM technique in smallholder farms is to develop the relatively coarse spatial resolution soil prediction maps or utilize available coarse spatial resolution soil maps at the regional scale and to disaggregate these maps to the fine spatial resolution downscaled soil maps at farm scale.

On the applicability of density dependent effective interactions in cluster-forming systems

NASA Astrophysics Data System (ADS)

Montes-Saralegui, Marta; Kahl, Gerhard; Nikoubashman, Arash

2017-02-01

We systematically studied the validity and transferability of the force-matching algorithm for computing effective pair potentials in a system of dendritic polymers, i.e., a particular class of ultrasoft colloids. We focused on amphiphilic dendrimers, macromolecules which can aggregate into clusters of overlapping particles to minimize the contact area with the surrounding implicit solvent. Simulations were performed for both the monomeric and coarse-grained models in the liquid phase at densities ranging from infinite dilution up to values close to the freezing point. The effective pair potentials for the coarse-grained simulations were computed from the monomeric simulations both in the zero-density limit (Φeff0) and at each investigated finite density (Φeff). Conducting the coarse-grained simulations with Φeff0 at higher densities is not appropriate as they failed at reproducing the structural properties of the monomeric simulations. In contrast, we found excellent agreement between the spatial dendrimer distributions obtained from the coarse-grained simulations with Φeff and the microscopically detailed simulations at low densities, where the macromolecules were distributed homogeneously in the system. However, the reliability of the coarse-grained simulations deteriorated significantly as the density was increased further and the cluster occupation became more polydisperse. Under these conditions, the effective pair potential of the coarse-grained model can no longer be computed by averaging over the whole system, but the local density needs to be taken into account instead.

Continuous data assimilation for downscaling large-footprint soil moisture retrievals

NASA Astrophysics Data System (ADS)

Altaf, Muhammad U.; Jana, Raghavendra B.; Hoteit, Ibrahim; McCabe, Matthew F.

2016-10-01

Soil moisture is a key component of the hydrologic cycle, influencing processes leading to runoff generation, infiltration and groundwater recharge, evaporation and transpiration. Generally, the measurement scale for soil moisture is found to be different from the modeling scales for these processes. Reducing this mismatch between observation and model scales in necessary for improved hydrological modeling. An innovative approach to downscaling coarse resolution soil moisture data by combining continuous data assimilation and physically based modeling is presented. In this approach, we exploit the features of Continuous Data Assimilation (CDA) which was initially designed for general dissipative dynamical systems and later tested numerically on the incompressible Navier-Stokes equation, and the Benard equation. A nudging term, estimated as the misfit between interpolants of the assimilated coarse grid measurements and the fine grid model solution, is added to the model equations to constrain the model's large scale variability by available measurements. Soil moisture fields generated at a fine resolution by a physically-based vadose zone model (HYDRUS) are subjected to data assimilation conditioned upon coarse resolution observations. This enables nudging of the model outputs towards values that honor the coarse resolution dynamics while still being generated at the fine scale. Results show that the approach is feasible to generate fine scale soil moisture fields across large extents, based on coarse scale observations. Application of this approach is likely in generating fine and intermediate resolution soil moisture fields conditioned on the radiometerbased, coarse resolution products from remote sensing satellites.

The grain-size lineup: A test of a novel eyewitness identification procedure.

PubMed

Horry, Ruth; Brewer, Neil; Weber, Nathan

2016-04-01

When making a memorial judgment, respondents can regulate their accuracy by adjusting the precision, or grain size, of their responses. In many circumstances, coarse-grained responses are less informative, but more likely to be accurate, than fine-grained responses. This study describes a novel eyewitness identification procedure, the grain-size lineup, in which participants eliminated any number of individuals from the lineup, creating a choice set of variable size. A decision was considered to be fine-grained if no more than 1 individual was left in the choice set or coarse-grained if more than 1 individual was left in the choice set. Participants (N = 384) watched 2 high-quality or low-quality videotaped mock crimes and then completed 4 standard simultaneous lineups or 4 grain-size lineups (2 target-present and 2 target-absent). There was some evidence of strategic regulation of grain size, as the most difficult lineup was associated with a greater proportion of coarse-grained responses than the other lineups. However, the grain-size lineup did not outperform the standard simultaneous lineup. Fine-grained suspect identifications were no more diagnostic than suspect identifications from standard lineups, whereas coarse-grained suspect identifications carried little probative value. Participants were generally reluctant to provide coarse-grained responses, which may have hampered the utility of the procedure. For a grain-size approach to be useful, participants may need to be trained or instructed to use the coarse-grained option effectively. (c) 2016 APA, all rights reserved).

A mass-conservative adaptive FAS multigrid solver for cell-centered finite difference methods on block-structured, locally-cartesian grids

NASA Astrophysics Data System (ADS)

Feng, Wenqiang; Guo, Zhenlin; Lowengrub, John S.; Wise, Steven M.

2018-01-01

We present a mass-conservative full approximation storage (FAS) multigrid solver for cell-centered finite difference methods on block-structured, locally cartesian grids. The algorithm is essentially a standard adaptive FAS (AFAS) scheme, but with a simple modification that comes in the form of a mass-conservative correction to the coarse-level force. This correction is facilitated by the creation of a zombie variable, analogous to a ghost variable, but defined on the coarse grid and lying under the fine grid refinement patch. We show that a number of different types of fine-level ghost cell interpolation strategies could be used in our framework, including low-order linear interpolation. In our approach, the smoother, prolongation, and restriction operations need never be aware of the mass conservation conditions at the coarse-fine interface. To maintain global mass conservation, we need only modify the usual FAS algorithm by correcting the coarse-level force function at points adjacent to the coarse-fine interface. We demonstrate through simulations that the solver converges geometrically, at a rate that is h-independent, and we show the generality of the solver, applying it to several nonlinear, time-dependent, and multi-dimensional problems. In several tests, we show that second-order asymptotic (h → 0) convergence is observed for the discretizations, provided that (1) at least linear interpolation of the ghost variables is employed, and (2) the mass conservation corrections are applied to the coarse-level force term.

Coarse-to-fine construction for high-resolution representation in visual working memory.

PubMed

Gao, Zaifeng; Ding, Xiaowei; Yang, Tong; Liang, Junying; Shui, Rende

2013-01-01

This study explored whether the high-resolution representations created by visual working memory (VWM) are constructed in a coarse-to-fine or all-or-none manner. The coarse-to-fine hypothesis suggests that coarse information precedes detailed information in entering VWM and that its resolution increases along with the processing time of the memory array, whereas the all-or-none hypothesis claims that either both enter into VWM simultaneously, or neither does. We tested the two hypotheses by asking participants to remember two or four complex objects. An ERP component, contralateral delay activity (CDA), was used as the neural marker. CDA is higher for four objects than for two objects when coarse information is primarily extracted; yet, this CDA difference vanishes when detailed information is encoded. Experiment 1 manipulated the comparison difficulty of the task under a 500-ms exposure time to determine a condition in which the detailed information was maintained. No CDA difference was found between two and four objects, even in an easy-comparison condition. Thus, Experiment 2 manipulated the memory array's exposure time under the easy-comparison condition and found a significant CDA difference at 100 ms while replicating Experiment 1's results at 500 ms. In Experiment 3, the 500-ms memory array was blurred to block the detailed information; this manipulation reestablished a significant CDA difference. These findings suggest that the creation of high-resolution representations in VWM is a coarse-to-fine process.

Partitioned learning of deep Boltzmann machines for SNP data.

PubMed

Hess, Moritz; Lenz, Stefan; Blätte, Tamara J; Bullinger, Lars; Binder, Harald

2017-10-15

Learning the joint distributions of measurements, and in particular identification of an appropriate low-dimensional manifold, has been found to be a powerful ingredient of deep leaning approaches. Yet, such approaches have hardly been applied to single nucleotide polymorphism (SNP) data, probably due to the high number of features typically exceeding the number of studied individuals. After a brief overview of how deep Boltzmann machines (DBMs), a deep learning approach, can be adapted to SNP data in principle, we specifically present a way to alleviate the dimensionality problem by partitioned learning. We propose a sparse regression approach to coarsely screen the joint distribution of SNPs, followed by training several DBMs on SNP partitions that were identified by the screening. Aggregate features representing SNP patterns and the corresponding SNPs are extracted from the DBMs by a combination of statistical tests and sparse regression. In simulated case-control data, we show how this can uncover complex SNP patterns and augment results from univariate approaches, while maintaining type 1 error control. Time-to-event endpoints are considered in an application with acute myeloid leukemia patients, where SNP patterns are modeled after a pre-screening based on gene expression data. The proposed approach identified three SNPs that seem to jointly influence survival in a validation dataset. This indicates the added value of jointly investigating SNPs compared to standard univariate analyses and makes partitioned learning of DBMs an interesting complementary approach when analyzing SNP data. A Julia package is provided at 'http://github.com/binderh/BoltzmannMachines.jl'. binderh@imbi.uni-freiburg.de. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Cone penetrometer testing and discrete-depth ground water sampling techniques: A cost-effective method of site characterization in a multiple-aquifer setting

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

Zemo, D.A.; Pierce, Y.G.; Gallinatti, J.D.

Cone penetrometer testing (CPT), combined with discrete-depth ground water sampling methods, can significantly reduce the time and expense required to characterize large sites that have multiple aquifers. Results from the screening site characterization can then be used to design and install a cost-effective monitoring well network. At a site in northern California, it was necessary to characterize the stratigraphy and the distribution of volatile organic compounds (VOCs). To expedite characterization, a five-week field screening program was implemented that consisted of a shallow ground water survey, CPT soundings and pore-pressure measurements, and discrete-depth ground water sampling. Based on continuous lithologic informationmore » provided by the CPT soundings, four predominantly coarse-grained, water yielding stratigraphic packages were identified. Seventy-nine discrete-depth ground water samples were collected using either shallow ground water survey techniques, the BAT Enviroprobe, or the QED HydroPunch I, depending on subsurface conditions. Using results from these efforts, a 20-well monitoring network was designed and installed to monitor critical points within each stratigraphic package. Good correlation was found for hydraulic head and chemical results between discrete-depth screening data and monitoring well data. Understanding the vertical VOC distribution and concentrations produced substantial time and cost savings by minimizing the number of permanent monitoring wells and reducing the number of costly conductor casings that had to be installed. Additionally, significant long-term cost savings will result from reduced sampling costs, because fewer wells comprise the monitoring network. The authors estimate these savings to be 50% for site characterization costs, 65% for site characterization time, and 60% for long-term monitoring costs.« less

Screening for thrombophilia in high-risk situations: a meta-analysis and cost-effectiveness analysis.

PubMed

Wu, Olivia; Robertson, Lindsay; Twaddle, Sara; Lowe, Gordon; Clark, Peter; Walker, Isobel; Brenkel, Ivan; Greaves, Mike; Langhorne, Peter; Regan, Lesley; Greer, Ian

2005-10-01

Laboratory testing for the identification of heritable thrombophilia in high-risk patient groups have become common practice; however, indiscriminate testing of all patients is unjustified. The objective of this study was to evaluate the cost-effectiveness of universal and selective history-based thrombophilia screening relative to no screening, from the perspective of the UK National Health Service, in women prior to prescribing combined oral contraceptives and hormone replacement therapy, women during pregnancy and patients prior to major orthopaedic surgery. A decision analysis model was developed, and data from meta-analysis, the literature and two Delphi studies were incorporated in the model. Incremental cost-effectiveness ratios (ICERs) for screening compared with no screening was calculated for each patient group. Of all the patient groups evaluated, universal screening of women prior to prescribing hormone replacement therapy was the most cost-effective (ICER 6824 pounds). In contrast, universal screening of women prior to prescribing combined oral contraceptives was the least cost-effective strategy (ICER 202,402 pounds). Selective thrombophilia screening based on previous personal and/or family history of venous thromboembolism was more cost-effective than universal screening in all the patient groups evaluated.

Pots, plates and provenance: sourcing Indian coarse wares from Mleiha using X-ray fluorescence (XRF) spectrometry analysis

NASA Astrophysics Data System (ADS)

Reddy, A.; Attaelmanan, A. G.; Mouton, M.

2012-07-01

The identification of more than 25% of the pottery sherds from the late PIR.D period (ca. 2nd - mid. 3rd c. AD) assemblage from the recently excavated building H at Mleiha as Indian is based on form and fabric, but using only visual assessment. Petrographic analysis of the fabrics can provide more precise indicators of the geographical origin of the wares. In this study, a total of 21 sherds from various key sites in Western India were compared with 7 different 'Indian' coarse-ware vessels sampled at Mleiha using X-ray fluorescence (XRF) spectrometry. The analyses were conducted on powdered samples collected from the core of each sherd. Each sample was irradiated for 1000 seconds using a 1.2 mm diameter X-ray beam. The resulting spectra were used for quantification of the X-ray intensity and elemental concentration. Levels of correlation in the elemental ratios of the sherds were statistically tested using an F-test as well as a Chi-test. Initial review of the XRF results indicates that the Maharashtra and Gujarat regions of India are probable source areas for at least two of the types of wares. Collection of additional samples from these areas and other regions of India, and further statistical analysis through methods such as Principal Component Analysis will help to isolate groups of wares from India and correlate them with types of vessels imported into the Oman peninsula in antiquity.

Adaptive resolution simulation of an atomistic protein in MARTINI water

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

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J., E-mail: s.j.marrink@rug.nl

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecularmore » dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.« less

Adaptive resolution simulation of an atomistic protein in MARTINI water.

PubMed

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J; Praprotnik, Matej

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

Local free energies for the coarse-graining of adsorption phenomena: The interacting pair approximation

NASA Astrophysics Data System (ADS)

Pazzona, Federico G.; Pireddu, Giovanni; Gabrieli, Andrea; Pintus, Alberto M.; Demontis, Pierfranco

2018-05-01

We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely accepted approach, in which the contributions to the free energy given by the molecules located in two neighboring pores are estimated through Monte Carlo simulations where the two pores are kept separated from the rest of the system, leads to inaccurate results at high sorbate densities. In the coarse-graining strategy that we propose, which is based on the Bethe-Peierls approximation, density-independent interaction terms are instead computed according to local effective potentials that take into account the correlations between the pore pair and its surroundings by means of mean-field correction terms without the need for simulating the pore pair separately. Use of the interaction parameters obtained this way allows the coarse-grained system to reproduce more closely the equilibrium properties of the original one. Results are shown for lattice-gases where the local free energy can be computed exactly and for a system of Lennard-Jones particles under the effect of a static confining field.

Coarse-grained simulations of cis- and trans-polybutadiene: A bottom-up approach

NASA Astrophysics Data System (ADS)

Lemarchand, Claire A.; Couty, Marc; Rousseau, Bernard

2017-02-01

We apply the dissipative particle dynamics strategy proposed by Hijón et al. [Faraday Discuss. 144, 301-322 (2010)] and based on an exact derivation of the generalized Langevin equation to cis- and trans-1,4-polybutadiene. We prove that it is able to reproduce not only the structural but also the dynamical properties of these polymers without any fitting parameter. A systematic study of the effect of the level of coarse-graining is done on cis-1,4-polybutadiene. We show that as the level of coarse-graining increases, the dynamical properties are better and better reproduced while the structural properties deviate more and more from those calculated in molecular dynamics (MD) simulations. We suggest two reasons for this behavior: the Markovian approximation is better satisfied as the level of coarse-graining increases, while the pair-wise approximation neglects important contributions due to the relative orientation of the beads at large levels of coarse-graining. Finally, we highlight a possible limit of the Markovian approximation: the fact that in constrained simulations, in which the centers-of-mass of the beads are kept constant, the bead rotational dynamics become extremely slow.

Mechanical Properties of Lightweight Concrete Using Recycled Cement-Sand Brick as Coarse Aggregates Replacement

NASA Astrophysics Data System (ADS)

Joohari, Ilya; Farhani Ishak, Nor; Amin, Norliyati Mohd

2018-03-01

This paper presents the result of replacing natural course aggregate with recycled cement-sand brick (CSB) towards the mechanical properties of concrete. Natural aggregates were used in this study as a control sample to compare with recycled coarse aggregates. This study was also carried to determine the optimum proportion of coarse aggregates replacement to produce lightweight concrete. Besides, this study was conducted to observe the crack and its behaviour development during the mechanical testing. Through this study, four types of concrete mixed were prepared, which were the control sample, 25%, 50% and 75% replacement of CSB. The test conducted to determine the effectiveness of recycled CSB as coarse aggregates replacement in this study were slump test, density measurement, compression test, and flexural test and. The strength of concrete was tested at 7 days and 28 days of curing. From the results obtained, the optimum proportion which produced the highest strength is 25% replacement of recycled CSB. The compressive and flexural strength has decreased by 10%-12% and 4%-34% respectively compared to the control sample. The presence of recycled coarse aggregates in sample has decreased the density of concrete by 0.8%-3% compared to the control sample.

An engineering closure for heavily under-resolved coarse-grid CFD in large applications

NASA Astrophysics Data System (ADS)

Class, Andreas G.; Yu, Fujiang; Jordan, Thomas

2016-11-01

Even though high performance computation allows very detailed description of a wide range of scales in scientific computations, engineering simulations used for design studies commonly merely resolve the large scales thus speeding up simulation time. The coarse-grid CFD (CGCFD) methodology is developed for flows with repeated flow patterns as often observed in heat exchangers or porous structures. It is proposed to use inviscid Euler equations on a very coarse numerical mesh. This coarse mesh needs not to conform to the geometry in all details. To reinstall physics on all smaller scales cheap subgrid models are employed. Subgrid models are systematically constructed by analyzing well-resolved generic representative simulations. By varying the flow conditions in these simulations correlations are obtained. These comprehend for each individual coarse mesh cell a volume force vector and volume porosity. Moreover, for all vertices, surface porosities are derived. CGCFD is related to the immersed boundary method as both exploit volume forces and non-body conformal meshes. Yet, CGCFD differs with respect to the coarser mesh and the use of Euler equations. We will describe the methodology based on a simple test case and the application of the method to a 127 pin wire-wrap fuel bundle.

A coarse-grid-projection acceleration method for finite-element incompressible flow computations

NASA Astrophysics Data System (ADS)

Kashefi, Ali; Staples, Anne; FiN Lab Team

2015-11-01

Coarse grid projection (CGP) methodology provides a framework for accelerating computations by performing some part of the computation on a coarsened grid. We apply the CGP to pressure projection methods for finite element-based incompressible flow simulations. Based on it, the predicted velocity field data is restricted to a coarsened grid, the pressure is determined by solving the Poisson equation on the coarse grid, and the resulting data are prolonged to the preset fine grid. The contributions of the CGP method to the pressure correction technique are twofold: first, it substantially lessens the computational cost devoted to the Poisson equation, which is the most time-consuming part of the simulation process. Second, it preserves the accuracy of the velocity field. The velocity and pressure spaces are approximated by Galerkin spectral element using piecewise linear basis functions. A restriction operator is designed so that fine data are directly injected into the coarse grid. The Laplacian and divergence matrices are driven by taking inner products of coarse grid shape functions. Linear interpolation is implemented to construct a prolongation operator. A study of the data accuracy and the CPU time for the CGP-based versus non-CGP computations is presented. Laboratory for Fluid Dynamics in Nature.

iScreen: Image-Based High-Content RNAi Screening Analysis Tools.

PubMed

Zhong, Rui; Dong, Xiaonan; Levine, Beth; Xie, Yang; Xiao, Guanghua

2015-09-01

High-throughput RNA interference (RNAi) screening has opened up a path to investigating functional genomics in a genome-wide pattern. However, such studies are often restricted to assays that have a single readout format. Recently, advanced image technologies have been coupled with high-throughput RNAi screening to develop high-content screening, in which one or more cell image(s), instead of a single readout, were generated from each well. This image-based high-content screening technology has led to genome-wide functional annotation in a wider spectrum of biological research studies, as well as in drug and target discovery, so that complex cellular phenotypes can be measured in a multiparametric format. Despite these advances, data analysis and visualization tools are still largely lacking for these types of experiments. Therefore, we developed iScreen (image-Based High-content RNAi Screening Analysis Tool), an R package for the statistical modeling and visualization of image-based high-content RNAi screening. Two case studies were used to demonstrate the capability and efficiency of the iScreen package. iScreen is available for download on CRAN (http://cran.cnr.berkeley.edu/web/packages/iScreen/index.html). The user manual is also available as a supplementary document. © 2014 Society for Laboratory Automation and Screening.

Invertebrates Associated with Coarse Woody Debris in Streams, Upland Forests, and Wetlands: A Review

Treesearch

A. Braccia; D.P. Batzer

1999-01-01

We reviewed literature on the inbvertebrate groups associated with coarse woody debris in forests, streams, and wetlands, and contrasted patterns of invertebrate community development and wood decomposition among ecosystems.

Characterization and mechanical separation of metals from computer Printed Circuit Boards (PCBs) based on mineral processing methods.

PubMed

Sarvar, Mojtaba; Salarirad, Mohammad Mehdi; Shabani, Mohammad Amin

2015-11-01

In this paper, a novel mechanical process is proposed for enriching metal content of computer Printed Circuit Boards (PCBs). The PCBs are crushed and divided into three different size fractions namely: -0.59, +0.59 to 1.68 and +1.68 mm. Wet jigging and froth flotation methods are selected for metal enrichment. The coarse size fraction (+1.68 mm) is processed by jigging. The plastic free product is grinded and screened. The oversized product is separated as the first concentrate. It was rich of metal because the grinding process was selective. The undersized product is processed by froth flotation. Based on the obtained results, the middle size fraction (+0.59 to 1.68 mm) and the small size fraction (-0.59 mm) are processed by wet jigging and froth flotation respectively. The wet jigging process is optimized by investigating the effect of pulsation frequency and water flow rate. The results of examining the effect of particle size, solid to liquid ratio, conditioning time and using apolar collector showed that collectorless flotation is a promising method for separating nonmetals of PCBs. 95.6%, 97.5% and 85% of metal content of coarse size, middle size and small size fraction are recovered. The grades of obtained concentrates were 63.3%, 92.5% and 75% respectively. The total recovery is calculated as 95.64% and the grade of the final concentrate was 71.26%. Determining the grade of copper and gold in the final product reveals that 4.95% of copper and 24.46% of gold are lost during the concentration. The major part of the lost gold is accumulated in froth flotation tail. Copyright © 2015 Elsevier Ltd. All rights reserved.

De novo inference of protein function from coarse-grained dynamics.

PubMed

Bhadra, Pratiti; Pal, Debnath

2014-10-01

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 µs coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. © 2014 Wiley Periodicals, Inc.

Dispersing Zwitterions into Comb Polymers for Nonviral Transfection: Experiments and Molecular Simulation.

PubMed

Ghobadi, Ahmadreza F; Letteri, Rachel; Parelkar, Sangram S; Zhao, Yue; Chan-Seng, Delphine; Emrick, Todd; Jayaraman, Arthi

2016-02-08

Polymer-based gene delivery vehicles benefit from the presence of hydrophilic groups that mitigate the inherent toxicity of polycations and that provide tunable polymer-DNA binding strength and stable complexes (polyplexes). However, hydrophilic groups screen charge, and as such can reduce cell uptake and transfection efficiency. We report the effect of embedding zwitterionic sulfobetaine (SB) groups in cationic comb polymers, using a combination of experiments and molecular simulations. Ring-opening metathesis polymerization (ROMP) produced comb polymers with tetralysine (K4) and SB pendent groups. Dynamic light scattering, zeta potential measurements, and fluorescence-based experiments, together with coarse-grained molecular dynamics simulations, described the effect of SB groups on the size, shape, surface charge, composition, and DNA binding strength of polyplexes formed using these comb polymers. Experiments and simulations showed that increasing SB composition in the comb polymers decreased polymer-DNA binding strength, while simulations indicated that the SB groups distributed throughout the polyplex. This allows polyplexes to maintain a positive surface charge and provide high levels of gene expression in live cells. Notably, comb polymers with nearly 50 mol % SB form polyplexes that exhibit positive surface charge similarly as polyplexes formed from purely cationic comb polymers, indicating the ability to introduce an appreciable amount of SB functionality without screening surface charge. This integrated simulation-experimental study demonstrates the effectiveness of incorporating zwitterions in polyplexes, while guiding the design of new and effective gene delivery vectors.

DARPA Advanced Cannon Propellant (ACP) Library User’s Guide. Appendix F. Patents Dealing with Fluid Propellant Technology

DTIC Science & Technology

1981-06-15

tallisation temperature were added 0.4 parts of hydrox- mannitol, and 15.0 parts coarse aluminium powder were ypropylated guar gum which was allowed to...3.0 parts of8 15 coarse aluminium powder , 0.5 parts of hydroxy- propylated guar gum , 0.2 parts of zinc chromate and A slurry was prepared by the mixing...4 molecules of ethylene oxide), 10 parts of foaming agent and entrapped air bubbles into the comn- coarse aluminium powder , 0.7 parts of guar gum

Coarse-grained hydrodynamics from correlation functions

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

Palmer, Bruce

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configuration from a molecular dynamics simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilbrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is applied to some simple hydrodynamic cases to determine the feasibility of applying this to realistic nanoscale systems.

Characterization of fly ash from low-sulfur and high-sulfur coal sources: Partitioning of carbon and trace elements with particle size

USGS Publications Warehouse

Hower, J.C.; Trimble, A.S.; Eble, C.F.; Palmer, C.A.; Kolker, A.

1999-01-01

Fly ash samples were collected in November and December of 1994, from generating units at a Kentucky power station using high- and low-sulfur feed coals. The samples are part of a two-year study of the coal and coal combustion byproducts from the power station. The ashes were wet screened at 100, 200, 325, and 500 mesh (150, 75, 42, and 25 ??m, respectively). The size fractions were then dried, weighed, split for petrographic and chemical analysis, and analyzed for ash yield and carbon content. The low-sulfur "heavy side" and "light side" ashes each have a similar size distribution in the November samples. In contrast, the December fly ashes showed the trend observed in later months, the light-side ash being finer (over 20 % more ash in the -500 mesh [-25 ??m] fraction) than the heavy-side ash. Carbon tended to be concentrated in the coarse fractions in the December samples. The dominance of the -325 mesh (-42 ??m) fractions in the overall size analysis implies, though, that carbon in the fine sizes may be an important consideration in the utilization of the fly ash. Element partitioning follows several patterns. Volatile elements, such as Zn and As, are enriched in the finer sizes, particularly in fly ashes collected at cooler, light-side electrostatic precipitator (ESP) temperatures. The latter trend is a function of precipitation at the cooler-ESP temperatures and of increasing concentration with the increased surface area of the finest fraction. Mercury concentrations are higher in high-carbon fly ashes, suggesting Hg adsorption on the fly ash carbon. Ni and Cr are associated, in part, with the spinel minerals in the fly ash. Copyright ?? 1999 Taylor & Francis.

Assessment of the effects of horizontal grid resolution on long ...

EPA Pesticide Factsheets

The objective of this study is to determine the adequacy of using a relatively coarse horizontal resolution (i.e. 36 km) to simulate long-term trends of pollutant concentrations and radiation variables with the coupled WRF-CMAQ model. WRF-CMAQ simulations over the continental United State are performed over the 2001 to 2010 time period at two different horizontal resolutions of 12 and 36 km. Both simulations used the same emission inventory and model configurations. Model results are compared both in space and time to assess the potential weaknesses and strengths of using coarse resolution in long-term air quality applications. The results show that the 36 km and 12 km simulations are comparable in terms of trends analysis for both pollutant concentrations and radiation variables. The advantage of using the coarser 36 km resolution is a significant reduction of computational cost, time and storage requirement which are key considerations when performing multiple years of simulations for trend analysis. However, if such simulations are to be used for local air quality analysis, finer horizontal resolution may be beneficial since it can provide information on local gradients. In particular, divergences between the two simulations are noticeable in urban, complex terrain and coastal regions. The National Exposure Research Laboratory’s Atmospheric Modeling Division (AMAD) conducts research in support of EPA’s mission to protect human health and the environment.

KOSMOS: a universal morph server for nucleic acids, proteins and their complexes

PubMed Central

Seo, Sangjae; Kim, Moon Ki

2012-01-01

KOSMOS is the first online morph server to be able to address the structural dynamics of DNA/RNA, proteins and even their complexes, such as ribosomes. The key functions of KOSMOS are the harmonic and anharmonic analyses of macromolecules. In the harmonic analysis, normal mode analysis (NMA) based on an elastic network model (ENM) is performed, yielding vibrational modes and B-factor calculations, which provide insight into the potential biological functions of macromolecules based on their structural features. Anharmonic analysis involving elastic network interpolation (ENI) is used to generate plausible transition pathways between two given conformations by optimizing a topology-oriented cost function that guarantees a smooth transition without steric clashes. The quality of the computed pathways is evaluated based on their various facets, including topology, energy cost and compatibility with the NMA results. There are also two unique features of KOSMOS that distinguish it from other morph servers: (i) the versatility in the coarse-graining methods and (ii) the various connection rules in the ENM. The models enable us to analyze macromolecular dynamics with the maximum degrees of freedom by combining a variety of ENMs from full-atom to coarse-grained, backbone and hybrid models with one connection rule, such as distance-cutoff, number-cutoff or chemical-cutoff. KOSMOS is available at http://bioengineering.skku.ac.kr/kosmos. PMID:22669912

Longitudinal Commercial Claims-Based Cost Analysis of Diabetic Retinopathy Screening Patterns.

PubMed

Fitch, Kathryn; Weisman, Thomas; Engel, Tyler; Turpcu, Adam; Blumen, Helen; Rajput, Yamina; Dave, Purav

2015-09-01

Diabetic retinopathy is one of the most common complications of diabetes. The screening of patients with diabetes to detect retinopathy is recommended by several professional guidelines but is an underutilized service. To analyze the relationship between the frequency of retinopathy screening and the cost of care in adult patients with diabetes. Truven Health MarketScan commercial databases (2000-2013) were used to identify the diabetic population aged 18 to 64 years for the performance of a 2001-2013 annual trend analysis of patients with type 1 and type 2 diabetes and a 10-year longitudinal analysis of patients with newly diagnosed type 2 diabetes. In the trend analysis, the prevalence of diabetes, screening rate, and allowed cost per member per month (PMPM) were calculated. In the longitudinal analysis, data from 4 index years (2001-2004) of patients newly diagnosed with type 2 diabetes were combined, and the costs were adjusted to be comparable to the 2004 index year cohort, using the annual diabetes population cost trends calculated in the trend analysis. The longitudinal population was segmented into the number of years of diabetic retinopathy screening (ie, 0, 1-4, 5-7, and 8-10), and the relationship between the years of screening and the PMPM allowed costs was analyzed. The difference in mean incremental cost between years 1 and 10 in each of the 4 cohorts was compared after adjusting for explanatory variables. In the trend analysis, between 2001 and 2013, the prevalence of diabetes increased from 3.93% to 5.08%, retinal screening increased from 26.27% to 29.58%, and the average total unadjusted allowed cost of care for each patient with diabetes increased from $822 to $1395 PMPM. In the longitudinal analysis, the difference between the screening cohorts' mean incremental cost increase was $185 between the 0- and 1-4-year cohorts (P <.003) and $202 between the 0- and 5-7-year cohorts (P <.023). The cost differences between the other cohorts, including $217 between the 0- and 8-10-year cohorts (P <.066), were not statistically significant. Based on our analysis, the annual retinopathy screening rate for patients with diabetes has remained low since 2001, and has been well below the guideline-recommended screening levels. For patients with type 2 diabetes, the mean increase in healthcare expenditures over a 10-year period after diagnosis is not statistically different among those with various retinopathy screening rates, although the increase in healthcare spending is lower for patients with diabetes who were not screened for retinopathy compared with patients who did get screened.

The balance between keystone clustering and bed roughness in experimental step-pool stabilization

NASA Astrophysics Data System (ADS)

Johnson, J. P.

2016-12-01

Predicting how mountain channels will respond to environmental perturbations such as floods requires an improved quantitative understanding of morphodynamic feedbacks among bed topography, surface grain size and sediment sorting. In boulder-rich gravel streams, transport and sorting often lead to the development of step pool morphologies, which are expressed both in bed topography and coarse grain clustering. Bed stability is difficult to measure, and is sometimes inferred from the presence of step pools. I use scaled flume experiments to explore feedbacks among surface grain sizes, coarse grain clustering, bed roughness and hydraulic roughness during progressive bed stabilization and over a range of sediment transport rates. While grain clusters are sometimes identified by subjective interpretation, I quantify the degree of coarse surface grain clustering using spatial statistics, including a novel normalization of Ripley's K function. This approach is objective and provides information on the strength of clustering over a range of length scales. Flume experiments start with an initial bed surface with a broad grain size distribution and spatially random positions. Flow causes the bed surface to progressively stabilize in response to erosion, surface coarsening, roughening and grain reorganization. At 95% confidence, many but not all beds stabilized with coarse grains becoming more clustered than complete spatial randomness (CSR). I observe a tradeoff between topographic roughness and clustering. Beds that stabilized with higher degrees of coarse-grain clustering were topographically smoother, and vice-versa. Initial conditions influenced the degree of clustering at stability: Beds that happened to have fewer initial coarse grains had more coarse grain reorganization during stabilization, leading to more clustering. Finally, regressions demonstrate that clustering statistics actually predict hydraulic roughness significantly better than does D84 (the size at which 84% of grains are smaller). In the experimental data, the spatial organization of surface grains is a stronger control on flow characteristics than the size of surface grains.

Possibilities for preservation of coarse particles in pelleting process to improve feed quality characteristics.

PubMed

Vukmirović, D; Fišteš, A; Lević, J; Čolović, R; Rakić, D; Brlek, T; Banjac, V

2017-10-01

Poultry diets are mainly used in pelleted form because pellets have many advantages compared to mash feed. On the other hand, pelleting causes reduction of feed particle size. The aim of this research was to investigate the possibility of increasing the content of coarse particles in pellets, and, at the same time, to produce pellets with satisfactory quality. In this research, the three grinding treatments of corn were applied using hammer mill with three sieve openings diameter: 3 mm (HM-3), 6 mm (HM-6) and 9 mm (HM-9). These grinding treatments were combined in pelleting process with three gaps between rollers and the die of pellet press (roller-die gap, RDG) (0.30, 1.15 and 2.00 mm) and three moisture contents of the pelleted material (14.5, 16.0 and 17.5%). The increased coarseness of grinding by the hammer mill resulted in the increased amount of coarse particles in pellets, especially when the smallest RDG was applied (0.30 mm), but pellet quality was greatly reduced. Increasing of RDG improved the quality of pellets produced from coarsely ground corn, but reduced the content of coarse particles in pellets and increased specific energy consumption of the pellet press. Increasing the moisture content of material to be pelleted (MC) significantly reduced energy consumption of the pellet press, but there was no significant influence of MC on particle size after pelleting and on the pellet quality. The optimal values of the pelleting process parameters were determined using desirability function method. The results of optimization process showed that to achieve the highest possible quantity of coarse particles in the pellets, and to produce pellets of satisfactory quality, with the lowest possible energy consumption of the pellet press, the coarsest grinding on hammer mill (HM-9), the largest RDG (2 mm) and the highest MC (17.5%) should be applied. Journal of Animal Physiology and Animal Nutrition © 2016 Blackwell Verlag GmbH.

Diet structure, butyric acid, and fermentable carbohydrates influence growth performance, gut morphology, and cecal fermentation characteristics in broilers.

PubMed

Qaisrani, S N; van Krimpen, M M; Kwakkel, R P; Verstegen, M W A; Hendriks, W H

2015-09-01

An experiment with 288 male (Ross 308) 1-d-old broilers was conducted to test the hypothesis that a coarse diet supplemented with butyric acid (BA) and fermentable carbohydrates (FC) improves performance of broilers with a poorly digestible protein source. The interaction effects of diet structure (fine or coarse), FC supplementation (with or without), and BA supplementation (with or without) in a poorly digestible diet based on rapeseed meal (RSM) were tested in a factorial arrangement of 8 (2×2×2) dietary treatments. The coarseness of the diet affected feed intake (FI) (P<0.001), BW gain (P=0.001), and the feed conversion ratio (FCR) (P=0.001) positively. Broilers fed the coarse diets had, on average, 14% heavier gizzards and 11, 7, 5, and 6% lower relative empty weights of the crop, duodenum, jejunum, and ileum, respectively, compared with those fed the fine diets. Dietary coarseness resulted in, on average, 6% greater ileal protein digestibility, 20% lower gizzard pH, 19% greater villus height, 18% lower crypt depth, and 23% reduced cecal branched chain fatty acids (BCFA) compared with chickens fed the fine diets. Broilers fed BA-supplemented diets had an improved FCR (P=0.004) and decreased crypt depth (P<0.001) compared with those fed diets without BA. Fermentable carbohydrate supplementation did not influence growth performance, gut development, or contents of total BCFA and total biogenic amines in the cecal digesta (P>0.05). Supplementation with FC, however, decreased the cecal concentration of spermine by approximately 31% compared with broilers fed diets without FC (P=0.002). In conclusion, feeding a coarse diet supplemented with BA improved performance of broilers fed a diet containing a poorly digestible protein source. The negative effects of a poorly digestible protein source can thus be partly counterbalanced by coarse grinding and BA supplementation in the diet. © The Author 2015. Published by Oxford University Press on behalf of Poultry Science Association.

Cell-Specific Oxidative Stress and Cytotoxicity after Wildfire Coarse Particulate Matter Instillation into Mouse Lung

PubMed Central

Williams, Keisha M.; Franzi, Lisa M.; Last, Jerold A.

2012-01-01

Our previous work has shown that coarse particulate matter (PM10-2.5) from wildfire smoke is more toxic to lung macrophages on an equal dose (by mass) basis than coarse PM isolated from normal ambient air, as evidenced by decreased numbers of macrophages in lung lavage fluid 6 and 24 hours after PM instillation into mouse lungs in vivo and by cytotoxicity to a macrophage cell line observed directly in vitro. We hypothesized that pulmonary macrophages from mice instilled with wildfire coarse PM would undergo more cytotoxicity than macrophages from controls, and that there would be an increase in oxidative stress in their lungs. Cytotoxicity was quantified as decreased viable macrophages and increased percentages of dead macrophages in the bronchoalveolar lavage fluid (BALF) of mice instilled with wildfire coarse PM. At one hour after PM instillation, we observed both decreased numbers of viable macrophages and increased dead macrophage percentages as compared to controls. An increase in free isoprostanes, an indicator of oxidative stress, from control values of 28.1±3.2 pg/mL to 83.9±12.2 pg/mL was observed a half-hour after PM instillation. By one hour after PM instillation, isoprostane values had returned to 30.4±7.6pg/mL, not significantly different from control concentrations. Lung sections from mice instilled with wildfire coarse PM showed rapid Clara cell responses, with decreased intracellular staining for the Clara cell secretory protein CCSP 1 hour after wildfire PM instillation. In conclusion, very rapid cytotoxicity occurs in pulmonary macrophages and oxidative stress responses are seen 0.5-1 hour after wildfire coarse PM instillation. These results define early cellular and biochemical events occurring in vivo and support the hypothesis that oxidative stress-mediated macrophage toxicity plays a key role in the initial response of the mouse lung to wildfire PM exposure. PMID:23142465

Cell-specific oxidative stress and cytotoxicity after wildfire coarse particulate matter instillation into mouse lung.

PubMed

Williams, Keisha M; Franzi, Lisa M; Last, Jerold A

2013-01-01

Our previous work has shown that coarse particulate matter (PM(10-2.5)) from wildfire smoke is more toxic to lung macrophages on an equal dose (by mass) basis than coarse PM isolated from normal ambient air, as evidenced by decreased numbers of macrophages in lung lavage fluid 6 and 24hours after PM instillation into mouse lungs in vivo and by cytotoxicity to a macrophage cell line observed directly in vitro. We hypothesized that pulmonary macrophages from mice instilled with wildfire coarse PM would undergo more cytotoxicity than macrophages from controls, and that there would be an increase in oxidative stress in their lungs. Cytotoxicity was quantified as decreased viable macrophages and increased percentages of dead macrophages in the bronchoalveolar lavage fluid (BALF) of mice instilled with wildfire coarse PM. At 1hour after PM instillation, we observed both decreased numbers of viable macrophages and increased dead macrophage percentages as compared to controls. An increase in free isoprostanes, an indicator of oxidative stress, from control values of 28.1±3.2pg/mL to 83.9±12.2pg/mL was observed a half-hour after PM instillation. By 1hour after PM instillation, isoprostane values had returned to 30.4±7.6pg/mL, not significantly different from control concentrations. Lung sections from mice instilled with wildfire coarse PM showed rapid Clara cell responses, with decreased intracellular staining for the Clara cell secretory protein CCSP 1hour after wildfire PM instillation. In conclusion, very rapid cytotoxicity occurs in pulmonary macrophages and oxidative stress responses are seen 0.5-1hour after wildfire coarse PM instillation. These results define early cellular and biochemical events occurring in vivo and support the hypothesis that oxidative stress-mediated macrophage toxicity plays a key role in the initial response of the mouse lung to wildfire PM exposure. Copyright © 2012 Elsevier Inc. All rights reserved.

Diet structure, butyric acid, and fermentable carbohydrates influence growth performance, gut morphology, and cecal fermentation characteristics in broilers

PubMed Central

Qaisrani, S. N.; van Krimpen, M. M.; Kwakkel, R. P.; Verstegen, M. W. A.; Hendriks, W. H.

2015-01-01

An experiment with 288 male (Ross 308) 1-d-old broilers was conducted to test the hypothesis that a coarse diet supplemented with butyric acid (BA) and fermentable carbohydrates (FC) improves performance of broilers with a poorly digestible protein source. The interaction effects of diet structure (fine or coarse), FC supplementation (with or without), and BA supplementation (with or without) in a poorly digestible diet based on rapeseed meal (RSM) were tested in a factorial arrangement of 8 (2 × 2 × 2) dietary treatments. The coarseness of the diet affected feed intake (FI) (P < 0.001), BW gain (P = 0.001), and the feed conversion ratio (FCR) (P = 0.001) positively. Broilers fed the coarse diets had, on average, 14% heavier gizzards and 11, 7, 5, and 6% lower relative empty weights of the crop, duodenum, jejunum, and ileum, respectively, compared with those fed the fine diets. Dietary coarseness resulted in, on average, 6% greater ileal protein digestibility, 20% lower gizzard pH, 19% greater villus height, 18% lower crypt depth, and 23% reduced cecal branched chain fatty acids (BCFA) compared with chickens fed the fine diets. Broilers fed BA-supplemented diets had an improved FCR (P = 0.004) and decreased crypt depth (P < 0.001) compared with those fed diets without BA. Fermentable carbohydrate supplementation did not influence growth performance, gut development, or contents of total BCFA and total biogenic amines in the cecal digesta (P > 0.05). Supplementation with FC, however, decreased the cecal concentration of spermine by approximately 31% compared with broilers fed diets without FC (P = 0.002). In conclusion, feeding a coarse diet supplemented with BA improved performance of broilers fed a diet containing a poorly digestible protein source. The negative effects of a poorly digestible protein source can thus be partly counterbalanced by coarse grinding and BA supplementation in the diet. PMID:26175052

Fine-coarse semantic processing in schizophrenia: a reversed pattern of hemispheric dominance.

PubMed

Zeev-Wolf, Maor; Goldstein, Abraham; Levkovitz, Yechiel; Faust, Miriam

2014-04-01

Left lateralization for language processing is a feature of neurotypical brains. In individuals with schizophrenia, lack of left lateralization is associated with the language impairments manifested in this population. Beeman׳s fine-coarse semantic coding model asserts left hemisphere specialization in fine (i.e., conventionalized) semantic coding and right hemisphere specialization in coarse (i.e., non-conventionalized) semantic coding. Applying this model to schizophrenia would suggest that language impairments in this population are a result of greater reliance on coarse semantic coding. We investigated this hypothesis and examined whether a reversed pattern of hemispheric involvement in fine-coarse semantic coding along the time course of activation could be detected in individuals with schizophrenia. Seventeen individuals with schizophrenia and 30 neurotypical participants were presented with two word expressions of four types: literal, conventional metaphoric, unrelated (exemplars of fine semantic coding) and novel metaphoric (an exemplar of coarse semantic coding). Expressions were separated by either a short (250 ms) or long (750 ms) delay. Findings indicate that whereas during novel metaphor processing, controls displayed a left hemisphere advantage at 250 ms delay and right hemisphere advantage at 750 ms, individuals with schizophrenia displayed the opposite. For conventional metaphoric and unrelated expressions, controls showed left hemisphere advantage across times, while individuals with schizophrenia showed a right hemisphere advantage. Furthermore, whereas individuals with schizophrenia were less accurate than control at judging literal, conventional metaphoric and unrelated expressions they were more accurate when judging novel metaphors. Results suggest that individuals with schizophrenia display a reversed pattern of lateralization for semantic coding which causes them to rely more heavily on coarse semantic coding. Thus, for individuals with schizophrenia, speech situation are always non-conventional, compelling them to constantly seek for meanings and prejudicing them toward novel or atypical speech acts. This, in turn, may disadvantage them in conventionalized communication and result in language impairment. Copyright © 2014 Elsevier Ltd. All rights reserved.

Soricid response to coarse woody debris manipulations in Coastal Plain loblolly pine forests.

Treesearch

Kurtis R. Moseley; Audrey K. Owens; Steven B. Castleberry; W. Mark Ford; John C. Kilgo; Timothy S. McCay

2009-01-01

We assessed shrew (soricids) response to coarse woody debris (CWD) manipulations in managed upland loblolly pine (Pinus taeda) stands in the upper Coastal Plain of South Carolina over multiple years and...

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

Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr; Harmandaris, Vagelis, E-mail: harman@uoc.gr; Institute of Applied and Computational Mathematics

Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce 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 grainingmore » mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems.« less

A Hybrid Coarse-graining Approach for Lipid Bilayers at Large Length and Time Scales

PubMed Central

Ayton, Gary S.; Voth, Gregory A.

2009-01-01

A hybrid analytic-systematic (HAS) coarse-grained (CG) lipid model is developed and employed in a large-scale simulation of a liposome. The methodology is termed hybrid analyticsystematic as one component of the interaction between CG sites is variationally determined from the multiscale coarse-graining (MS-CG) methodology, while the remaining component utilizes an analytic potential. The systematic component models the in-plane center of mass interaction of the lipids as determined from an atomistic-level MD simulation of a bilayer. The analytic component is based on the well known Gay-Berne ellipsoid of revolution liquid crystal model, and is designed to model the highly anisotropic interactions at a highly coarse-grained level. The HAS CG approach is the first step in an “aggressive” CG methodology designed to model multi-component biological membranes at very large length and timescales. PMID:19281167

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.

Fast coarse-fine locating method for φ-OTDR.

PubMed

Mei, Xuanwei; Pang, Fufei; Liu, Huanhuan; Yu, Guoqin; Shao, Yuying; Qian, Tianyu; Mou, Chengbo; Lv, Longbao; Wang, Tingyun

2018-02-05

We proposed and demonstrated a coarse-fine method to achieve fast locating of external vibration for the phase-sensitive optical time-domain reflectometer (φ-OTDR) sensing system. Firstly, the acquired backscattered traces from heterodyne coherent φ-OTDR systems are spatially divided into a few segments along a sensing fiber for coarse locating, and most of the acquired data can be excluded by comparing the phase difference between the endpoints in adjacent segments. Secondly, the amplitude-based locating is implemented within the target segments for fine locating. By using the proposed coarse-fine locating method, we have numerically and experimentally investigated a distributed vibration sensor based on the heterodyne coherent φ-OTDR system with a 50-km-long sensing fiber. We find that the computation cost of signal processing for locating is significantly reduced in the long-haul sensing fiber, showing a potential application in real-time locating of external vibration.

Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

PubMed

Shen, Lin; Hu, Hao

2014-06-10

We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

PubMed Central

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

2013-01-01

A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridization rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering. PMID:24116642

A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters: Theory and application to microfilaments

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

Li, Tong; Gu, YuanTong, E-mail: yuantong.gu@qut.edu.au

As all-atom molecular dynamics method is limited by its enormous computational cost, various coarse-grained strategies have been developed to extend the length scale of soft matters in the modeling of mechanical behaviors. However, the classical thermostat algorithm in highly coarse-grained molecular dynamics method would underestimate the thermodynamic behaviors of soft matters (e.g. microfilaments in cells), which can weaken the ability of materials to overcome local energy traps in granular modeling. Based on all-atom molecular dynamics modeling of microfilament fragments (G-actin clusters), a new stochastic thermostat algorithm is developed to retain the representation of thermodynamic properties of microfilaments at extra coarse-grainedmore » level. The accuracy of this stochastic thermostat algorithm is validated by all-atom MD simulation. This new stochastic thermostat algorithm provides an efficient way to investigate the thermomechanical properties of large-scale soft matters.« less

Optimal Design of Experiments by Combining Coarse and Fine Measurements

NASA Astrophysics Data System (ADS)

Lee, Alpha A.; Brenner, Michael P.; Colwell, Lucy J.

2017-11-01

In many contexts, it is extremely costly to perform enough high-quality experimental measurements to accurately parametrize a predictive quantitative model. However, it is often much easier to carry out large numbers of experiments that indicate whether each sample is above or below a given threshold. Can many such categorical or "coarse" measurements be combined with a much smaller number of high-resolution or "fine" measurements to yield accurate models? Here, we demonstrate an intuitive strategy, inspired by statistical physics, wherein the coarse measurements are used to identify the salient features of the data, while the fine measurements determine the relative importance of these features. A linear model is inferred from the fine measurements, augmented by a quadratic term that captures the correlation structure of the coarse data. We illustrate our strategy by considering the problems of predicting the antimalarial potency and aqueous solubility of small organic molecules from their 2D molecular structure.

Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications.

PubMed

Henrich, Oliver; Gutiérrez Fosado, Yair Augusto; Curk, Tine; Ouldridge, Thomas E

2018-05-10

During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.

The basis of orientation decoding in human primary visual cortex: fine- or coarse-scale biases?

PubMed

Maloney, Ryan T

2015-01-01

Orientation signals in human primary visual cortex (V1) can be reliably decoded from the multivariate pattern of activity as measured with functional magnetic resonance imaging (fMRI). The precise underlying source of these decoded signals (whether by orientation biases at a fine or coarse scale in cortex) remains a matter of some controversy, however. Freeman and colleagues (J Neurosci 33: 19695-19703, 2013) recently showed that the accuracy of decoding of spiral patterns in V1 can be predicted by a voxel's preferred spatial position (the population receptive field) and its coarse orientation preference, suggesting that coarse-scale biases are sufficient for orientation decoding. Whether they are also necessary for decoding remains an open question, and one with implications for the broader interpretation of multivariate decoding results in fMRI studies. Copyright © 2015 the American Physiological Society.

Investigation of strength characteristics of aluminum alloy under dynamic tension

NASA Astrophysics Data System (ADS)

Evstifeev, A. D.

2018-04-01

The study presents the results of experimental-theoretical analysis for aluminum alloy subjected to static and dynamic tension on samples of different types. The material was tested under initial coarse-grained (CG) and in ultrafine-grained (UFG) condition. The time dependence of the tensile strength is calculated using an incubation time fracture criterion based on a set of fixed constants of the material.

Seasonal variability of PM2.5 and PM10 composition and sources in an urban background site in Southern Italy.

PubMed

Cesari, D; De Benedetto, G E; Bonasoni, P; Busetto, M; Dinoi, A; Merico, E; Chirizzi, D; Cristofanelli, P; Donateo, A; Grasso, F M; Marinoni, A; Pennetta, A; Contini, D

2018-01-15

Comparison of fine and coarse fractions in terms of sources and dynamics is scarce in southeast Mediterranean countries; differences are relevant because of the importance of natural sources like sea spray and Saharan dust advection, because most of the monitoring networks are limited to PM 10 . In this work, the main seasonal variabilities of sources and processes involving fine and coarse PM (particulate matter) were studied at the Environmental-Climate Observatory of Lecce (Southern Italy). Simultaneous PM 2.5 and PM 10 samples were collected between July 2013 and July 2014 and chemically analysed to determine concentrations of several species: OC (organic carbon) and EC (elemental carbon) via thermo-optical analysis, 9 major ions via IC, and 23 metals via ICP-MS. Data was processed through mass closure analysis and Positive Matrix Factorization (PMF) receptor model characterizing seasonal variabilities of nine sources contributions. Organic and inorganic secondary aerosol accounts for 43% of PM 2.5 and 12% of PM 2.5-10 with small seasonal changes. SIA (secondary inorganic aerosol) seasonal pattern is opposite to that of SOC (secondary organic carbon). SOC is larger during the cold period, sulphate (the major contributor to SIA) is larger during summer. Two forms of nitrate were identified: NaNO 3 , correlated with chloride depletion and aging of sea-spray, mainly present in PM 2.5-10 ; NH 4 NO 3 more abundant in PM 2.5 . Biomass burning is a relevant source with larger contribution during autumn and winter because of the influence of domestic heating, however, is not negligible in spring and summer, because of the contributions of fires and agricultural practices. Mass closure analysis and PMF results identify two soil sources: crustal associated to long range transport and carbonates associated to local resuspended dust. Both sources contributes to the coarse fraction and have different dynamics with crustal source contributing mainly in high winds from SE conditions and carbonates during high winds from North direction. Copyright © 2017 Elsevier B.V. All rights reserved.