Free energy calculations to estimate ligand-binding affinities in structure-based drug design.
Reddy, M Rami; Reddy, C Ravikumar; Rathore, R S; Erion, Mark D; Aparoy, P; Reddy, R Nageswara; Reddanna, P
2014-01-01
Post-genomic era has led to the discovery of several new targets posing challenges for structure-based drug design efforts to identify lead compounds. Multiple computational methodologies exist to predict the high ranking hit/lead compounds. Among them, free energy methods provide the most accurate estimate of predicted binding affinity. Pathway-based Free Energy Perturbation (FEP), Thermodynamic Integration (TI) and Slow Growth (SG) as well as less rigorous end-point methods such as Linear interaction energy (LIE), Molecular Mechanics-Poisson Boltzmann./Generalized Born Surface Area (MM-PBSA/GBSA) and λ-dynamics have been applied to a variety of biologically relevant problems. The recent advances in free energy methods and their applications including the prediction of protein-ligand binding affinity for some of the important drug targets have been elaborated. Results using a recently developed Quantum Mechanics (QM)/Molecular Mechanics (MM) based Free Energy Perturbation (FEP) method, which has the potential to provide a very accurate estimation of binding affinities to date has been discussed. A case study for the optimization of inhibitors for the fructose 1,6- bisphosphatase inhibitors has been described. PMID:23947646
Ga(+) Basicity and Affinity Scales Based on High-Level Ab Initio Calculations.
Brea, Oriana; Mó, Otilia; Yáñez, Manuel
2015-10-26
The structure, relative stability and bonding of complexes formed by the interaction between Ga(+) and a large set of compounds, including hydrocarbons, aromatic systems, and oxygen-, nitrogen-, fluorine and sulfur-containing Lewis bases have been investigated through the use of the high-level composite ab initio Gaussian-4 theory. This allowed us to establish rather accurate Ga(+) cation affinity (GaCA) and Ga(+) cation basicity (GaCB) scales. The bonding analysis of the complexes under scrutiny shows that, even though one of the main ingredients of the Ga(+) -base interaction is electrostatic, it exhibits a non-negligible covalent character triggered by the presence of the low-lying empty 4p orbital of Ga(+) , which favors a charge donation from occupied orbitals of the base to the metal ion. This partial covalent character, also observed in AlCA scales, is behind the dissimilarities observed when GaCA are compared with Li(+) cation affinities, where these covalent contributions are practically nonexistent. Quite unexpectedly, there are some dissimilarities between several Ga(+) -complexes and the corresponding Al(+) -analogues, mainly affecting the relative stability of π-complexes involving aromatic compounds.
Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model
Muddana, Hari S.; Gilson, Michael K.
2012-01-01
The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy functi...
Reflectable bases for affine reflection systems
Azam, Saeid; Yousofzadeh, Malihe
2011-01-01
The notion of a "root base" together with its geometry plays a crucial role in the theory of finite and affine Lie theory. However, it is known that such a notion does not exist for the recent generalizations of finite and affine root systems such as extended affine root systems and affine reflection systems. As an alternative, we introduce the notion of a "reflectable base", a minimal subset $\\Pi$ of roots such that the non-isotropic part of the root system can be recovered by reflecting roots of $\\Pi$ relative to the hyperplanes determined by $\\Pi$. We give a full characterization of reflectable bases for tame irreducible affine reflection systems of reduced types, excluding types $E_{6,7,8}$. As a byproduct of our results, we show that if the root system under consideration is locally finite then any reflectable base is an integral base.
Protein-protein binding affinities calculated using the LIE method
Andberg, Tor Arne Heim
2011-01-01
Absolute binding free energies for the third domain of the turkey ovomucoid inhibitor in complex with Streptomyces griseus proteinase B and porcine pancreatic elastase has been calculated using the linear interaction energy method.
Stanke, Monika; Kedziera, Dariusz; Bubin, Sergiy; Adamowicz, Ludwik
2007-10-01
Explicitly correlated Gaussian functions have been used to perform very accurate variational calculations for the ground states of (7)Li and (7)Li(-). The nuclear motion has been explicitly included in the calculations (i.e., they have been done without assuming the Born-Oppenheimer (BO) approximation). An approach based on the analytical energy gradient calculated with respect to the Gaussian exponential parameters was employed. This led to a noticeable improvement of the previously determined variational upper bound to the nonrelativistic energy of Li(-). The Li energy obtained in the calculations matches those of the most accurate results obtained with Hylleraas functions. The finite-mass (non-BO) wave functions were used to calculate the alpha(2) relativistic corrections (alpha=1c). With those corrections and the alpha(3) and alpha(4) corrections taken from Pachucki and Komasa [J. Chem. Phys. 125, 204304 (2006)], the electron affinity (EA) of (7)Li was determined. It agrees very well with the most recent experimental EA. PMID:17919011
Genetic Algorithm-based Affine Parameter Estimation for Shape Recognition
Directory of Open Access Journals (Sweden)
Yuxing Mao
2014-06-01
Full Text Available Shape recognition is a classically difficult problem because of the affine transformation between two shapes. The current study proposes an affine parameter estimation method for shape recognition based on a genetic algorithm (GA. The contributions of this study are focused on the extraction of affine- invariant features, the individual encoding scheme, and the fitness function construction policy for a GA. First, the affine-invariant characteristics of the centroid distance ratios (CDRs of any two opposite contour points to the barycentre are analysed. Using different intervals along the azimuth angle, the different numbers of CDRs of two candidate shapes are computed as representations of the shapes, respectively. Then, the CDRs are selected based on predesigned affine parameters to construct the fitness function. After that, a GA is used to search for the affine parameters with optimal matching between candidate shapes, which serve as actual descriptions of the affine transformation between the shapes. Finally, the CDRs are resampled based on the estimated parameters to evaluate the similarity of the shapes for classification. The experimental results demonstrate the robust performance of the proposed method in shape recognition with translation, scaling, rotation and distortion.
Betowski, Leon D; Enlow, Mark; Riddick, Lee; Aue, Donald H
2006-11-30
Electron affinities (EAs) and free energies for electron attachment (DeltaGo(a,298K)) have been directly calculated for 45 polynuclear aromatic hydrocarbons (PAHs) and related molecules by a variety of theoretical methods, with standard regression errors of about 0.07 eV (mean unsigned error = 0.05 eV) at the B3LYP/6-31 + G(d,p) level and larger errors with HF or MP2 methods or using Koopmans' Theorem. Comparison of gas-phase free energies with solution-phase reduction potentials provides a measure of solvation energy differences between the radical anion and neutral PAH. A simple Born-charging model approximates the solvation effects on the radical anions, leading to a good correlation with experimental solvation energy differences. This is used to estimate unknown or questionable EAs from reduction potentials. Two independent methods are used to predict DeltaGo(a,298K) values: (1) based upon DFT methods, or (2) based upon reduction potentials and the Born model. They suggest reassignments or a resolution of conflicting experimental EAs for nearly one-half (17 of 38) of the PAH molecules for which experimental EAs have been reported. For the antiaromatic molecules, 1,3,5-tri-tert-butylpentalene and the dithia-substituted cyclobutadiene 1, the reduction potentials lead to estimated EAs close to those expected from DFT calculations and provide a basis for the prediction of the EAs and reduction potentials of pentalene and cyclobutadiene. The Born model has been used to relate the electrostatic solvation energies of PAH and hydrocarbon radical anions, and spherical halide anions, alkali metal cations, and ammonium ions to effective ionic radii from DFT electron-density envelopes. The Born model used for PAHs has been successfully extended here to quantitatively explain the solvation energy of the C60 radical anion.
Hyperspherical Calculations on Electron Affinity and Geometry for Li-and Na-
Institute of Scientific and Technical Information of China (English)
HAN Hui-Li; ZHANG Xian-zhou; SHI Ting-Yun
2007-01-01
Using a model potential to describe the interaction between the core and the valence electron,we perform hyperspherical calculations for electron affinity and geometry of the weakly bound Li-and Na-systems.In ourcalculation.channel functions are expanded in terms of B-splines.Using the special properties of B-splines,we make the knot distributions more precisely,characterizing the behaviour of channel functions.This improves the convergence greatly.Our results are in good agreement with the other theoretical and experimental values.
DFT Calculations of the Ionization Potential and Electron Affinity of Alaninamide
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
Adiabatic and vertical ionization potentials (IPs) and valence electron affinities (EAs) of alaninamide in gas phase have been determined using density functional theory (BLYP, B3LYP, B3P86) methods with 6-311++G(d, p) basis set, respectively. IPs and EAs of alaninamide in solutions have been calculated at the B3LYP/6-311++G(d, p) level. Five possible conformers of alaninamide and their charged states have been optimized employing density functional theory B3LYP method with 6-311++(d, p) basis set, respectively.
Enhancing Community Detection By Affinity-based Edge Weighting Scheme
Energy Technology Data Exchange (ETDEWEB)
Yoo, Andy [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sanders, Geoffrey [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Henson, Van [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vassilevski, Panayot [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-10-05
Community detection refers to an important graph analytics problem of finding a set of densely-connected subgraphs in a graph and has gained a great deal of interest recently. The performance of current community detection algorithms is limited by an inherent constraint of unweighted graphs that offer very little information on their internal community structures. In this paper, we propose a new scheme to address this issue that weights the edges in a given graph based on recently proposed vertex affinity. The vertex affinity quantifies the proximity between two vertices in terms of their clustering strength, and therefore, it is ideal for graph analytics applications such as community detection. We also demonstrate that the affinity-based edge weighting scheme can improve the performance of community detection algorithms significantly.
Semisupervised Clustering for Networks Based on Fast Affinity Propagation
Directory of Open Access Journals (Sweden)
Mu Zhu
2013-01-01
Full Text Available Most of the existing clustering algorithms for networks are unsupervised, which cannot help improve the clustering quality by utilizing a small number of prior knowledge. We propose a semisupervised clustering algorithm for networks based on fast affinity propagation (SCAN-FAP, which is essentially a kind of similarity metric learning method. Firstly, we define a new constraint similarity measure integrating the structural information and the pairwise constraints, which reflects the effective similarities between nodes in networks. Then, taking the constraint similarities as input, we propose a fast affinity propagation algorithm which keeps the advantages of the original affinity propagation algorithm while increasing the time efficiency by passing only the messages between certain nodes. Finally, by extensive experimental studies, we demonstrate that the proposed algorithm can take fully advantage of the prior knowledge and improve the clustering quality significantly. Furthermore, our algorithm has a superior performance to some of the state-of-art approaches.
Canonical bases and affine Hecke algebras of type B
Varagnolo, Michela
2009-01-01
We prove a series of conjectures of Enomoto and Kashiwara on canonical bases and branching rules of affine Hecke algebras of type B. The main ingredient of the proof is a new graded Ext-algebra associated with quiver with involutions that we compute explicitly.
Calculation of the enthalpies of formation and proton affinities of some isoquinoline derivatives
Energy Technology Data Exchange (ETDEWEB)
Namazian, Mansoor [ARC Centre of Excellence for Free-Radical Chemistry and Biotechnology, Research School of Chemistry, Australian National University, Canberra ACT 0200 (Australia)], E-mail: namazian@rsc.anu.edu.au; Coote, Michelle L. [ARC Centre of Excellence for Free-Radical Chemistry and Biotechnology, Research School of Chemistry, Australian National University, Canberra ACT 0200 (Australia)], E-mail: mcoote@rsc.anu.edu.au
2008-12-15
Ab initio molecular orbital theory has been used to calculate enthalpies of formation of isoquinoline, 1-hydroxyisoquinoline, 5-hydroxyisoquinoline, and 1,5-dihydroxyisoquinoline as well as some pyridine and quinoline derivatives. The proton affinities of the four isoquinoline derivatives were also obtained. The high-level composite methods G3(MP2), G3(MP2)//B3LYP, G3//B3LYP, and CBS-QB3 have been used for this study, and the results have been compared with available experimental values. For six of the eight studied compounds, the theoretical enthalpies of formation were very close to the experimental values (to within 4.3 kJ . mol{sup -1}); where comparison was possible, the theoretical and experimental proton affinities were also in excellent agreement with one another. However, there is an extraordinary discrepancy between theory and experiment for the enthalpies of formation of 1-hydroxyisoquinoline and 1,5-dihydroxyisoquinoline, suggesting that the experimental values for these two compounds should perhaps be re-examined. We also show that popular low cost computational methods such as B3LYP and MP2 show very large deviations from the benchmark values.
Dai, Lu; Li, Weikang; Sun, Fei; Li, Baizhi; Li, Hongrui; Zhang, Hongxing; Zheng, Qingchuan; Liang, Chongyang
2016-09-01
Designing affinity ligands has always been the development focus of affinity chromatography. Previous antibody affinity ligand designs were mostly based on the crystal structure of protein A (UniProt code number: P38507), and the antibody-binding domains were modified according to the properties of amino acid residues. Currently, more effective bioinformatic prediction and experimental validation has been used to improve the design of antibody affinity ligands. In the present study, the complex crystal structure (the domain D of protein A and the Fab segment of IgM, PDB code: 1DEE) was used as the model. The vital site that inhibits the binding between domain D and IgM was estimated by means of molecular dynamics (MD) simulation, then MM-GBSA calculations were used to design a mutant of domain D (K46E) for improving affinity on the above vital site. The binding analysis using Biacore showed the association and dissociation parameters of K46E mutant that were optimized with IgM. The affinity increase of K46E mutant preferred for IgM, the affinity order is K46E tetramer (KD=6.02×10(-9)M)>K46E mutant (KD=6.66×10(-8)M)>domain D (KD=2.17×10(-7)M). Similar results were obtained when the optimized ligands were immobilized to the chromatography medium. A complete designing strategy was validated in this study, which will provide a novel insight into designing new ligands of antibody affinity chromatography media.
Dai, Lu; Li, Weikang; Sun, Fei; Li, Baizhi; Li, Hongrui; Zhang, Hongxing; Zheng, Qingchuan; Liang, Chongyang
2016-09-01
Designing affinity ligands has always been the development focus of affinity chromatography. Previous antibody affinity ligand designs were mostly based on the crystal structure of protein A (UniProt code number: P38507), and the antibody-binding domains were modified according to the properties of amino acid residues. Currently, more effective bioinformatic prediction and experimental validation has been used to improve the design of antibody affinity ligands. In the present study, the complex crystal structure (the domain D of protein A and the Fab segment of IgM, PDB code: 1DEE) was used as the model. The vital site that inhibits the binding between domain D and IgM was estimated by means of molecular dynamics (MD) simulation, then MM-GBSA calculations were used to design a mutant of domain D (K46E) for improving affinity on the above vital site. The binding analysis using Biacore showed the association and dissociation parameters of K46E mutant that were optimized with IgM. The affinity increase of K46E mutant preferred for IgM, the affinity order is K46E tetramer (KD=6.02×10(-9)M)>K46E mutant (KD=6.66×10(-8)M)>domain D (KD=2.17×10(-7)M). Similar results were obtained when the optimized ligands were immobilized to the chromatography medium. A complete designing strategy was validated in this study, which will provide a novel insight into designing new ligands of antibody affinity chromatography media. PMID:27524303
Evolution based on chromosome affinity from a network perspective
Monteiro, R. L. S.; Fontoura, J. R. A.; Carneiro, T. K. G.; Moret, M. A.; Pereira, H. B. B.
2014-06-01
Recent studies have focused on models to simulate the complex phenomenon of evolution of species. Several studies have been performed with theoretical models based on Darwin's theories to associate them with the actual evolution of species. However, none of the existing models include the affinity between individuals using network properties. In this paper, we present a new model based on the concept of affinity. The model is used to simulate the evolution of species in an ecosystem composed of individuals and their relationships. We propose an evolutive algorithm that incorporates the degree centrality and efficiency network properties to perform the crossover process and to obtain the network topology objective, respectively. Using a real network as a starting point, we simulate its evolution and compare its results with the results of 5788 computer-generated networks.
Kong, Gang; Dai, Dao-Qing; Zou, Lu-Min
2008-07-01
In order to remove the artifacts of peripheral digital subtraction angiography (DSA), an affine transformation-based automatic image registration algorithm is introduced here. The whole process is described as follows: First, rectangle feature templates are constructed with their centers of the extracted Harris corners in the mask, and motion vectors of the central feature points are estimated using template matching technology with the similarity measure of maximum histogram energy. And then the optimal parameters of the affine transformation are calculated with the matrix singular value decomposition (SVD) method. Finally, bilinear intensity interpolation is taken to the mask according to the specific affine transformation. More than 30 peripheral DSA registrations are performed with the presented algorithm, and as the result, moving artifacts of the images are removed with sub-pixel precision, and the time consumption is less enough to satisfy the clinical requirements. Experimental results show the efficiency and robustness of the algorithm.
Flexible Molybdenum Electrodes towards Designing Affinity Based Protein Biosensors.
Kamakoti, Vikramshankar; Panneer Selvam, Anjan; Radha Shanmugam, Nandhinee; Muthukumar, Sriram; Prasad, Shalini
2016-01-01
Molybdenum electrode based flexible biosensor on porous polyamide substrates has been fabricated and tested for its functionality as a protein affinity based biosensor. The biosensor performance was evaluated using a key cardiac biomarker; cardiac Troponin-I (cTnI). Molybdenum is a transition metal and demonstrates electrochemical behavior upon interaction with an electrolyte. We have leveraged this property of molybdenum for designing an affinity based biosensor using electrochemical impedance spectroscopy. We have evaluated the feasibility of detection of cTnI in phosphate-buffered saline (PBS) and human serum (HS) by measuring impedance changes over a frequency window from 100 mHz to 1 MHz. Increasing changes to the measured impedance was correlated to the increased dose of cTnI molecules binding to the cTnI antibody functionalized molybdenum surface. We achieved cTnI detection limit of 10 pg/mL in PBS and 1 ng/mL in HS medium. The use of flexible substrates for designing the biosensor demonstrates promise for integration with a large-scale batch manufacturing process. PMID:27438863
Talon, Laurent; Hansen, Alex
2010-01-01
We propose a method for calculating the effective permeability of two-dimensional self-affine permeability fields based on generalizing the one-dimensional concept of a bottleneck. We test the method on fracture faults where the local permeability field is given by the cube of the aperture field. The method remains accurate even when there is substantial mechanical overlap between the two fracture surfaces. The computational efficiency of the method is comparable to calculating a simple average and is more than two orders of magnitude faster than solving the Reynolds equations using a finite-difference scheme.
Felfli, Z
2015-01-01
Core-polarization interactions are investigated in low-energy electron elastic scattering from the atoms In,Sn,Eu,Au and At through the calculation of their electron affinities. The complex angular momentum method wherein is embedded the vital electron-electron correlations is used. The core-polarization effects are studied through the well investigated rational function approximation of the Thomas-Fermi potential,which can be analytically continued into the complex plane. The EAs are extracted from the large resonance peaks in the calculated low-energy electron atom scattering total cross sections and compared with those from measurements and sophisticated theoretical methods. It is concluded that when the electron-electron correlation effects and core polarization interactions are accounted for adequately the importance of relativity on the calculation of the electron affinities of atoms can be assessed. For At, relativistic effects are estimated to contribute a maximum of about 3.6 percent to its (non-rela...
Affinity sensor based on immobilized molecular imprinted synthetic recognition elements.
Lenain, Pieterjan; De Saeger, Sarah; Mattiasson, Bo; Hedström, Martin
2015-07-15
An affinity sensor based on capacitive transduction was developed to detect a model compound, metergoline, in a continuous flow system. This system simulates the monitoring of low-molecular weight organic compounds in natural flowing waters, i.e. rivers and streams. During operation in such scenarios, control of the experimental parameters is not possible, which poses a true analytical challenge. A two-step approach was used to produce a sensor for metergoline. Submicron spherical molecularly imprinted polymers, used as recognition elements, were obtained through emulsion polymerization and subsequently coupled to the sensor surface by electropolymerization. This way, a robust and reusable sensor was obtained that regenerated spontaneously under the natural conditions in a river. Small organic compounds could be analyzed in water without manipulating the binding or regeneration conditions, thereby offering a viable tool for on-site application. PMID:25703726
Capillary electrophoresis-based assessment of nanobody affinity and purity
Haselberg, Rob; Oliveira, Sabrina; van der Meel, Roy; Somsen, Govert W; de Jong, Gerhardus J
2014-01-01
Drug purity and affinity are essential attributes during development and production of therapeutic proteins. In this work, capillary electrophoresis (CE) was used to determine both the affinity and composition of the biotechnologically produced "nanobody" EGa1, the binding fragment of a heavy-chain-
PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity.
Liu, Xiao; Liu, Jinfeng; Zhu, Tong; Zhang, Lujia; He, Xiao; Zhang, John Z H
2016-05-23
Improving the accuracy of scoring functions for estimating protein-ligand binding affinity is of significant interest as well as practical utility in drug discovery. In this work, PBSA_E, a new free energy estimator based on the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) descriptors, has been developed. This free energy estimator was optimized using high-quality experimental data from a training set consisting of 145 protein-ligand complexes. The method was validated on two separate test sets containing 121 and 130 complexes. Comparison of the binding affinities predicted using the present method with those obtained using three popular scoring functions, i.e., GlideXP, GlideSP, and SYBYL_F, demonstrated that the PBSA_E method is more accurate. This new energy estimator requires a MM/PBSA calculation of the protein-ligand binding energy for a single complex configuration, which is typically obtained by optimizing the crystal structure. The present study shows that PBSA_E has the potential to become a robust tool for more reliable estimation of protein-ligand binding affinity in structure-based drug design. PMID:27088302
Affinity functions: recognizing essential parameters in fuzzy connectedness based image segmentation
Ciesielski, Krzysztof C.; Udupa, Jayaram K.
2009-02-01
Fuzzy connectedness (FC) constitutes an important class of image segmentation schemas. Although affinity functions represent the core aspect (main variability parameter) of FC algorithms, they have not been studied systematically in the literature. In this paper, we present a thorough study to fill this gap. Our analysis is based on the notion of equivalent affinities: if any two equivalent affinities are used in the same FC schema to produce two versions of the algorithm, then these algorithms are equivalent in the sense that they lead to identical segmentations. We give a complete characterization of the affinity equivalence and show that many natural definitions of affinity functions and their parameters used in the literature are redundant in the sense that different definitions and values of such parameters lead to equivalent affinities. We also show that two main affinity types - homogeneity based and object feature based - are equivalent, respectively, to the difference quotient of the intensity function and Rosenfeld's degree of connectivity. In addition, we demonstrate that any segmentation obtained via relative fuzzy connectedness (RFC) algorithm can be viewed as segmentation obtained via absolute fuzzy connectedness (AFC) algorithm with an automatic and adaptive threshold detection. We finish with an analysis of possible ways of combining different component affinities that result in non equivalent affinities.
DEFF Research Database (Denmark)
Poongavanam, Vasanthanathan; Svendsen, Casper Steinmann; Kongsted, Jacob
2014-01-01
Quantum mechanical (QM) calculations have been used to predict the binding affinity of a set of ligands towards HIV-1 RT associated RNase H (RNH). The QM based chelation calculations show improved binding affinity prediction for the inhibitors compared to using an empirical scoring function....... Thus, the computational models tested in this study could be useful as high throughput filters for searching HIV-1 RNase H active-site molecules in the virtual screening process....
Affinity chromatography based on a combinatorial strategy for rerythropoietin purification.
Martínez-Ceron, María C; Marani, Mariela M; Taulés, Marta; Etcheverrigaray, Marina; Albericio, Fernando; Cascone, Osvaldo; Camperi, Silvia A
2011-05-01
Small peptides containing fewer than 10 amino acids are promising ligand candidates with which to build affinity chromatographic systems for industrial protein purification. The application of combinatorial peptide synthesis strategies greatly facilitates the discovery of suitable ligands for any given protein of interest. Here we sought to identify peptide ligands with affinity for recombinant human erythropoietin (rhEPO), which is used for the treatment of anemia. A combinatorial library containing the octapeptides X-X-X-Phe-X-X-Ala-Gly, where X = Ala, Asp, Glu, Phe, His, Leu, Asn, Pro, Ser, or Thr, was synthesized on HMBA-ChemMatrix resin by the divide-couple-recombine method. For the library screening, rhEPO was coupled to either Texas Red or biotin. Fluorescent beads or beads showing a positive reaction with streptavidin-peroxidase were isolated. After cleavage, peptides were sequenced by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Fifty-seven beads showed a positive reaction. Peptides showing more consensuses were synthesized, and their affinity to rhEPO was assessed using a plasma resonance biosensor. Dissociation constant values in the range of 1-18 μM were obtained. The best two peptides were immobilized on Sepharose, and the resultant chromatographic matrixes showed affinity for rhEPO with dissociation constant values between 1.8 and 2.7 μM. Chinese hamster ovary (CHO) cell culture supernatant was spiked with rhEPO, and the artificial mixture was loaded on Peptide-Sepharose columns. The rhEPO was recovered in the elution fraction with a yield of 90% and a purity of 95% and 97% for P1-Sepharose and P2-Sepharose, respectively. PMID:21495625
Su, Neil Qiang; Xu, Xin
2016-05-10
Recently, we have developed an integration approach for the calculations of ionization potentials (IPs) and electron affinities (EAs) of molecular systems at the level of second-order Møller-Plesset (MP2) (Su, N. Q.; Xu, X. J. Chem. Theory Comput. 11, 4677, 2015), where the full MP2 energy gradient with respect to the orbital occupation numbers was derived but only at integer occupations. The theory is completed here to cover the fractional occupation systems, such that Slater's transition state concept can be used to have accurate predictions of IPs and EAs. Antisymmetrized Goldstone diagrams have been employed for interpretations and better understanding of the derived equations, where two additional rules were introduced in the present work specifically for hole or particle lines with fractional occupation numbers.
Su, Neil Qiang; Xu, Xin
2016-05-10
Recently, we have developed an integration approach for the calculations of ionization potentials (IPs) and electron affinities (EAs) of molecular systems at the level of second-order Møller-Plesset (MP2) (Su, N. Q.; Xu, X. J. Chem. Theory Comput. 11, 4677, 2015), where the full MP2 energy gradient with respect to the orbital occupation numbers was derived but only at integer occupations. The theory is completed here to cover the fractional occupation systems, such that Slater's transition state concept can be used to have accurate predictions of IPs and EAs. Antisymmetrized Goldstone diagrams have been employed for interpretations and better understanding of the derived equations, where two additional rules were introduced in the present work specifically for hole or particle lines with fractional occupation numbers. PMID:27010405
Moghaddam, Sarvin; Yang, Cheng; Rekharsky, Mikhail; Ko, Young Ho; Kim, Kimoon; Inoue, Yoshihisa; Gilson, Michael K.
2011-01-01
A dicationic ferrocene derivative has previously been shown to bind cucurbit[7]uril (CB[7]) in water with ultra-high affinity (ΔGo= −21 kcal/mol). Here, we describe new compounds that bind aqueous CB[7] equally well, validating our prior suggestion that they, too, would be ultra-high affinity CB[7] guests. The present guests, which are based upon either a bicyclo[2.2.2]octane or adamantane core, have no metal atoms, so these results also confirm that the remarkably high affinities of the ferr...
An Affinity Propagation-Based DNA Motif Discovery Algorithm.
Sun, Chunxiao; Huo, Hongwei; Yu, Qiang; Guo, Haitao; Sun, Zhigang
2015-01-01
The planted (l, d) motif search (PMS) is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs) in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP) clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM) refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.
An Affinity Propagation-Based DNA Motif Discovery Algorithm
Directory of Open Access Journals (Sweden)
Chunxiao Sun
2015-01-01
Full Text Available The planted (l,d motif search (PMS is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.
Indian Academy of Sciences (India)
Younes Valadbeigi; Hossein Farrokhpour; Mahmoud Tabrizchi
2014-07-01
The proton affinities, gas phase basicities and adiabatic ionization energies and electron affinities of some important hydroxylamines and alkanolamines were calculated using B3LYP, CBS-Q and G4MP2 methods. Also, the B3LYP method was used to calculate vertical ionization energies and electron affinities of the molecules. The calculated ionization energies are in the range of 8-10.5 eV and they decrease as the number of carbon atoms increases. Computational results and ion mobility spectrometry study confirm that some alkanolamines lose a water molecule due to protonation at oxygen site and form cationic cyclic compounds. Effect of different substitutions on the cyclization of ethanolamine was studied theoretically.
Oberlin, Michael; Kroemer, Romano; Mikol, Vincent; Minoux, Hervé; Tastan, Erdogan; Baurin, Nicolas
2012-08-27
The implementation of a structure based virtual affinity maturation protocol and evaluation of its predictivity are presented. The in silico protocol is based on conformational sampling of the interface residues (using the Dead End Elimination/A* algorithm), followed by the estimation of the change of free energy of binding due to a point mutation, applying MM/PBSA calculations. Several implementations of the protocol have been evaluated for 173 mutations in 7 different protein complexes for which experimental data were available: the use of the Boltzamnn averaged predictor based on the free energy of binding (ΔΔG(*)) combined with the one based on its polar component only (ΔΔE(pol*)) led to the proposal of a subset of mutations out of which 45% would have successfully enhanced the binding. When focusing on those mutations that are less likely to be introduced by natural in vivo maturation methods (99 mutations with at least two base changes in the codon), the success rate is increased to 63%. In another evaluation, focusing on 56 alanine scanning mutations, the in silico protocol was able to detect 89% of the hot-spots. PMID:22788756
Quantum image encryption based on generalized affine transform and logistic map
Liang, Hao-Ran; Tao, Xiang-Yang; Zhou, Nan-Run
2016-07-01
Quantum circuits of the generalized affine transform are devised based on the novel enhanced quantum representation of digital images. A novel quantum image encryption algorithm combining the generalized affine transform with logistic map is suggested. The gray-level information of the quantum image is encrypted by the XOR operation with a key generator controlled by the logistic map, while the position information of the quantum image is encoded by the generalized affine transform. The encryption keys include the independent control parameters used in the generalized affine transform and the logistic map. Thus, the key space is large enough to frustrate the possible brute-force attack. Numerical simulations and analyses indicate that the proposed algorithm is realizable, robust and has a better performance than its classical counterpart in terms of computational complexity.
International Nuclear Information System (INIS)
Full text: Therapy of hypercholesterolemia using immunoadsorption of Low Density Lipoprotein (LDL) to a gel substrate is a current clinical technique (Bosch T., Biomat., Art. Cells and Immob. Biotech, 20: 1165- 1169, 1992). Recently, Affinity Membranes have been proposed as an alternate substrate for immunoadsorption (Brandt S and others, Bio Technology, 6:779-782, 1988). Potentially, the overall rate of adsorption to a membrane may be faster than to a gel because of the different geometry (ibid). This implies that for the same conditions, a membrane-based device will have a higher Number of Transfer Units, more efficient adsorption and a smaller device size than a gel. To test this hypothesis, we calculated two key theoretical design parameters: Separation Factor, R, and the Number of Transfer Units, N, for a functioning clinical-scale affinity membrane device: R=Kd/Kd+C0. Kd: Equilibrium Dissociation Constant (M) and Co: Feed Concentration (M) N=kaQmaxVm/F. ka: Intrinsic reaction rate constant (M-1 min-1), Qmax: Substrate capacity (M), Vm: Membrane volume (m1) and F: Flow Rate (m1 min-1). We assumed 1 hr treatment time during which 1 plasma volume (3L) is treated, hence F=50 (m1 min-1). If we assume 2/3 of LDL is removed from an initial level of 3 g/L, we can calculate an average feed concentration Co = 2 g / L. There is some data available in the literature for typical values of Kd (10-8 M) and ka ( 103 M-1s-1 to 3 x 105 M-1 s-1 ) (Olsen WC and others, Molec. Immun: 26: 129-136, 1989). Since the intrinsic reaction kinetics may vary from very slow (103 M) to very fast (3 x 105 M), the Number of Transfer Units, N may vary from small (2) to large (650). Hence for a membrane device, we must select the antibody with the fastest reaction, ka, and highest capacity (Qmax) otherwise, there may be no advantage in a membrane-based device over a gel-based device
Architecture of high-affinity unnatural-base DNA aptamers toward pharmaceutical applications
Ken-ichiro Matsunaga; Michiko Kimoto; Charlotte Hanson; Michael Sanford; Young, Howard A.; Ichiro Hirao
2015-01-01
We present a remodeling method for high-affinity unnatural-base DNA aptamers to augment their thermal stability and nuclease resistance, for use as drug candidates targeting specific proteins. Introducing a unique mini-hairpin DNA provides robust stability to unnatural-base DNA aptamers generated by SELEX using genetic alphabet expansion, without reducing their high affinity. By this method, >80% of the remodeled DNA aptamer targeting interferon-γ (K D of 33 pM) survived in human serum at 37 ...
Data base to compare calculations and observations
Energy Technology Data Exchange (ETDEWEB)
Tichler, J.L.
1985-01-01
Meteorological and climatological data bases were compared with known tritium release points and diffusion calculations to determine if calculated concentrations could replace measure concentrations at the monitoring stations. Daily tritium concentrations were monitored at 8 stations and 16 possible receptors. Automated data retrieval strategies are listed. (PSB)
Gaussian Affine Feature Detector
Xu, Xiaopeng; Zhang, Xiaochun
2011-01-01
A new method is proposed to get image features' geometric information. Using Gaussian as an input signal, a theoretical optimal solution to calculate feature's affine shape is proposed. Based on analytic result of a feature model, the method is different from conventional iterative approaches. From the model, feature's parameters such as position, orientation, background luminance, contrast, area and aspect ratio can be extracted. Tested with synthesized and benchmark data, the method achieve...
Affinity-based methodologies and ligands for antibody purification: advances and perspectives.
Roque, Ana C A; Silva, Cláudia S O; Taipa, M Angela
2007-08-10
Many successful, recent therapies for life-threatening diseases such as cancer and rheumatoid arthritis are based on the recognition between native or genetically engineered antibodies and cell-surface receptors. Although naturally produced by the immune system, the need for antibodies with unique specificities and designed for single application, has encouraged the search for novel antibody purification strategies. The availability of these products to the end-consumer is strictly related to manufacture costs, particularly those attributed to downstream processing. Over the last decades, academia and industry have developed different types of interactions and separation techniques for antibody purification, affinity-based strategies being the most common and efficient methodologies. The affinity ligands utilized range from biological to synthetic designed molecules with enhanced resistance and stability. Despite the successes achieved, the purification "paradigm" still moves interests and efforts in the continuous demand for improved separation performances. This review will focus on recent advances and perspectives in antibody purification by affinity interactions using different techniques, with particular emphasis on affinity chromatography. PMID:17618635
Affinity-based methodologies and ligands for antibody purification: advances and perspectives.
Roque, Ana C A; Silva, Cláudia S O; Taipa, M Angela
2007-08-10
Many successful, recent therapies for life-threatening diseases such as cancer and rheumatoid arthritis are based on the recognition between native or genetically engineered antibodies and cell-surface receptors. Although naturally produced by the immune system, the need for antibodies with unique specificities and designed for single application, has encouraged the search for novel antibody purification strategies. The availability of these products to the end-consumer is strictly related to manufacture costs, particularly those attributed to downstream processing. Over the last decades, academia and industry have developed different types of interactions and separation techniques for antibody purification, affinity-based strategies being the most common and efficient methodologies. The affinity ligands utilized range from biological to synthetic designed molecules with enhanced resistance and stability. Despite the successes achieved, the purification "paradigm" still moves interests and efforts in the continuous demand for improved separation performances. This review will focus on recent advances and perspectives in antibody purification by affinity interactions using different techniques, with particular emphasis on affinity chromatography.
Upper Subcritical Calculations Based on Correlated Data
Energy Technology Data Exchange (ETDEWEB)
Sobes, Vladimir [ORNL; Rearden, Bradley T [ORNL; Mueller, Don [ORNL; Marshall, William BJ J [ORNL; Scaglione, John M [ORNL; Dunn, Michael E [ORNL
2015-01-01
The American National Standards Institute and American Nuclear Society standard for Validation of Neutron Transport Methods for Nuclear Criticality Safety Calculations defines the upper subcritical limit (USL) as “a limit on the calculated k-effective value established to ensure that conditions calculated to be subcritical will actually be subcritical.” Often, USL calculations are based on statistical techniques that infer information about a nuclear system of interest from a set of known/well-characterized similar systems. The work in this paper is part of an active area of research to investigate the way traditional trending analysis is used in the nuclear industry, and in particular, the research is assessing the impact of the underlying assumption that the experimental data being analyzed for USL calculations are statistically independent. In contrast, the multiple experiments typically used for USL calculations can be correlated because they are often performed at the same facilities using the same materials and measurement techniques. This paper addresses this issue by providing a set of statistical inference methods to calculate the bias and bias uncertainty based on the underlying assumption that the experimental data are correlated. Methods to quantify these correlations are the subject of a companion paper and will not be discussed here. The newly proposed USL methodology is based on the assumption that the integral experiments selected for use in the establishment of the USL are sufficiently applicable and that experimental correlations are known. Under the assumption of uncorrelated data, the new methods collapse directly to familiar USL equations currently used. We will demonstrate our proposed methods on real data and compare them to calculations of currently used methods such as USLSTATS and NUREG/CR-6698. Lastly, we will also demonstrate the effect experiment correlations can have on USL calculations.
Wickstrom, Lauren; He, Peng; Gallicchio, Emilio; Ronald M Levy
2013-01-01
Host-guest inclusion complexes are useful models for understanding the structural and energetic aspects of molecular recognition. Due to their small size relative to much larger protein-ligand complexes, converged results can be obtained rapidly for these systems thus offering the opportunity to more reliably study fundamental aspects of the thermodynamics of binding. In this work, we have performed a large scale binding affinity survey of 57 β-cyclodextrin (CD) host guest systems using the b...
Affine with B-Spline Registration based Retrieval using Distance Metrics
Directory of Open Access Journals (Sweden)
Swarnambiga AYYACHAMY
2014-06-01
Full Text Available Developing a two stage framework is the purpose dealt in this paper. This rely on the Affine transformation and B –Spline for registration of medical images as the first stage of the framework and retrieval of medical images using distance metrics as the second stage in the framework. Affine with B-Spline registration based retrieval methods have been dealt in this paper. Evaluation of the framework using images extracted from the Affine with B-Spline registration are applied for the retrieval of medical images performing registration based retrieval. Quantitative analysis is performed to show the registration based retrieval methods perform well with comparable results and presents a summary of the results obtained. This work brings three major advantages as conclusion. First, medical images are conveniently retrieved from the database for effective clinical comparison, diagnosis and verification and also serving as a guidance tool. Second, coping registration techniques with monomodal medical images for more detailed view of images. Third, driving and tracking the entire lifecycle of this medical process would be easier with this application which permits immediate access to all patients’ data stored in a medical repository. Conclusions drawn out of the proposed schemes are listed and justified.
Serizawa, Takeshi; Fukuta, Hiroki; Date, Takaaki; Sawada, Toshiki
2016-02-01
Peptides with affinities for the target segments of polymer hydrogels were identified by biological screening using phage-displayed peptide libraries, and these peptides exhibited an affinity-based release capability from hydrogels. The results from cell culture assays demonstrated the sustained anticancer effects of the drug-conjugated peptides that were released from the hydrogels.
Novel cyclen-based linear polymer as a high-affinity binding material for DNA condensation
Institute of Scientific and Technical Information of China (English)
无
2009-01-01
A novel cyclen-based linear polyamine (POGEC) was designed and synthesized from the reaction between 1,3-propanediol diglycidyl ether and 1,7-bis(diethoxyphosphory)-1,4,7,10-tetraazacyclod-odecane. High-affinity binding between POGEC and DNA was demonstrated by agarose gel electrophoresis and scanning electron microscopy (SEM). Moreover,the formed POGEC/DNA complex (termed polyplex) could be disassociated to release the free DNA through addition of the physiological concentration of NaCl solution. Fluorescence spectrum was used to measure the high-affinity binding and DNA condensation capability of POGEC. Circular dichroism (CD) spectrum indicates that the DNA conformation did not change after binding to POEGC.
Novel cyclen-based linear polymer as a high-affinity binding material for DNA condensation
Institute of Scientific and Technical Information of China (English)
XIANG YongZhe; WANG Na; ZHANG Ji; LI Kun; ZHANG ZhongWei; LIN HongHui; YU XiaoQi
2009-01-01
A novel cyclen-based linear polyamine (POGEC) was designed and synthesized from the reaction be-tween 1,3-propanediol diglycidyl ether and 1,7-bis(diethoxyphosphory)-1,4,7,10-tetraazacyclod- odecane.High-affinity binding between POGEC and DNA was demonstrated by agarose gel electrophoresis and scanning electron microscopy (SEM). Moreover, the formed POGEC/DNA complex (termed polyplex) could be disassociated to release the free DNA through addition of the physiological concentration of NaCl solution. Fluorescence spectrum was used to measure the high-affinity binding and DNA con-densation capability of POGEC. Circular dichroism (CD) spectrum indicates that the DNA conformation did not change after binding to POEGC.
Numerical inductance calculations based on first principles.
Shatz, Lisa F; Christensen, Craig W
2014-01-01
A method of calculating inductances based on first principles is presented, which has the advantage over the more popular simulators in that fundamental formulas are explicitly used so that a deeper understanding of the inductance calculation is obtained with no need for explicit discretization of the inductor. It also has the advantage over the traditional method of formulas or table lookups in that it can be used for a wider range of configurations. It relies on the use of fast computers with a sophisticated mathematical computing language such as Mathematica to perform the required integration numerically so that the researcher can focus on the physics of the inductance calculation and not on the numerical integration.
Bi, Xiaodong; Liu, Zhen
2014-12-16
Enzyme activity assay is an important method in clinical diagnostics. However, conventional enzyme activity assay suffers from apparent interference from the sample matrix. Herein, we present a new format of enzyme activity assay that can effectively eliminate the effects of the sample matrix. The key is a 96-well microplate modified with molecularly imprinted polymer (MIP) prepared according to a newly proposed method called boronate affinity-based oriented surface imprinting. Alkaline phosphatase (ALP), a glycoprotein enzyme that has been routinely used as an indicator for several diseases in clinical tests, was taken as a representative target enzyme. The prepared MIP exhibited strong affinity toward the template enzyme (with a dissociation constant of 10(-10) M) as well as superb tolerance for interference. Thus, the enzyme molecules in a complicated sample matrix could be specifically captured and cleaned up for enzyme activity assay, which eliminated the interference from the sample matrix. On the other hand, because the boronate affinity MIP could well retain the enzymatic activity of glycoprotein enzymes, the enzyme captured by the MIP was directly used for activity assay. Thus, additional assay time and possible enzyme or activity loss due to an enzyme release step required by other methods were avoided. Assay of ALP in human serum was successfully demonstrated, suggesting a promising prospect of the proposed method in real-world applications.
Color-weak compensation using local affine isometry based on discrimination threshold matching
Mochizuki, Rika; Kojima, Takanori; Lenz, Reiner; Chao, Jinhui
2015-01-01
We develop algorithms for color-weak compensation and color-weak simulation based on Riemannian geometry models of color spaces. The objective function introduced measures the match of color discrimination thresholds of average normal observers and a color-weak observer. The developed matching process makes use of local affine maps between color spaces of color-normal and color-weak observers. The method can be used to generate displays of images that provide color-normal and color-weak obser...
Affine Invariant, Model-Based Object Recognition Using Robust Metrics and Bayesian Statistics
Zografos, Vasileios; 10.1007/11559573_51
2010-01-01
We revisit the problem of model-based object recognition for intensity images and attempt to address some of the shortcomings of existing Bayesian methods, such as unsuitable priors and the treatment of residuals with a non-robust error norm. We do so by using a refor- mulation of the Huber metric and carefully chosen prior distributions. Our proposed method is invariant to 2-dimensional affine transforma- tions and, because it is relatively easy to train and use, it is suited for general object matching problems.
High-throughput and multiplexed regeneration buffer scouting for affinity-based interactions.
Geuijen, Karin P M; Schasfoort, Richard B; Wijffels, Rene H; Eppink, Michel H M
2014-06-01
Affinity-based analyses on biosensors depend partly on regeneration between measurements. Regeneration is performed with a buffer that efficiently breaks all interactions between ligand and analyte while maintaining the active binding site of the ligand. We demonstrated a regeneration buffer scouting using the combination of a continuous flow microspotter with a surface plasmon resonance imaging platform to simultaneously test 48 different regeneration buffers on a single biosensor. Optimal regeneration conditions are found within hours and consume little amounts of buffers, analyte, and ligand. This workflow can be applied to any ligand that is coupled through amine, thiol, or streptavidin immobilization.
Inulin-based glycopolymer: its preparation, lectin-affinity and gellation property.
Izawa, Kazumi; Akiyama, Kento; Abe, Haruka; Togashi, Yosuke; Hasegawa, Teruaki
2013-06-01
The glycopolymer composed of an inulin scaffold and pendent β-lactosides was developed from commercially available inulin through sequential chemical modification processes composed of tosylation, azidation, and the subsequent Huisgen cyclocoupling with an alkyne-terminated β-lactoside. The resultant inulin-based glycopolymer has unique dual affinity towards β-galactoside and α-glucoside specific lectins which is attributable to its pendent β-lactosides and terminal α-glucoside. Its gellation property was also accessed to find that the inulin-based glycopolymer forms hydrogels whose critical gellation concentration (CGC) was lower than that required for hydrogels made from native inulin. Drug release properties of the inulin-based glycopolymer were also discussed in this paper.
Energy Technology Data Exchange (ETDEWEB)
Moaddel, Ruin [Gerontology Research Center, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224-6825 (United States); Wainer, Irving W. [Gerontology Research Center, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224-6825 (United States)]. E-mail: Wainerir@grc.nia.nih.gov
2006-03-30
Membranes obtained from cell lines that express or do not express a target membrane bound protein have been immobilized on a silica-based liquid chromatographic support or on the surface of an activated glass capillary. The resulting chromatographic columns have been placed in liquid chromatographic systems and used to characterize the target proteins and to identify small molecules that bind to the target. Membranes containing ligand gated ion channels, G-protein coupled receptors and drug transporters have been prepared and characterized. If a marker ligand has been identified for the target protein, frontal or zonal displacement chromatographic techniques can be used to determine binding affinities (K {sub d} values) and non-linear chromatography can be used to assess the association (k {sub on}) and dissociation (k {sub off}) rate constants and the thermodynamics of the binding process. Membrane-based affinity columns have been created using membranes from a cell line that does not express the target protein (control) and the same cell line that expresses the target protein (experimental) after genomic transfection. The resulting columns can be placed in a parallel chromatography system and the differential retention between the control and experimental columns can be used to identify small molecules and protein that bind to the target protein. These applications will be illustrated using columns created using cellular membranes containing nicotinic acetylcholine receptors and the drug transporter P-glycoprotein.
Nguyen, Ha P; Koutsoukas, Alexios; Mohd Fauzi, Fazlin; Drakakis, Georgios; Maciejewski, Mateusz; Glen, Robert C; Bender, Andreas
2013-09-01
Diversity selection is a frequently applied strategy for assembling high-throughput screening libraries, making the assumption that a diverse compound set increases chances of finding bioactive molecules. Based on previous work on experimental 'affinity fingerprints', in this study, a novel diversity selection method is benchmarked that utilizes predicted bioactivity profiles as descriptors. Compounds were selected based on their predicted activity against half of the targets (training set), and diversity was assessed based on coverage of the remaining (test set) targets. Simultaneously, fingerprint-based diversity selection was performed. An original version of the method exhibited on average 5% and an improved version on average 10% increase in target space coverage compared with the fingerprint-based methods. As a typical case, bioactivity-based selection of 231 compounds (2%) from a particular data set ('Cutoff-40') resulted in 47.0% and 50.1% coverage, while fingerprint-based selection only achieved 38.4% target coverage for the same subset size. In conclusion, the novel bioactivity-based selection method outperformed the fingerprint-based method in sampling bioactive chemical space on the data sets considered. The structures retrieved were structurally more acceptable to medicinal chemists while at the same time being more lipophilic, hence bioactivity-based diversity selection of compounds would best be combined with physicochemical property filters in practice.
A multiobjective evolutionary algorithm to find community structures based on affinity propagation
Shang, Ronghua; Luo, Shuang; Zhang, Weitong; Stolkin, Rustam; Jiao, Licheng
2016-07-01
Community detection plays an important role in reflecting and understanding the topological structure of complex networks, and can be used to help mine the potential information in networks. This paper presents a Multiobjective Evolutionary Algorithm based on Affinity Propagation (APMOEA) which improves the accuracy of community detection. Firstly, APMOEA takes the method of affinity propagation (AP) to initially divide the network. To accelerate its convergence, the multiobjective evolutionary algorithm selects nondominated solutions from the preliminary partitioning results as its initial population. Secondly, the multiobjective evolutionary algorithm finds solutions approximating the true Pareto optimal front through constantly selecting nondominated solutions from the population after crossover and mutation in iterations, which overcomes the tendency of data clustering methods to fall into local optima. Finally, APMOEA uses an elitist strategy, called "external archive", to prevent degeneration during the process of searching using the multiobjective evolutionary algorithm. According to this strategy, the preliminary partitioning results obtained by AP will be archived and participate in the final selection of Pareto-optimal solutions. Experiments on benchmark test data, including both computer-generated networks and eight real-world networks, show that the proposed algorithm achieves more accurate results and has faster convergence speed compared with seven other state-of-art algorithms.
DEFF Research Database (Denmark)
Poongavanam, Vasanthanathan; Olsen, Lars; Jørgensen, Flemming Steen;
2010-01-01
, and methods based on statistical mechanics. In the present investigation, we started from an LIE model to predict the binding free energy of structurally diverse compounds of cytochrome P450 1A2 ligands, one of the important human metabolizing isoforms of the cytochrome P450 family. The data set includes both...... substrates and inhibitors. It appears that the electrostatic contribution to the binding free energy becomes negligible in this particular protein and a simple empirical model was derived, based on a training set of eight compounds. The root mean square error for the training set was 3.7 kJ/mol. Subsequent...
Functional group based Ligand binding affinity scoring function at atomic environmental level
Varadwaj, Pritish Kumar; Lahiri, Tapobrata
2009-01-01
Use of knowledge based scoring function (KBSF) for virtual screening and molecular docking has become an established method for drug discovery. Lack of a precise and reliable free energy function that describes several interactions including water-mediated atomic interaction between amino-acid residues and ligand makes distance based statistical measure as the only alternative. Till now all the distance based scoring functions in KBSF arena use atom singularity concept, which neglects the environmental effect of the atom under consideration. We have developed a novel knowledge-based statistical energy function for protein-ligand complexes which takes atomic environment in to account hence functional group as a singular entity. The proposed knowledge based scoring function is fast, simple to construct, easy to use and moreover it tackle the existing problem of handling molecular orientation in active site pocket. We have designed and used Functional group based Ligand retrieval (FBLR) system which can identify and detect the orientation of functional groups in ligand. This decoy searching was used to build the above KBSF to quantify the activity and affinity of high resolution protein-ligand complexes. We have proposed the probable use of these decoys in molecular build-up as a de-novo drug designing approach. We have also discussed the possible use of the said KSBF in pharmacophore fragment detection and pseudo center based fragment alignment procedure. PMID:19255647
New Mathematical Model Based on Affine Transformation for Remote Sensing Image with High Resolution
Institute of Scientific and Technical Information of China (English)
无
2003-01-01
This paper calculates the parameters of image position and orientation,proposes a mathematical model and adopts a new method with three steps of transformations based on parallel ray projection.Every step of the model is strict,and the map function of each transformation is the first order polynomials and other simple function.The final calculation of the parameters is for the linear equations with good status.As a result,the problem of the relativity of image parameter calculation is solved completely.Some experiments are carried out.
Energy Technology Data Exchange (ETDEWEB)
Haruyama, Tetsuya; Wakabayashi, Ryo; Cho, Takeshi; Matsuyama, Sho-taro, E-mail: haruyama@life.kyutech.as.jp [Kyushu Institute of Technology, Department of Biological Functions and Engineering, Kitakyushu Science and Research Park, Hibikino, Kitakyushu, Fukuoka 808-0196 (Japan)
2011-10-29
Photo-excited current can be generated at a molecular interface between a photo-excited molecules and a semi-conductive material in appropriate condition. The system has been recognized for promoting photo-energy devices such as an organic dye sensitized solar-cell. The photo-current generated reactions are totally dependent on the interfacial energy reactions, which are in a highly fluctuated interfacial environment. The authors investigated the photo-excited current reaction to develop a smart affinity detection method. However, in order to perform both an affinity reaction and a photo-excited current reaction at a molecular interface, ordered fabrications of the functional (affinity, photo-excitation, etc.) molecules layer on a semi-conductive surface is required. In the present research, we would like to present the fabrication and functional performance of photo-excited current-based affinity assay device and its application for detection of endocrine disrupting chemicals. On the FTO surface, fluorescent pigment labelled affinity peptide was immobilized through the EC tag (electrochemical-tag) method. The modified FTO produced a current when it was irradiated with diode laser light. However, the photo current decreased drastically when estrogen (ES) coexisted in the reaction solution. In this case, immobilized affinity probe molecules formed a complex with ES and estrogen receptor (ER). The result strongly suggests that the photo-excited current transduction between probe molecule-labelled cyanine pigment and the FTO surface was partly inhibited by a complex that formed at the affinity oligo-peptide region in a probe molecule on the FTO electrode. The bound bulky complex may act as an impediment to perform smooth transduction of photo-excited current in the molecular interface. The present system is new type of photo-reaction-based analysis. This system can be used to perform simple high-sensitive homogeneous assays.
Determining the ice-binding planes of antifreeze proteins by fluorescence-based ice plane affinity.
Basu, Koli; Garnham, Christopher P; Nishimiya, Yoshiyuki; Tsuda, Sakae; Braslavsky, Ido; Davies, Peter
2014-01-15
Antifreeze proteins (AFPs) are expressed in a variety of cold-hardy organisms to prevent or slow internal ice growth. AFPs bind to specific planes of ice through their ice-binding surfaces. Fluorescence-based ice plane affinity (FIPA) analysis is a modified technique used to determine the ice planes to which the AFPs bind. FIPA is based on the original ice-etching method for determining AFP-bound ice-planes. It produces clearer images in a shortened experimental time. In FIPA analysis, AFPs are fluorescently labeled with a chimeric tag or a covalent dye then slowly incorporated into a macroscopic single ice crystal, which has been preformed into a hemisphere and oriented to determine the a- and c-axes. The AFP-bound ice hemisphere is imaged under UV light to visualize AFP-bound planes using filters to block out nonspecific light. Fluorescent labeling of the AFPs allows real-time monitoring of AFP adsorption into ice. The labels have been found not to influence the planes to which AFPs bind. FIPA analysis also introduces the option to bind more than one differently tagged AFP on the same single ice crystal to help differentiate their binding planes. These applications of FIPA are helping to advance our understanding of how AFPs bind to ice to halt its growth and why many AFP-producing organisms express multiple AFP isoforms.
Affinity-Based Network Interfaces for Efficient Communication on Multicore Architectures
Institute of Scientific and Technical Information of China (English)
Andrés Ortiz; Julio Ortega; Antonio F.Díaz; Alberto Prieto
2013-01-01
Improving the network interface performance is needed by the demand of applications with high communication requirements (for example,some multimedia,real-time,and high-performance computing applications),and the availability of network links providing multiple gigabits per second bandwidths that could require many processor cycles for communication tasks.Multicore architectures,the current trend in the microprocessor development to cope with the difficulties to further increase clock frequencies and microarchitecture efficiencies,provide new opportunities to exploit the parallelism available in the nodes for designing efficient communication architectures.Nevertheless,although present OS network stacks include multiple threals that make it possible to execute network tasks concurrently in the kernel,the implementations of packet-based or connection-based parallelism are not trivial as they have to take into account issues related with the cost of synchronization in the access to shared resources and the efficient use of caches.Therefore,a common trend in many recent researches on this topic is to assign network interrupts and the corresponding protocol and network application processing to the same core,as with this affinity scheduling it would be possible to reduce the contention for shared resources and the cache misses.In this paper we propose and analyze several configurations to distribute the network interface among the different cores available in the server.These alternatives have been devised according to the affinity of the corresponding communication tasks with the location (proximity to the memories where the different data structures are stored) and characteristics of the processing core.As this approach uses several cores to accelerate the communication path of a given connection,it can be seen as complementary to those that consider several cores to simultaneously process packets belonging to either the same or different connections.Message passing
Development of an aptamer-based affinity purification method for vascular endothelial growth factor
Directory of Open Access Journals (Sweden)
Maren Lönne
2015-12-01
Full Text Available Since aptamers bind their targets with high affinity and specificity, they are promising alternative ligands in protein affinity purification. As aptamers are chemically synthesized oligonucleotides, they can be easily produced in large quantities regarding GMP conditions allowing their application in protein production for therapeutic purposes. Several advantages of aptamers compared to antibodies are described in general within this paper. Here, an aptamer directed against the human Vascular Endothelial Growth Factor (VEGF was used as affinity ligand for establishing a purification platform for VEGF in small scale. The aptamer was covalently immobilized on magnetic beads in a controlled orientation resulting in a functional active affinity matrix. Target binding was optimized by introduction of spacer molecules and variation of aptamer density. Further, salt-induced target elution was demonstrated as well as VEGF purification from a complex protein mixture proving the specificity of protein-aptamer binding.
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
The dioxygen affinities and biomimetic catalytic performance of transition-metal complexes with (15-crown-5) salophen and its substituted derivatives were examined. The oxygenation constants of Co(II) complexes with crowned bis-Schiff bases were measured and their Mn(III) complexes were employed as models to mimic monooxygenase in catalytic epoxidation of styrene. The highest conversion and selectivity were up to 57.2% and 100% respectively at ambient temperature and pressure. The effects of crown ether ring and substituents R on the dioxygen affinities and catalytic activities were also investigated through comparing with the uncrowned analogues.
Calculating Traffic based on Road Sensor Data
Bisseling, Rob; Gao, Fengnan; Hafkenscheid, Patrick; Idema, Reijer; Jetka, Tomasz; Guerra Ones, Valia; Sikora, Monika
2014-01-01
Road sensors gather a lot of statistical data about traffic. In this paper, we discuss how a measure for the amount of traffic on the roads can be derived from this data, such that the measure is independent of the number and placement of sensors, and the calculations can be performed quickly for la
Multicarrier Communications Based on the Affine Fourier Transform in Doubly-Dispersive Channels
Directory of Open Access Journals (Sweden)
Djurović Igor
2010-01-01
Full Text Available The affine Fourier transform (AFT, a general formulation of chirp transforms, has been recently proposed for use in multicarrier communications. The AFT-based multicarrier (AFT-MC system can be considered as a generalization of the orthogonal frequency division multiplexing (OFDM, frequently used in modern wireless communications. AFT-MC keeps all important properties of OFDM and, in addition, gives a new degree of freedom in suppressing interference caused by Doppler spreading in time-varying multipath channels. We present a general interference analysis of the AFT-MC system that models both time and frequency dispersion effects. Upper and lower bounds on interference power are given, followed by interference power approximation that significantly simplifies interference analysis. The optimal parameters are obtained in the closed form followed by the analysis of the effects of synchronization errors and the optimal symbol period. A detailed interference analysis and optimal parameters are given for different aeronautical and land-mobile satellite (LMS channel scenarios. It is shown that the AFT-MC system is able to match changes in these channels and efficiently reduce interference with high-spectral efficiency.
Physics-based enzyme design: predicting binding affinity and catalytic activity.
Sirin, Sarah; Pearlman, David A; Sherman, Woody
2014-12-01
Computational enzyme design is an emerging field that has yielded promising success stories, but where numerous challenges remain. Accurate methods to rapidly evaluate possible enzyme design variants could provide significant value when combined with experimental efforts by reducing the number of variants needed to be synthesized and speeding the time to reach the desired endpoint of the design. To that end, extending our computational methods to model the fundamental physical-chemical principles that regulate activity in a protocol that is automated and accessible to a broad population of enzyme design researchers is essential. Here, we apply a physics-based implicit solvent MM-GBSA scoring approach to enzyme design and benchmark the computational predictions against experimentally determined activities. Specifically, we evaluate the ability of MM-GBSA to predict changes in affinity for a steroid binder protein, catalytic turnover for a Kemp eliminase, and catalytic activity for α-Gliadin peptidase variants. Using the enzyme design framework developed here, we accurately rank the most experimentally active enzyme variants, suggesting that this approach could provide enrichment of active variants in real-world enzyme design applications.
Design of Bcl-2 and Bcl-xL Inhibitors with Subnanomolar Binding Affinities Based upon a New Scaffold
Energy Technology Data Exchange (ETDEWEB)
Zhou, Haibin; Chen, Jianfang; Meagher, Jennifer L.; Yang, Chao-Yie; Aguilar, Angelo; Liu, Liu; Bai, Longchuan; Cong, Xin; Cai, Qian; Fang, Xueliang; Stuckey, Jeanne A.; Wang, Shaomeng (Michigan)
2014-10-02
Employing a structure-based strategy, we have designed a new class of potent small-molecule inhibitors of the anti-apoptotic proteins Bcl-2 and Bcl-xL. An initial lead compound with a new scaffold was designed based upon the crystal structure of Bcl-xL and U.S. Food and Drug Administration (FDA) approved drugs and was found to have an affinity of 100 {micro}M for both Bcl-2 and Bcl-xL. Linking this weak lead to another weak-affinity fragment derived from Abbott's ABT-737 led to an improvement of the binding affinity by a factor of >10,000. Further optimization ultimately yielded compounds with subnanomolar binding affinities for both Bcl-2 and Bcl-xL and potent cellular activity. The best compound (21) binds to Bcl-xL and Bcl-2 with K{sub i} < 1 nM, inhibits cell growth in the H146 and H1417 small-cell lung cancer cell lines with IC{sub 50} values of 60-90 nM, and induces robust cell death in the H146 cancer cell line at 30-100 nM.
An Activation Force-based Affinity Measure for Analyzing Complex Networks
Jun Guo; Hanliang Guo; Zhanyi Wang
2011-01-01
Affinity measure is a key factor that determines the quality of the analysis of a complex network. Here, we introduce a type of statistics, activation forces, to weight the links of a complex network and thereby develop a desired affinity measure. We show that the approach is superior in facilitating the analysis through experiments on a large-scale word network and a protein-protein interaction (PPI) network consisting of ∼5,000 human proteins. The experiment on the word network verifies tha...
Image-Moment Based Affine Invariant Watermarking Scheme Utilizing Neural Networks
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
A new image watermarking scheme is proposed to resist rotation, scaling and translation (RST) attacks. Six combined low order image moments are utilized to represent image information on rotation, scaling and translation. Affine transform parameters are registered by feedforward neural networks. Watermark is adaptively embedded in discrete wavelet transform (DWT) domain while watermark extraction is carried out without original image after attacked watermarked image has been synchronized by making inverse transform through parameters learned by neural networks. Experimental results show that the proposed scheme can effectively register affine transform parameters, embed watermark more robustly and resist geometric attacks as well as JPEG2000 compression.
Luo, Man; Wang, Xiang S; Tropsha, Alexander
2016-01-01
Ligand based virtual screening (LBVS) approaches could be broadly divided into those relying on chemical similarity searches and those employing Quantitative Structure-Activity Relationship (QSAR) models. We have compared the predictive power of these approaches using some datasets of compounds tested against several G-Protein Coupled Receptors (GPCRs). The k-Nearest Neighbors (kNN) QSAR models were built for known ligands of each GPCR target independently, with a fraction of tested ligands for each target set aside as a validation set. The prediction accuracies of QSAR models for making active/inactive calls for compounds in both training and validation sets were compared to those achieved by the Prediction of Activity Spectra for Substances' (PASS) and the Similarity Ensemble Approach (SEA) tools both available online. Models developed with the kNN QSAR method showed the highest predictive power for almost all tested GPCR datasets. The PASS software, which incorporates multiple end-point specific QSAR models demonstrated a moderate predictive power, while SEA, a chemical similarity based approach, had the lowest prediction power. Our studies suggest that when sufficient amount of data is available to develop and rigorously validate QSAR models such models should be chosen as the preferred virtual screening tool in ligand-based computational drug discovery as compared to chemical similarity based approaches. PMID:27491652
Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.
Brylinski, Michal
2013-11-25
A common strategy for virtual screening considers a systematic docking of a large library of organic compounds into the target sites in protein receptors with promising leads selected based on favorable intermolecular interactions. Despite a continuous progress in the modeling of protein-ligand interactions for pharmaceutical design, important challenges still remain, thus the development of novel techniques is required. In this communication, we describe eSimDock, a new approach to ligand docking and binding affinity prediction. eSimDock employs nonlinear machine learning-based scoring functions to improve the accuracy of ligand ranking and similarity-based binding pose prediction, and to increase the tolerance to structural imperfections in the target structures. In large-scale benchmarking using the Astex/CCDC data set, we show that 53.9% (67.9%) of the predicted ligand poses have RMSD of <2 Å (<3 Å). Moreover, using binding sites predicted by recently developed eFindSite, eSimDock models ligand binding poses with an RMSD of 4 Å for 50.0-39.7% of the complexes at the protein homology level limited to 80-40%. Simulations against non-native receptor structures, whose mean backbone rearrangements vary from 0.5 to 5.0 Å Cα-RMSD, show that the ratio of docking accuracy and the estimated upper bound is at a constant level of ∼0.65. Pearson correlation coefficient between experimental and predicted by eSimDock Ki values for a large data set of the crystal structures of protein-ligand complexes from BindingDB is 0.58, which decreases only to 0.46 when target structures distorted to 3.0 Å Cα-RMSD are used. Finally, two case studies demonstrate that eSimDock can be customized to specific applications as well. These encouraging results show that the performance of eSimDock is largely unaffected by the deformations of ligand binding regions, thus it represents a practical strategy for across-proteome virtual screening using protein models. eSimDock is freely
Bioanalytical applications of affinity-based nanotube membranes for sensing and separations
Caicedo, Hector Mario
2008-11-01
Nanotechnology has played an important role in the development of research and technology during the last two decades. The contribution of nanotechnology in different fields, along with the versatility of the constructed nanoscale materials, have made nanotechnology one of the most suitable tools to develop particular nanostructures to realize a desired function and application. A nanostructure is simply an entity at the nanometer scale with one, two or three dimensional features. Since nanotechnology covers a broad range of nanoscale materials, to simplify nanotechnology, it can be classified into two categories based on how the nanostructures are prepared: top-down and bottom-up. In the top-down methods, the nanostructures are constructed by chiseling larger bulk materials into entities of smaller size. Conversely, in the bottom-up case, small units are grown or assembled into their desired size and shape. The nanoporous materials specifically have attracted a lot of attention because they can be used for the synthesis of a variety of functional nanostructures of great usefulness in technology. These porous nanostructures usually combine many of the advantages of the top-down and bottom-up methodologies such as flexibility, size controllability, and cost. The research presented in this work utilizes nanoporous membranes to develop porous nanostructured platforms with potential applications in sensing and separations. In particular, this work is centered in fundamental studies for bioanalytical applications of affinity-based nanotube membranes for sensing and separations. A bottom-up methodology like the template synthesis was used to produce silica nanotubes inside of the pores of alumina membrane. The functionalization of the inside walls of these silica nanotube membranes allowed control of the functional behavior and properties of the nanostructured membrane during membrane-based separations and sensing. The general scheme of the work presented here, is
Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.
Brylinski, Michal
2013-11-25
A common strategy for virtual screening considers a systematic docking of a large library of organic compounds into the target sites in protein receptors with promising leads selected based on favorable intermolecular interactions. Despite a continuous progress in the modeling of protein-ligand interactions for pharmaceutical design, important challenges still remain, thus the development of novel techniques is required. In this communication, we describe eSimDock, a new approach to ligand docking and binding affinity prediction. eSimDock employs nonlinear machine learning-based scoring functions to improve the accuracy of ligand ranking and similarity-based binding pose prediction, and to increase the tolerance to structural imperfections in the target structures. In large-scale benchmarking using the Astex/CCDC data set, we show that 53.9% (67.9%) of the predicted ligand poses have RMSD of <2 Å (<3 Å). Moreover, using binding sites predicted by recently developed eFindSite, eSimDock models ligand binding poses with an RMSD of 4 Å for 50.0-39.7% of the complexes at the protein homology level limited to 80-40%. Simulations against non-native receptor structures, whose mean backbone rearrangements vary from 0.5 to 5.0 Å Cα-RMSD, show that the ratio of docking accuracy and the estimated upper bound is at a constant level of ∼0.65. Pearson correlation coefficient between experimental and predicted by eSimDock Ki values for a large data set of the crystal structures of protein-ligand complexes from BindingDB is 0.58, which decreases only to 0.46 when target structures distorted to 3.0 Å Cα-RMSD are used. Finally, two case studies demonstrate that eSimDock can be customized to specific applications as well. These encouraging results show that the performance of eSimDock is largely unaffected by the deformations of ligand binding regions, thus it represents a practical strategy for across-proteome virtual screening using protein models. eSimDock is freely
Writing in the Wild: Writers' Motivation in Fan-Based Affinity Spaces
Curwood, Jen Scott; Magnifico, Alecia Marie; Lammers, Jayne C.
2013-01-01
In order to understand the culture of the physical, virtual, and blended spheres that adolescents inhabit, we build on Gee's concept of affinity spaces. Drawing on our ethnographic research of adolescent literacies related to The Hunger Games novels, the Neopets online game, and The Sims videogames, this article explores the nature of…
A note on geometric method-based procedures to calculate the Hurst exponent
Trinidad Segovia, J. E.; Fernández-Martínez, M.; Sánchez-Granero, M. A.
2012-03-01
Geometric method-based procedures, which we will call GM algorithms hereafter, were introduced in M.A. Sánchez-Granero, J.E. Trinidad Segovia, J. García Pérez, Some comments on Hurst exponent and the long memory processes on capital markets, Phys. A 387 (2008) 5543-5551, to calculate the Hurst exponent of a time series. The authors proved that GM algorithms, based on a geometrical approach, are more accurate than classical algorithms, especially with short length time series. The main contribution of this paper is to provide a mathematical background for the validity of these two algorithms to calculate the Hurst exponent H of random processes with stationary and self-affine increments. In particular, we show that these procedures are valid not only for exploring long memory in classical processes such as (fractional) Brownian motions, but also for estimating the Hurst exponent of (fractional) Lévy stable motions.
Passive Fault Tolerant Control of Piecewise Affine Systems Based on H Infinity Synthesis
DEFF Research Database (Denmark)
Gholami, Mehdi; Cocquempot, vincent; Schiøler, Henrik;
2011-01-01
In this paper we design a passive fault tolerant controller against actuator faults for discretetime piecewise affine (PWA) systems. By using dissipativity theory and H analysis, fault tolerant state feedback controller design is expressed as a set of Linear Matrix Inequalities (LMIs). In the cur......In this paper we design a passive fault tolerant controller against actuator faults for discretetime piecewise affine (PWA) systems. By using dissipativity theory and H analysis, fault tolerant state feedback controller design is expressed as a set of Linear Matrix Inequalities (LMIs......). In the current paper, the PWA system switches not only due to the state but also due to the control input. The method is applied on a large scale livestock ventilation model....
Fractal-Based Exponential Distribution of Urban Density and Self-Affine Fractal Forms of Cities
Chen, Yanguang
2016-01-01
Urban population density always follows the exponential distribution and can be described with Clark's model. Because of this, the spatial distribution of urban population used to be regarded as non-fractal pattern. However, Clark's model differs from the exponential function in mathematics because that urban population is distributed on the fractal support of landform and land-use form. By using mathematical transform and empirical evidence, we argue that there are self-affine scaling relations and local power laws behind the exponential distribution of urban density. The scale parameter of Clark's model indicating the characteristic radius of cities is not a real constant, but depends on the urban field we defined. So the exponential model suggests local fractal structure with two kinds of fractal parameters. The parameters can be used to characterize urban space filling, spatial correlation, self-affine properties, and self-organized evolution. The case study of the city of Hangzhou, China, is employed to ...
Nanotechnology-Based Surface Plasmon Resonance Affinity Biosensors for In Vitro Diagnostics
Antiochia, Riccarda; Bollella, Paolo; Favero, Gabriele
2016-01-01
In the last decades, in vitro diagnostic devices (IVDDs) became a very important tool in medicine for an early and correct diagnosis, a proper screening of targeted population, and also assessing the efficiency of a specific therapy. In this review, the most recent developments regarding different configurations of surface plasmon resonance affinity biosensors modified by using several nanostructured materials for in vitro diagnostics are critically discussed. Both assembly and performances of the IVDDs tested in biological samples are reported and compared. PMID:27594884
Nanotechnology-Based Surface Plasmon Resonance Affinity Biosensors for In Vitro Diagnostics.
Antiochia, Riccarda; Bollella, Paolo; Favero, Gabriele; Mazzei, Franco
2016-01-01
In the last decades, in vitro diagnostic devices (IVDDs) became a very important tool in medicine for an early and correct diagnosis, a proper screening of targeted population, and also assessing the efficiency of a specific therapy. In this review, the most recent developments regarding different configurations of surface plasmon resonance affinity biosensors modified by using several nanostructured materials for in vitro diagnostics are critically discussed. Both assembly and performances of the IVDDs tested in biological samples are reported and compared. PMID:27594884
Energy Technology Data Exchange (ETDEWEB)
Gueltekin, Kemal [Izmir Institute of Technology, Department of Physics, Izmir (Turkey)
2016-03-15
In this study, we give a thorough analysis of a general affine gravity with torsion. After a brief exposition of the affine gravities considered by Eddington and Schroedinger, we construct and analyze different affine gravities based on the determinants of the Ricci tensor, the torsion tensor, the Riemann tensor, and their combinations. In each case we reduce equations of motion to their simplest forms and give a detailed analysis of their solutions. Our analyses lead to the construction of the affine connection in terms of the curvature and torsion tensors. Our solutions of the dynamical equations show that the curvature tensors at different points are correlated via non-local, exponential rescaling factors determined by the torsion tensor. (orig.)
Institute of Scientific and Technical Information of China (English)
LIU Jia-Ming; LIU Zhen-Bo; LI Zhi-Ming; HE Hang-Xia; LIN Wei-Nü; HUANG Ya-Hong; WANG Fang-Mei
2008-01-01
In the presence of heavy atom perturber Pb2+,silicon dioxide nanoparticle containing fluorescein isothiocyanate (FITC-SiO2) could emit a strong and stable room temperature phosphorescence (RTP) signal on the surface of acetyl cellulose membrane (ACM).It was found in the research that a quantitative specific affinity adsorption (AA) reaction between triticum vulgare lectin (WGA) labeled with luminescent nanoparticle and glucose (g)could be carried on the surface of ACM.The product (WGA-G-WGA-FITC-SiO2) of the reaction could emit a stronger RTP signal,and the △Ip had linear correlation to the content of G.According to the facts above,a new method to determine G by affinity adsorption solid substrate room temperature phosphorimetry (AA-SS-RTP) was established,based on WGA labeled with FITC-SiO2.The detection limit (LD) of this method calculated by 3Sb/k was 0.47 pg·spot-1 (corresponding to a concentration value 1.2 × 10-9 g·mL-1,namely 5.3 × 10-9 mol·L-1),the sensitivity was high.Meanwhile,the mechanism for the determination of G by AA-SS-RTP was discussed.
Adjoint affine fusion and tadpoles
Urichuk, Andrew; Walton, Mark A.
2016-06-01
We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.
Adjoint affine fusion and tadpoles
Urichuk, Andrew
2016-01-01
We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows, and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.
Wenhua Han; Xiaohui Shen; Jun Xu; Ping Wang; Guiyun Tian; Zhengyang Wu
2014-01-01
Magnetic flux leakage (MFL) inspection is one of the most important and sensitive nondestructive testing approaches. For online MFL inspection of a long-range railway track or oil pipeline, a fast and effective defect profile estimating method based on a multi-power affine projection algorithm (MAPA) is proposed, where the depth of a sampling point is related with not only the MFL signals before it, but also the ones after it, and all of the sampling points related to one point appear as seri...
A Poisson-based adaptive affinity propagation clustering for SAGE data.
Tang, DongMing; Zhu, QingXin; Yang, Fan
2010-02-01
Serial analysis of gene expression (SAGE) is a powerful tool to obtain gene expression profiles. Clustering analysis is a valuable technique for analyzing SAGE data. In this paper, we propose an adaptive clustering method for SAGE data analysis, namely, PoissonAPS. The method incorporates a novel clustering algorithm, Affinity Propagation (AP). While AP algorithm has demonstrated good performance on many different data sets, it also faces several limitations. PoissonAPS overcomes the limitations of AP using the clustering validation measure as a cost function of merging and splitting, and as a result, it can automatically cluster SAGE data without user-specified parameters. We evaluated PoissonAPS and compared its performance with other methods on several real life SAGE datasets. The experimental results show that PoissonAPS can produce meaningful and interpretable clusters for SAGE data.
Calculation of electromagnetic parameter based on interpolation algorithm
International Nuclear Information System (INIS)
Wave-absorbing material is an important functional material of electromagnetic protection. The wave-absorbing characteristics depend on the electromagnetic parameter of mixed media. In order to accurately predict the electromagnetic parameter of mixed media and facilitate the design of wave-absorbing material, based on the electromagnetic parameters of spherical and flaky carbonyl iron mixture of paraffin base, this paper studied two different interpolation methods: Lagrange interpolation and Hermite interpolation of electromagnetic parameters. The results showed that Hermite interpolation is more accurate than the Lagrange interpolation, and the reflectance calculated with the electromagnetic parameter obtained by interpolation is consistent with that obtained through experiment on the whole. - Highlights: • We use interpolation algorithm on calculation of EM-parameter with limited samples. • Interpolation method can predict EM-parameter well with different particles added. • Hermite interpolation is more accurate than Lagrange interpolation. • Calculating RL based on interpolation is consistent with calculating RL from experiment
Calculation of electromagnetic parameter based on interpolation algorithm
Energy Technology Data Exchange (ETDEWEB)
Zhang, Wenqiang, E-mail: zwqcau@gmail.com [College of Engineering, China Agricultural University, Beijing 100083 (China); Bionic and Micro/Nano/Bio Manufacturing Technology Research Center, Beihang University, Beijing 100191 (China); Yuan, Liming; Zhang, Deyuan [Bionic and Micro/Nano/Bio Manufacturing Technology Research Center, Beihang University, Beijing 100191 (China)
2015-11-01
Wave-absorbing material is an important functional material of electromagnetic protection. The wave-absorbing characteristics depend on the electromagnetic parameter of mixed media. In order to accurately predict the electromagnetic parameter of mixed media and facilitate the design of wave-absorbing material, based on the electromagnetic parameters of spherical and flaky carbonyl iron mixture of paraffin base, this paper studied two different interpolation methods: Lagrange interpolation and Hermite interpolation of electromagnetic parameters. The results showed that Hermite interpolation is more accurate than the Lagrange interpolation, and the reflectance calculated with the electromagnetic parameter obtained by interpolation is consistent with that obtained through experiment on the whole. - Highlights: • We use interpolation algorithm on calculation of EM-parameter with limited samples. • Interpolation method can predict EM-parameter well with different particles added. • Hermite interpolation is more accurate than Lagrange interpolation. • Calculating RL based on interpolation is consistent with calculating RL from experiment.
Dukler, A; Freeman, A
1998-01-01
In situ product removal (ISPR) involves actions taken for the fast removal of a product from the producing cell. ISPR is implemented to improve yield and productivity via minimization of product inhibition, minimization of product losses due to degradation or evaporation, and reduction of the number of subsequent downstream processing steps. Here we describe the implementation of affinity-based, specific ISPR as a crucial component of an integrative approach to problems associated with the biocatalytic production of a product exhibiting poor water solubility from an oily, water-insoluble precursor. Our integrative ISPR-based approach consists of co-immobilization of the oily substrate emulsion and the biocatalyst within bilayered alginate beads. A particulate-specific adsorbent, exhibiting high binding capacity of the product, is suspended in the reaction medium with periodical replacements. According to this approach, ISPR implementation is expected to shift the equilibration of product distribution between the co-immobilized oily substrate and the outer medium via specific product immobilization onto the added adsorbent. The product may subsequently be readily recovered via single-step final purification. This integrative approach was successfully demonstrated by the affinity-based ISPR of gamma-decalactone (4-decanolide). gamma-Decalactone was produced from castor oil via its beta-oxidation by the filamentous fungus Tyromyces sambuceus, co-immobilized with emulsified substrate within bilayered alginate beads. Product immobilization onto medium-suspended epichlorohydrin-crosslinked beta-cyclodextrin resulted in higher yield and easy pure product recovery. PMID:10076845
Directory of Open Access Journals (Sweden)
Jieun Han
Full Text Available Repeat proteins are increasingly attracting much attention as alternative scaffolds to immunoglobulin antibodies due to their unique structural features. Nonetheless, engineering interaction interface and understanding molecular basis for affinity maturation of repeat proteins still remain a challenge. Here, we present a structure-based rational design of a repeat protein with high binding affinity for a target protein. As a model repeat protein, a Toll-like receptor4 (TLR4 decoy receptor composed of leucine-rich repeat (LRR modules was used, and its interaction interface was rationally engineered to increase the binding affinity for myeloid differentiation protein 2 (MD2. Based on the complex crystal structure of the decoy receptor with MD2, we first designed single amino acid substitutions in the decoy receptor, and obtained three variants showing a binding affinity (K(D one-order of magnitude higher than the wild-type decoy receptor. The interacting modes and contributions of individual residues were elucidated by analyzing the crystal structures of the single variants. To further increase the binding affinity, single positive mutations were combined, and two double mutants were shown to have about 3000- and 565-fold higher binding affinities than the wild-type decoy receptor. Molecular dynamics simulations and energetic analysis indicate that an additive effect by two mutations occurring at nearby modules was the major contributor to the remarkable increase in the binding affinities.
Marchenko, N Iu; Marchenkov, V V; Kaĭsheva, A L; Kashparov, I A; Kotova, N V; Kaliman, P A; Semisotnov, G V
2006-12-01
The chaperonin GroEL of the heat shock protein family from Escherichia coli cells can bind various polypeptides lacking rigid tertiary structure and thus prevent their nonspecific association and provide for acquisition of native conformation. In the present work we studied the interaction of GroEL with six denatured proteins (alpha-lactalbumin, ribonuclease A, egg lysozyme in the presence of dithiothreitol, pepsin, beta-casein, and apocytochrome c) possessing negative or positive total charge at neutral pH values and different in hydrophobicity (affinity for a hydrophobic probe ANS). To prevent the influence of nonspecific association of non-native proteins on their interaction with GroEL and make easier the recording of the complexing, the proteins were covalently attached to BrCN-activated Sepharose. At low ionic strength (lower than 60 mM), tight binding of the negatively charged denatured proteins with GroEL (which is also negatively charged) needed relatively low concentrations (approximately 10 mM) of bivalent cations Mg2+ or Ca2+. At the high ionic strength (approximately 600 mM), a tight complex was produced also in the absence of bivalent cations. In contrast, positively charged denatured proteins tightly interacted with GroEL irrespectively of the presence of bivalent cations and ionic strength of the solution (from 20 to 600 mM). These features of GroEL interaction with positively and negatively charged denatured proteins were confirmed by polarized fluorescence (fluorescence anisotropy). The findings suggest that the affinity of GroEL for denatured proteins can be determined by the balance of hydrophobic and electrostatic interactions. PMID:17223789
Yuan, Mingquan; Alocilja, Evangelyn C; Chakrabartty, Shantanu
2016-08-01
This paper presents a wireless, self-powered, affinity-based biosensor based on the integration of paper-based microfluidics with our previously reported method for self-assembling radio-frequency (RF) antennas. At the core of the proposed approach is a silver-enhancement technique that grows portions of a RF antenna in regions where target antigens hybridize with target specific affinity probes. The hybridization regions are defined by a network of nitrocellulose based microfluidic channels which implement a self-powered approach to sample the reagent and control its flow and mixing. The integration substrate for the biosensor has been constructed using polyethylene and the patterning of the antenna on the substrate has been achieved using a low-cost ink-jet printing technique. The substrate has been integrated with passive radio-frequency identification (RFID) tags to demonstrate that the resulting sensor-tag can be used for continuous monitoring in a food supply-chain where direct measurement of analytes is typically considered to be impractical. We validate the proof-of-concept operation of the proposed sensor-tag using IgG as a model analyte and using a 915 MHz Ultra-high-frequency (UHF) RFID tagging technology.
Yuan, Mingquan; Alocilja, Evangelyn C; Chakrabartty, Shantanu
2016-08-01
This paper presents a wireless, self-powered, affinity-based biosensor based on the integration of paper-based microfluidics with our previously reported method for self-assembling radio-frequency (RF) antennas. At the core of the proposed approach is a silver-enhancement technique that grows portions of a RF antenna in regions where target antigens hybridize with target specific affinity probes. The hybridization regions are defined by a network of nitrocellulose based microfluidic channels which implement a self-powered approach to sample the reagent and control its flow and mixing. The integration substrate for the biosensor has been constructed using polyethylene and the patterning of the antenna on the substrate has been achieved using a low-cost ink-jet printing technique. The substrate has been integrated with passive radio-frequency identification (RFID) tags to demonstrate that the resulting sensor-tag can be used for continuous monitoring in a food supply-chain where direct measurement of analytes is typically considered to be impractical. We validate the proof-of-concept operation of the proposed sensor-tag using IgG as a model analyte and using a 915 MHz Ultra-high-frequency (UHF) RFID tagging technology. PMID:27214914
Innovative Product Design Based on Customer Requirement Weight Calculation Model
Institute of Scientific and Technical Information of China (English)
Chen-Guang Guo; Yong-Xian Liu; Shou-Ming Hou; Wei Wang
2010-01-01
In the processes of product innovation and design, it is important for the designers to find and capture customer's focus through customer requirement weight calculation and ranking. Based on the fuzzy set theory and Euclidean space distance, this paper puts forward a method for customer requirement weight calculation called Euclidean space distances weighting ranking method. This method is used in the fuzzy analytic hierarchy process that satisfies the additive consistent fuzzy matrix. A model for the weight calculation steps is constructed;meanwhile, a product innovation design module on the basis of the customer requirement weight calculation model is developed. Finally, combined with the instance of titanium sponge production, the customer requirement weight calculation model is validated. By the innovation design module, the structure of the titanium sponge reactor has been improved and made innovative.
Calculating Track-Based Observables for the LHC
Chang, Hsi-Ming(Department of Physics, University of California at San Diego, La Jolla, CA 92093, USA); Procura, Massimiliano; Thaler, Jesse; Waalewijn, Wouter J.
2013-01-01
By using observables that only depend on charged particles (tracks), one can efficiently suppress pile-up contamination at the LHC. Such measurements are not infrared safe in perturbation theory, so any calculation of track-based observables must account for hadronization effects. We develop a formalism to perform these calculations in QCD, by matching partonic cross sections onto new non-perturbative objects called track functions which absorb infrared divergences. The track function T_i(x) ...
An extended affinity propagation clustering method based on different data density types.
Zhao, XiuLi; Xu, WeiXiang
2015-01-01
Affinity propagation (AP) algorithm, as a novel clustering method, does not require the users to specify the initial cluster centers in advance, which regards all data points as potential exemplars (cluster centers) equally and groups the clusters totally by the similar degree among the data points. But in many cases there exist some different intensive areas within the same data set, which means that the data set does not distribute homogeneously. In such situation the AP algorithm cannot group the data points into ideal clusters. In this paper, we proposed an extended AP clustering algorithm to deal with such a problem. There are two steps in our method: firstly the data set is partitioned into several data density types according to the nearest distances of each data point; and then the AP clustering method is, respectively, used to group the data points into clusters in each data density type. Two experiments are carried out to evaluate the performance of our algorithm: one utilizes an artificial data set and the other uses a real seismic data set. The experiment results show that groups are obtained more accurately by our algorithm than OPTICS and AP clustering algorithm itself.
Directory of Open Access Journals (Sweden)
Masato Kiyoshi
Full Text Available The optimization of antibodies is a desirable goal towards the development of better therapeutic strategies. The antibody 11K2 was previously developed as a therapeutic tool for inflammatory diseases, and displays very high affinity (4.6 pM for its antigen the chemokine MCP-1 (monocyte chemo-attractant protein-1. We have employed a virtual library of mutations of 11K2 to identify antibody variants of potentially higher affinity, and to establish benchmarks in the engineering of a mature therapeutic antibody. The most promising candidates identified in the virtual screening were examined by surface plasmon resonance to validate the computational predictions, and to characterize their binding affinity and key thermodynamic properties in detail. Only mutations in the light-chain of the antibody are effective at enhancing its affinity for the antigen in vitro, suggesting that the interaction surface of the heavy-chain (dominated by the hot-spot residue Phe101 is not amenable to optimization. The single-mutation with the highest affinity is L-N31R (4.6-fold higher affinity than wild-type antibody. Importantly, all the single-mutations showing increase affinity incorporate a charged residue (Arg, Asp, or Glu. The characterization of the relevant thermodynamic parameters clarifies the energetic mechanism. Essentially, the formation of new electrostatic interactions early in the binding reaction coordinate (transition state or earlier benefits the durability of the antibody-antigen complex. The combination of in silico calculations and thermodynamic analysis is an effective strategy to improve the affinity of a matured therapeutic antibody.
Affinity Purification of Insulin by Peptide-Ligand Affinity Chromatography
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
The affinity heptapeptide (HWWWPAS) for insulin, selected from phage display library,was coupled to EAH Sepharose 4B gel and packed to a 1-mL column. The column was used for the affinity purification of insulin from protein mixture and commercial insulin preparation. It was observed that the minor impurity in the commercial insulin was removed by the affinity chromatography. Nearly 40 mg of insulin could be purified with the 1-mL affinity column. The results revealed the high specificity and capacity of the affinity column for insulin purification. Moreover, based on the analysis of the amino acids in the peptide sequence, shorter peptides were designed and synthesized for insulin chromatography. As a result, HWWPS was found to be a good alternative to HWWWPAS, while the other two peptides with three or four amino acids showed weak affinity for insulin. The results indicated that the peptide sequence of HWWWPAS was quite conservative for specific binding of insulin.
Oss-Ronen, Liat; Seliktar, Dror
2011-01-01
Serum albumin was conjugated to poly-(ethylene glycol) (PEG) and cross-linked to form mono-PEGylated albumin hydrogels. These hydrogels were used as a basis for drug carrying tissue engineering scaffold materials, based on the natural affinity of various drugs and compounds for the tethered albumin in the polymer network. The results of the drug release validation experiments showed that the release kinetics of the drugs from the mono-PEGylated albumin hydrogels were controlled by the molecular weight (MW) of PEG conjugated to the albumin protein, the drug MW and its inherent affinity for albumin. Composite hydrogels containing both mono-PEGylated albumin and PEGylated fibrinogen were used specifically for three-dimensional (3D) cell culture scaffolds, with inherent bioactivity, proteolytic biodegradability and controlled drug release properties. The specific characteristics of these complex hydrogels were governed by the ratio between the concentrations of each protein, the addition of free PEG diacrylate (PEG DA) molecules to the hydrogel matrix and the MW of the PEG conjugated to each protein. Comprehensive characterization of the drug release and degradation properties, as well as 3D cell culture experiments using these composite materials, demonstrated the effectiveness of this combined approach in creating a tissue engineering scaffold material with controlled drug release features. PMID:20643230
Directory of Open Access Journals (Sweden)
Yansheng Li
2016-08-01
Full Text Available With the urgent demand for automatic management of large numbers of high-resolution remote sensing images, content-based high-resolution remote sensing image retrieval (CB-HRRS-IR has attracted much research interest. Accordingly, this paper proposes a novel high-resolution remote sensing image retrieval approach via multiple feature representation and collaborative affinity metric fusion (IRMFRCAMF. In IRMFRCAMF, we design four unsupervised convolutional neural networks with different layers to generate four types of unsupervised features from the fine level to the coarse level. In addition to these four types of unsupervised features, we also implement four traditional feature descriptors, including local binary pattern (LBP, gray level co-occurrence (GLCM, maximal response 8 (MR8, and scale-invariant feature transform (SIFT. In order to fully incorporate the complementary information among multiple features of one image and the mutual information across auxiliary images in the image dataset, this paper advocates collaborative affinity metric fusion to measure the similarity between images. The performance evaluation of high-resolution remote sensing image retrieval is implemented on two public datasets, the UC Merced (UCM dataset and the Wuhan University (WH dataset. Large numbers of experiments show that our proposed IRMFRCAMF can significantly outperform the state-of-the-art approaches.
D.F. Schrager
2006-01-01
We propose a new model for stochastic mortality. The model is based on the literature on affine term structure models. It satisfies three important requirements for application in practice: analytical tractibility, clear interpretation of the factors and compatibility with financial option pricing m
Caso, Giuseppe; de Nardis, Luca; di Benedetto, Maria-Gabriella
2015-01-01
The weighted k-nearest neighbors (WkNN) algorithm is by far the most popular choice in the design of fingerprinting indoor positioning systems based on WiFi received signal strength (RSS). WkNN estimates the position of a target device by selecting k reference points (RPs) based on the similarity of their fingerprints with the measured RSS values. The position of the target device is then obtained as a weighted sum of the positions of the k RPs. Two-step WkNN positioning algorithms were recently proposed, in which RPs are divided into clusters using the affinity propagation clustering algorithm, and one representative for each cluster is selected. Only cluster representatives are then considered during the position estimation, leading to a significant computational complexity reduction compared to traditional, flat WkNN. Flat and two-step WkNN share the issue of properly selecting the similarity metric so as to guarantee good positioning accuracy: in two-step WkNN, in particular, the metric impacts three different steps in the position estimation, that is cluster formation, cluster selection and RP selection and weighting. So far, however, the only similarity metric considered in the literature was the one proposed in the original formulation of the affinity propagation algorithm. This paper fills this gap by comparing different metrics and, based on this comparison, proposes a novel mixed approach in which different metrics are adopted in the different steps of the position estimation procedure. The analysis is supported by an extensive experimental campaign carried out in a multi-floor 3D indoor positioning testbed. The impact of similarity metrics and their combinations on the structure and size of the resulting clusters, 3D positioning accuracy and computational complexity are investigated. Results show that the adoption of metrics different from the one proposed in the original affinity propagation algorithm and, in particular, the combination of different
A density gradient theory based method for surface tension calculations
DEFF Research Database (Denmark)
Liang, Xiaodong; Michelsen, Michael Locht; Kontogeorgis, Georgios
2016-01-01
The density gradient theory has been becoming a widely used framework for calculating surface tension, within which the same equation of state is used for the interface and bulk phases, because it is a theoretically sound, consistent and computationally affordable approach. Based on the observati...
An improved LMI-based approach for stability of piecewise affine time-delay systems with uncertainty
Duan, Shiming; Ni, Jun; Galip Ulsoy, A.
2012-09-01
The stability problem for uncertain piecewise affine (PWA) time-delay systems is investigated in this article. It is assumed that there exists a known constant time delay in the system and the uncertainly is norm-bounded. Sufficient conditions for the stability of nominal systems and the stability of systems subject to uncertainty are derived using the Lyapunov-Krasovskii functional with a triple integration term. This approach handles switching based on the delayed states (in addition to the states) for a PWA time-delay system, considers structured as well as unstructured uncertainty and reduces the conservativeness of previous approaches. The effectiveness of the proposed approach is demonstrated by comparing with the existing methods through numerical examples.
Han, Wenhua; Shen, Xiaohui; Xu, Jun; Wang, Ping; Tian, Guiyun; Wu, Zhengyang
2014-01-01
Magnetic flux leakage (MFL) inspection is one of the most important and sensitive nondestructive testing approaches. For online MFL inspection of a long-range railway track or oil pipeline, a fast and effective defect profile estimating method based on a multi-power affine projection algorithm (MAPA) is proposed, where the depth of a sampling point is related with not only the MFL signals before it, but also the ones after it, and all of the sampling points related to one point appear as serials or multi-power. Defect profile estimation has two steps: regulating a weight vector in an MAPA filter and estimating a defect profile with the MAPA filter. Both simulation and experimental data are used to test the performance of the proposed method. The results demonstrate that the proposed method exhibits high speed while maintaining the estimated profiles clearly close to the desired ones in a noisy environment, thereby meeting the demand of accurate online inspection. PMID:25192314
Software-Based Visual Loan Calculator For Banking Industry
Isizoh, A. N.; Anazia, A. E.; Okide, S. O. 3; Onyeyili, T. I.; Okwaraoka, C. A. P.
2012-03-01
industry is very necessary in modern day banking system using many design techniques for security reasons. This paper thus presents the software-based design and implementation of a Visual Loan calculator for banking industry using Visual Basic .Net (VB.Net). The fundamental approach to this is to develop a Graphical User Interface (GUI) using VB.Net operating tools, and then developing a working program which calculates the interest of any loan obtained. The VB.Net programming was done, implemented and the software proved satisfactory.
Functional group based Ligand binding affinity scoring function at atomic environmental level
Varadwaj, Pritish Kumar; Lahiri, Tapobrata
2009-01-01
Use of knowledge based scoring function (KBSF) for virtual screening and molecular docking has become an established method for drug discovery. Lack of a precise and reliable free energy function that describes several interactions including water-mediated atomic interaction between amino-acid residues and ligand makes distance based statistical measure as the only alternative. Till now all the distance based scoring functions in KBSF arena use atom singularity concept, which neglects the env...
Electric field calculations in brain stimulation based on finite elements
DEFF Research Database (Denmark)
Windhoff, Mirko; Opitz, Alexander; Thielscher, Axel
2013-01-01
The need for realistic electric field calculations in human noninvasive brain stimulation is undisputed to more accurately determine the affected brain areas. However, using numerical techniques such as the finite element method (FEM) is methodologically complex, starting with the creation...... high-quality head models from magnetic resonance images and their usage in subsequent field calculations based on the FEM. The pipeline starts by extracting the borders between skin, skull, cerebrospinal fluid, gray and white matter. The quality of the resulting surfaces is subsequently improved...... the successful usage of the pipeline in six subjects, including field calculations for transcranial magnetic stimulation and transcranial direct current stimulation. The quality of the head volume meshes is validated both in terms of capturing the underlying anatomy and of the well-shapedness of the mesh...
Structure-based virtual screening of novel, high-affinity BRD4 inhibitors.
Muvva, Charuvaka; Singam, E R Azhagiya; Raman, S Sundar; Subramanian, V
2014-07-29
Bromodomains (BRDs) are a diverse family of evolutionarily conserved protein-interaction modules. Among various members of the bromodomain and extra terminal domain family, BRD4 is found to be an important target for many diseases such as cancer, acute myeloid leukemia, multiple myeloma, Burkitt's lymphoma, etc. Therefore, in this study an attempt has been made to screen compounds from NCI Diversity, Drug Bank and Toslab Databases targeting the Kac binding site of BRD4 using molecular docking, molecular dynamics simulations, MM-PB/GBSA binding free energy calculations and steered molecular dynamics simulations. Using virtual screening and docking, we have identified 11 inhibitors. These new inhibitors exhibit binding energy values higher than that of the (+)JQ1 inhibitor which is effective against BRD4. However, due to the toxicity of (+)JQ1, the designing of new inhibitors becomes significantly important. Thus, these new 11 ligands were systematically analyzed using other computational investigations. Results reveal that the compounds ZINC01411240, ZINC19632618 and ZINC04818522 could be potential drug candidates for targeting BRD4. It can also be seen from the results that there is a linear relationship between the results obtained from the SMD simulation and free energy obtained from the MM-PBSA/GBSA approach. This study clearly illustrates that the steered molecular dynamics can be effectively used for the design of new inhibitors. PMID:24976024
Alternative affinity tools: more attractive than antibodies?
Ruigrok, V.J.B.; Levisson, M.; Eppink, M.H.M.; Smidt, H.; Oost, van der J.
2011-01-01
Antibodies are the most successful affinity tools used today, in both fundamental and applied research (diagnostics, purification and therapeutics). Nonetheless, antibodies do have their limitations, including high production costs and low stability. Alternative affinity tools based on nucleic acids
Novel and high affinity fluorescent ligands for the serotonin transporter based on (s)-citalopram
DEFF Research Database (Denmark)
Kumar, Vivek; Rahbek-Clemmensen, Troels; Billesbølle, Christian B;
2014-01-01
Novel rhodamine-labeled ligands, based on (S)-citalopram, were synthesized and evaluated for uptake inhibition at the human serotonin, dopamine, and norepinephrine transporters (hSERT, hDAT, and hNET, respectively) and for binding at SERT, in transiently transfected COS7 cells. Compound 14 demons...
Highly sensitive voltammetric biosensor for nitric oxide based on its high affinity with hemoglobin
International Nuclear Information System (INIS)
Although heme protein-based, amperometric nitric oxide (NO) biosensors have been well documented in previous studies, most have been conducted in anaerobic conditions. Herein we report a novel hemoglobin-based NO biosensor that is not only very sensitive but also usable in air. The heme protein was entrapped in a sodium montmorillonite film, which was immobilized at a pyrolytic graphite electrode surface. Film-entrapped hemoglobin can directly exchange electrons with the electrode, and this process has proven to favor the catalytic reduction of oxygen. In addition, NO induced a cathodic potential shift of the catalytic reduction peak of oxygen. This potential shift was proportional to the logarithm of NO concentration ranging from 4.0 x 10-11 to 5.0 x 10-6 mol/L. The detection limit has been estimated to be 20 pM, approximately four orders lower than previously reported amperometric detectors
The role of taste affinity in agent-based models for social recommendation
Cimini, Giulio; Medo, Matus; Chen, Duanbing
2013-01-01
In the Internet era, online social media emerged as the main tool for sharing opinions and information among individuals. In this work we study an adaptive model of a social network where directed links connect users with similar tastes, and over which information propagates through social recommendation. Agent-based simulations of two different artificial settings for modeling user tastes are compared with patterns seen in real data, suggesting that users differing in their scope of interests is a more realistic assumption than users differing only in their particular interests. We further introduce an extensive set of similarity metrics based on users' past assessments, and evaluate their use in the given social recommendation model with both artificial simulations and real data. Superior recommendation performance is observed for similarity metrics that give preference to users with small scope---who thus act as selective filters in social recommendation.
New Products and Technologies, Based on Calculations Developed Areas
Directory of Open Access Journals (Sweden)
Gheorghe Vertan
2013-09-01
Full Text Available Following statistics, currently prosperous and have high GDP / capita, only countries that have and fructify intensively large natural resources and/or produce and export products massive based on patented inventions accordingly. Without great natural wealth and the lowest GDP / capita in the EU, Romania will prosper only with such products. Starting from the top experience in the country, some patented, can develop new and competitive technologies and patentable and exportable products, based on exact calculations of developed areas, such as that double shells welded assemblies and plating of ships' propellers and blade pump and hydraulic turbines.
DEFF Research Database (Denmark)
Skjødt, Mette Louise
linker for yeast surface display of scFv and scFab fragments, we compared a series of different Gly-Ser-based linkers in display and antigen binding proficiency. We show that these formats of the model antibody can accommodate linkers of different lengths and that introduction of alanine or glutamate......-2. Based on the presented data we suggest that affinity maturation of the model antibody proceeds through multiple incremental steps of subtle improvements. We moreover conclude that the best affinity improved candidates are likely to be obtained through optimization of both the antigen...... fragments by in vivo homologous recombination large combinatorial antibody libraries can easily be generated. We have optimized ordered assembly of three CDR fragments into a gapped vector and observed increased transformation efficiency in a yeast strain carrying a deletion of the SGS1 helicase...
Vertical emission profiles for Europe based on plume rise calculations.
Bieser, J; Aulinger, A; Matthias, V; Quante, M; Denier van der Gon, H A C
2011-10-01
The vertical allocation of emissions has a major impact on results of Chemistry Transport Models. However, in Europe it is still common to use fixed vertical profiles based on rough estimates to determine the emission height of point sources. This publication introduces a set of new vertical profiles for the use in chemistry transport modeling that were created from hourly gridded emissions calculated by the SMOKE for Europe emission model. SMOKE uses plume rise calculations to determine effective emission heights. Out of more than 40,000 different vertical emission profiles 73 have been chosen by means of hierarchical cluster analysis. These profiles show large differences to those currently used in many emission models. Emissions from combustion processes are released in much lower altitudes while those from production processes are allocated to higher altitudes. The profiles have a high temporal and spatial variability which is not represented by currently used profiles. PMID:21561695
Chen, Zheng; Jagannathan, Sarangapani
2008-01-01
In this paper, we consider the use of nonlinear networks towards obtaining nearly optimal solutions to the control of nonlinear discrete-time (DT) systems. The method is based on least squares successive approximation solution of the generalized Hamilton-Jacobi-Bellman (GHJB) equation which appears in optimization problems. Successive approximation using the GHJB has not been applied for nonlinear DT systems. The proposed recursive method solves the GHJB equation in DT on a well-defined region of attraction. The definition of GHJB, pre-Hamiltonian function, HJB equation, and method of updating the control function for the affine nonlinear DT systems under small perturbation assumption are proposed. A neural network (NN) is used to approximate the GHJB solution. It is shown that the result is a closed-loop control based on an NN that has been tuned a priori in offline mode. Numerical examples show that, for the linear DT system, the updated control laws will converge to the optimal control, and for nonlinear DT systems, the updated control laws will converge to the suboptimal control. PMID:18269941
Hu, Fangxin; Chen, Shihong; Wang, Chengyan; Yuan, Ruo; Xiang, Yun; Wang, Cun
2012-04-15
In this paper, a novel method for detecting concanavalin A (Con A) was developed based on lectin-carbohydrate biospecific interactions. Multi-wall carbon nanotube-polyaniline (MWNT-PANI) nanocomposites, synthesized by in situ polymerization, were chosen to immobilize d-glucose through the Schiff-base reaction. The immobilized D-glucose showed high binding sensitivity and excellent selectivity to its target lectin, Con A. Cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), transmission electron microscopy (TEM) and atomic force microscopy (AFM) were applied to characterize the assembly process of the modified electrode. Due to the high affinity of Con A for D-glucose and high stability of the propounded sensing platform, the fabricated biosensor achieved ultrasensitive detection of Con A with good sensitivity, acceptable reproducibility and stability. The changes of response current were proportional to the Con A concentrations from 3.3 pM to 9.3 nM, with a detection limit of 1.0 pM. Therefore, the combination of MWNT-PANI nanocomposites and the special binding force between lectin and carbohydrate provides an efficient and promising platform for the fabrication of bioelectrochemical devices.
Zhao, Qiming; Xu, Hao; Jagannathan, Sarangapani
2015-03-01
In this paper, the finite-horizon optimal control design for nonlinear discrete-time systems in affine form is presented. In contrast with the traditional approximate dynamic programming methodology, which requires at least partial knowledge of the system dynamics, in this paper, the complete system dynamics are relaxed utilizing a neural network (NN)-based identifier to learn the control coefficient matrix. The identifier is then used together with the actor-critic-based scheme to learn the time-varying solution, referred to as the value function, of the Hamilton-Jacobi-Bellman (HJB) equation in an online and forward-in-time manner. Since the solution of HJB is time-varying, NNs with constant weights and time-varying activation functions are considered. To properly satisfy the terminal constraint, an additional error term is incorporated in the novel update law such that the terminal constraint error is also minimized over time. Policy and/or value iterations are not needed and the NN weights are updated once a sampling instant. The uniform ultimate boundedness of the closed-loop system is verified by standard Lyapunov stability theory under nonautonomous analysis. Numerical examples are provided to illustrate the effectiveness of the proposed method. PMID:25720005
Calculation of the debris flow concentration based on clay content
Institute of Scientific and Technical Information of China (English)
CHEN; Ningsheng; CUI; Peng; LIU; Zhonggang; WEI; Fangqiang
2003-01-01
The debris flow clay content has very tremendous influence on its concentration (γC). It is reported that the concentration can be calculated by applying the relative polynomial based on the clay content. Here one polynomial model and one logarithm model to calculate the concentration based on the clay content for both the ordinary debris flow and viscous debris flow are obtained. The result derives from the statistics and analysis of the relationship between the debris flow concentrations and clay content in 45 debris flow sites located in the southwest of China. The models can be applied for the concentration calculation to those debris flows that are impossible to observe. The models are available to calculate the debris flow concentration, the principles of which are in the clay content affecting on the debris flow formation, movement and suspending particle diameter. The mechanism of the relationship of the clay content and concentration is clear and reliable. The debris flow is usually of micro-viscous when the clay content is low (<3%), by analyzing the developing tendency on the basics of the relationship between the clay content and debris flow concentration. Indeed, the less the clay content, the less the concentration for most debris flows. The debris flow tends to become the water rock flow or the hyperconcentrated flow with the clay content decrease. Through statistics it is apt to transform the soil into the viscous debris flow when the clay content of ranges is in 3%-18%. Its concentration increases with the increasing of the clay content when the clay content is between 5% and 10%. But the value decreases with the increasing of the clay content when the clay content is between 10% and 18%. It is apt to transform the soil into the mudflow, when the clay content exceeds 18%. The concentration of the mudflow usually decreases with the increase of the clay content, and this developing tendency reverses to that of the micro-viscous debris flow. There is
Craig, Hugh; Berretta, Regina; Moscato, Pablo
2016-01-01
In this study we propose a novel, unsupervised clustering methodology for analyzing large datasets. This new, efficient methodology converts the general clustering problem into the community detection problem in graph by using the Jensen-Shannon distance, a dissimilarity measure originating in Information Theory. Moreover, we use graph theoretic concepts for the generation and analysis of proximity graphs. Our methodology is based on a newly proposed memetic algorithm (iMA-Net) for discovering clusters of data elements by maximizing the modularity function in proximity graphs of literary works. To test the effectiveness of this general methodology, we apply it to a text corpus dataset, which contains frequencies of approximately 55,114 unique words across all 168 written in the Shakespearean era (16th and 17th centuries), to analyze and detect clusters of similar plays. Experimental results and comparison with state-of-the-art clustering methods demonstrate the remarkable performance of our new method for identifying high quality clusters which reflect the commonalities in the literary style of the plays. PMID:27571416
Naeni, Leila M; Craig, Hugh; Berretta, Regina; Moscato, Pablo
2016-01-01
In this study we propose a novel, unsupervised clustering methodology for analyzing large datasets. This new, efficient methodology converts the general clustering problem into the community detection problem in graph by using the Jensen-Shannon distance, a dissimilarity measure originating in Information Theory. Moreover, we use graph theoretic concepts for the generation and analysis of proximity graphs. Our methodology is based on a newly proposed memetic algorithm (iMA-Net) for discovering clusters of data elements by maximizing the modularity function in proximity graphs of literary works. To test the effectiveness of this general methodology, we apply it to a text corpus dataset, which contains frequencies of approximately 55,114 unique words across all 168 written in the Shakespearean era (16th and 17th centuries), to analyze and detect clusters of similar plays. Experimental results and comparison with state-of-the-art clustering methods demonstrate the remarkable performance of our new method for identifying high quality clusters which reflect the commonalities in the literary style of the plays. PMID:27571416
Erdas, Ozlem; Andac, Cenk A; Gurkan-Alp, A Selen; Alpaslan, Ferda Nur; Buyukbingol, Erdem
2015-01-01
The aim of this study is to propose an improved computational methodology, which is called Compressed Images for Affinity Prediction-2 (CIFAP-2) to predict binding affinities of structurally related protein-ligand complexes. CIFAP-2 method is established based on a protein-ligand model from which computational affinity information is obtained by utilizing 2D electrostatic potential images determined for the binding site of protein-ligand complexes. The quality of the prediction of the CIFAP-2 algorithm was tested using partial least squares regression (PLSR) as well as support vector regression (SVR) and adaptive neuro-fuzzy ınference system (ANFIS), which are highly promising prediction methods in drug design. CIFAP-2 was applied on a protein-ligand complex system involving Caspase 3 (CASP3) and its 35 inhibitors possessing a common isatin sulfonamide pharmacophore. As a result, PLSR affinity prediction for the CASP3-ligand complexes gave rise to the most consistent information with reported empirical binding affinities (pIC(50)) of the CASP3 inhibitors. PMID:25578823
Ruiz-May, Eliel; Hucko, Simon; Kevin J. Howe; Zhang, Sheng; Sherwood, Robert W.; Thannhauser, Theodore W; Rose, Jocelyn K. C.
2013-01-01
Lectin affinity chromatography (LAC) can provide a valuable front-end enrichment strategy for the study of N-glycoproteins and has been used to characterize a broad range eukaryotic N-glycoproteomes. Moreover, studies with mammalian systems have suggested that the use of multiple lectins with different affinities can be particularly effective. A multi-lectin approach has also been reported to provide a significant benefit for the analysis of plant N-glycoproteins; however, it has yet to be de...
DEFF Research Database (Denmark)
Pinto, Andrea; Conti, Paola; Grazioso, Giovanni;
2011-01-01
The synthesis of four new isoxazoline-based amino acids being analogues of previously described glutamate receptor ligands is reported and their affinity for ionotropic glutamate receptors is analyzed in comparison with that of selected model compounds. Molecular modelling investigations have bee...
A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders.
Cui, Naiwen; Zhang, Huidan; Schneider, Nils; Tao, Ye; Asahara, Haruichi; Sun, Zhiyi; Cai, Yamei; Koehler, Stephan A; de Greef, Tom F A; Abbaspourrad, Alireza; Weitz, David A; Chong, Shaorong
2016-01-01
Drop-based microfluidics have recently become a novel tool by providing a stable linkage between phenotype and genotype for high throughput screening. However, use of drop-based microfluidics for screening high-affinity peptide binders has not been demonstrated due to the lack of a sensitive functional assay that can detect single DNA molecules in drops. To address this sensitivity issue, we introduced in vitro two-hybrid system (IVT2H) into microfluidic drops and developed a streamlined mix-and-read drop-IVT2H method to screen a random DNA library. Drop-IVT2H was based on the correlation between the binding affinity of two interacting protein domains and transcriptional activation of a fluorescent reporter. A DNA library encoding potential peptide binders was encapsulated with IVT2H such that single DNA molecules were distributed in individual drops. We validated drop-IVT2H by screening a three-random-residue library derived from a high-affinity MDM2 inhibitor PMI. The current drop-IVT2H platform is ideally suited for affinity screening of small-to-medium-sized libraries (10(3)-10(6)). It can obtain hits within a single day while consuming minimal amounts of reagents. Drop-IVT2H simplifies and accelerates the drop-based microfluidics workflow for screening random DNA libraries, and represents a novel alternative method for protein engineering and in vitro directed protein evolution. PMID:26940078
Hierarchical Affinity Propagation
Givoni, Inmar; Frey, Brendan J
2012-01-01
Affinity propagation is an exemplar-based clustering algorithm that finds a set of data-points that best exemplify the data, and associates each datapoint with one exemplar. We extend affinity propagation in a principled way to solve the hierarchical clustering problem, which arises in a variety of domains including biology, sensor networks and decision making in operational research. We derive an inference algorithm that operates by propagating information up and down the hierarchy, and is efficient despite the high-order potentials required for the graphical model formulation. We demonstrate that our method outperforms greedy techniques that cluster one layer at a time. We show that on an artificial dataset designed to mimic the HIV-strain mutation dynamics, our method outperforms related methods. For real HIV sequences, where the ground truth is not available, we show our method achieves better results, in terms of the underlying objective function, and show the results correspond meaningfully to geographi...
DEFF Research Database (Denmark)
Guglielmi, Michel; Johannesen, Hl
2004-01-01
and potential situations but also virtual events that calls for an undeterminated process of resolution. This process is activated by the user who co-produces the actualisation as an answer to a virtual reality that we defined at the first place. The potential situations or the possible it is a fantomatic real...... of belonging to people sharing deterritorialized synchronic experiences. But at the same time, the immersion experience is highly low tech and desperately analog, mainly based on fabulation, cartoons, and mushrooms growing in local forests. It ultimately appeals to the experienced sense of tangible reality....
Jantra, Jongjit; Kanatharana, Proespichaya; Asawatreratanakul, Punnee; Hedström, Martin; Mattiasson, Bo; Thavarungkul, Panote
2011-01-01
This work presents the results of the use of flow injection surface plasmon resonance and impedimetric affinity biosensors for detecting and enumerating total bacteria based on the binding between E. coli and Con A, immobilized on a modified gold electrode. The single analysis time for both techniques was less than 20 min. Dissociation between the immobilized Con A and the E. coli using 200 mM of glucose in HCl at pH of 2.00 enabling the sensor to be reused for between 29-35 times. Impedimetric detection provided a much lower limit of detection (12 CFU mL(-1)) than the surface plasmon resonance method (6.1 × 10(7) CFU mL(-1)). Using the impedimetric system, real sample analysis was performed and the results were compared to the plate count agar method. Cell concentrations obtained by the biosensor were only slightly different from the result obtained from the plate count agar. The proposed system offers a rapid and useful tool for screening detection and enumeration of total bacteria. PMID:21961522
Arabzadeh, Abbas; Salimi, Abdollah
2015-12-15
In this study, we reported iminodiacetic acid-copper ion complex (IDA-Cu) immobilized onto gold nanoparticles (GNPs)-modified glassy carbon electrode as a novel electrochemical platform for selective and sensitive determination of lysozyme (Lys). IDA-Cu complex acted as an efficient recognition element capable of capturing Lys molecules. GNPs acts as a substrate to immobilize IDA-Cu coordinative complex and its interaction with Lys leds to a great signal amplification through measuring changes in differential pulse voltammetric (DPV) peak current of [Fe(CN)6](3-/4-) redox probe. Upon the recognition of the Lys to the IDA-Cu, the peak current decreased due to the hindered electron transfer reaction on the electrode surface. Under optimum condition, it was found that the proposed method could detect Lys at wide linear concentration range (0.1 pM to 0.10 mM) with detection limit of 60 fM. Furthermore, electrochemical impedance spectroscopy (EIS) detection of Lys was demonstrated as a simple and rapid alternative analytical technique with detection limit of 80 fM at concentration range up to 0.1mM. In addition, the proposed sensor was satisfactorily applied to the determination of Lys in real samples such as hen egg white. The proposed modified electrode showing the high selectivity, good sensitivity and stability toward Lys detection may hold a great promise in developing other electrochemical sensors based on metal-chelate affinity complexes.
Aronoff-Spencer, Eliah; Venkatesh, A G; Sun, Alex; Brickner, Howard; Looney, David; Hall, Drew A
2016-12-15
Yeast cell lines were genetically engineered to display Hepatitis C virus (HCV) core antigen linked to gold binding peptide (GBP) as a dual-affinity biobrick chimera. These multifunctional yeast cells adhere to the gold sensor surface while simultaneously acting as a "renewable" capture reagent for anti-HCV core antibody. This streamlined functionalization and detection strategy removes the need for traditional purification and immobilization techniques. With this biobrick construct, both optical and electrochemical immunoassays were developed. The optical immunoassays demonstrated detection of anti-HCV core antibody down to 12.3pM concentrations while the electrochemical assay demonstrated higher binding constants and dynamic range. The electrochemical format and a custom, low-cost smartphone-based potentiostat ($20 USD) yielded comparable results to assays performed on a state-of-the-art electrochemical workstation. We propose this combination of synthetic biology and scalable, point-of-care sensing has potential to provide low-cost, cutting edge diagnostic capability for many pathogens in a variety of settings.
Directory of Open Access Journals (Sweden)
Wenhua Han
2014-09-01
Full Text Available Magnetic flux leakage (MFL inspection is one of the most important and sensitive nondestructive testing approaches. For online MFL inspection of a long-range railway track or oil pipeline, a fast and effective defect profile estimating method based on a multi-power affine projection algorithm (MAPA is proposed, where the depth of a sampling point is related with not only the MFL signals before it, but also the ones after it, and all of the sampling points related to one point appear as serials or multi-power. Defect profile estimation has two steps: regulating a weight vector in an MAPA filter and estimating a defect profile with the MAPA filter. Both simulation and experimental data are used to test the performance of the proposed method. The results demonstrate that the proposed method exhibits high speed while maintaining the estimated profiles clearly close to the desired ones in a noisy environment, thereby meeting the demand of accurate online inspection.
Aronoff-Spencer, Eliah; Venkatesh, A G; Sun, Alex; Brickner, Howard; Looney, David; Hall, Drew A
2016-12-15
Yeast cell lines were genetically engineered to display Hepatitis C virus (HCV) core antigen linked to gold binding peptide (GBP) as a dual-affinity biobrick chimera. These multifunctional yeast cells adhere to the gold sensor surface while simultaneously acting as a "renewable" capture reagent for anti-HCV core antibody. This streamlined functionalization and detection strategy removes the need for traditional purification and immobilization techniques. With this biobrick construct, both optical and electrochemical immunoassays were developed. The optical immunoassays demonstrated detection of anti-HCV core antibody down to 12.3pM concentrations while the electrochemical assay demonstrated higher binding constants and dynamic range. The electrochemical format and a custom, low-cost smartphone-based potentiostat ($20 USD) yielded comparable results to assays performed on a state-of-the-art electrochemical workstation. We propose this combination of synthetic biology and scalable, point-of-care sensing has potential to provide low-cost, cutting edge diagnostic capability for many pathogens in a variety of settings. PMID:27472403
International Nuclear Information System (INIS)
The aim of this study was to develop a software application that performs calculation shields in radiology room depending on the type of equipment. The calculation will be done by selecting the user, the method proposed in the Guide 5.11, the Report 144 and 147 and also for the methodology given by the Portuguese Health Ministry. (Author)
Lifeline system network reliability calculation based on GIS and FTA
Institute of Scientific and Technical Information of China (English)
TANG Ai-ping; OU Jin-ping; LU Qin-nian; ZHANG Ke-xu
2006-01-01
Lifelines, such as pipeline, transportation, communication, electric transmission and medical rescue systems, are complicated networks that always distribute spatially over large geological and geographic units.The quantification of their reliability under an earthquake occurrence should be highly regarded, because the performance of these systems during a destructive earthquake is vital in order to estimate direct and indirect economic losses from lifeline failures, and is also related to laying out a rescue plan. The research in this paper aims to develop a new earthquake reliability calculation methodology for lifeline systems. The methodology of the network reliability for lifeline systems is based on fault tree analysis (FTA) and geological information system(GIS). The interactions existing in a lifeline system are considered herein. The lifeline systems are idealized as equivalent networks, consisting of nodes and links, and are described by network analysis in GIS. Firstly, the node is divided into two types: simple node and complicated node, where the reliability of the complicated node is calculated by FTA and interaction is regarded as one factor to affect performance of the nodes. The reliability of simple node and link is evaluated by code. Then, the reliability of the entire network is assessed based on GIS and FTA. Lastly, an illustration is given to show the methodology.
Density functional calculations of planar DNA base-pairs
Machado, M V T; Artacho, E; Sánchez-Portál, D; Soler, J M; Machado, Maider; Ordejon, Pablo; Artacho, Emilio; Sanchez-Portal, Daniel; Soler, Jose M.
1999-01-01
We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT scheme, which is specially suited for systems with large numbers of atoms. As a first step towards the study of large DNA systems, in this work: (i) We establish the reliability of the approximations of our method (including pseudopotentials and basis sets) for the description of the hydrogen-bonded base pairs, by comparing our results with those of former calculations. We show that the interaction energies at Hartree-Fock geometries are in very good agreement with those of second order M{ø}ller-Plesset (MP2) perturbation theory (the most accurate technique that can be applied at present for system of the sizes of the base-pairs). (ii) We perform DFT structural optimizations for the 30 different DNA base-pairs, only three of which had been previously studied with DFT. Our ...
Children base their investment on calculated pay-off.
Directory of Open Access Journals (Sweden)
Sophie Steelandt
Full Text Available To investigate the rise of economic abilities during development we studied children aged between 3 and 10 in an exchange situation requiring them to calculate their investment based on different offers. One experimenter gave back a reward twice the amount given by the children, and a second always gave back the same quantity regardless of the amount received. To maximize pay-offs children had to invest a maximal amount with the first, and a minimal amount with the second. About one third of the 5-year-olds and most 7- and 10-year-olds were able to adjust their investment according to the partner, while all 3-year-olds failed. Such performances should be related to the rise of cognitive and social skills after 4 years.
Goal based mesh adaptivity for fixed source radiation transport calculations
International Nuclear Information System (INIS)
Highlights: ► Derives an anisotropic goal based error measure for shielding problems. ► Reduces the error in the detector response by optimizing the finite element mesh. ► Anisotropic adaptivity captures material interfaces using fewer elements than AMR. ► A new residual based on the numerical scheme chosen forms the error measure. ► The error measure also combines the forward and adjoint metrics in a novel way. - Abstract: In this paper, the application of goal based error measures for anisotropic adaptivity applied to shielding problems in which a detector is present is explored. Goal based adaptivity is important when the response of a detector is required to ensure that dose limits are adhered to. To achieve this, a dual (adjoint) problem is solved which solves the neutron transport equation in terms of the response variables, in this case the detector response. The methods presented can be applied to general finite element solvers, however, the derivation of the residuals are dependent on the underlying finite element scheme which is also discussed in this paper. Once error metrics for the forward and adjoint solutions have been formed they are combined using a novel approach. The two metrics are combined by forming the minimum ellipsoid that covers both the error metrics rather than taking the maximum ellipsoid that is contained within the metrics. Another novel approach used within this paper is the construction of the residual. The residual, used to form the goal based error metrics, is calculated from the subgrid scale correction which is inherent in the underlying spatial discretisation employed
Representations of affine Hecke algebras
Xi, Nanhua
1994-01-01
Kazhdan and Lusztig classified the simple modules of an affine Hecke algebra Hq (q E C*) provided that q is not a root of 1 (Invent. Math. 1987). Ginzburg had some very interesting work on affine Hecke algebras. Combining these results simple Hq-modules can be classified provided that the order of q is not too small. These Lecture Notes of N. Xi show that the classification of simple Hq-modules is essentially different from general cases when q is a root of 1 of certain orders. In addition the based rings of affine Weyl groups are shown to be of interest in understanding irreducible representations of affine Hecke algebras. Basic knowledge of abstract algebra is enough to read one third of the book. Some knowledge of K-theory, algebraic group, and Kazhdan-Lusztig cell of Cexeter group is useful for the rest
Wang, Xiaofang; Li, Huibin; Bichot, Charles-Edmond; Masnou, Simon; Chen, Liming
2013-01-01
International audience We propose a graph-cut based image segmentation method by constructing an affinity graph using l0 sparse representation. Computing first oversegmented images, we associate with all segments, that we call superpixels, a collection of features. We find the sparse representation of each set of features over the dictionary of all features by solving a l0-minimization problem. Then, the connection information between superpixels is encoded as the non-zero representation c...
Seismic response based on transient calculations. Spectral and stochastic methods
International Nuclear Information System (INIS)
Further to the recent development in the ASTER code of functionalities enabling random dynamic responses to be calculated, notably a stochastic type seismic analysis, we propose a combination of three calculation methods to estimate a probabilistic seismic response on an N4 reactor building stick-model. Transient calculations involves time-and cost-consuming repetition. The conventional oscillator response spectrum calculation yields only the maximum response expectation. On the other hand, the stochastic approach in this context gives the response corresponding to selected probabilities. (authors). 12 figs., 3 tabs., 4 refs
Application of CFD based wave loads in aeroelastic calculations
DEFF Research Database (Denmark)
Schløer, Signe; Paulsen, Bo Terp; Bredmose, Henrik
2014-01-01
realizations compare well with corresponding surface elevations from laboratory experiments. In aeroelastic calculations of an offshore wind turbine on a monopile foundation the hydrodynamic loads due to the potential flow solver and Morison’s equation and the hydrodynamic loads calculated by the coupled......Two fully nonlinear irregular wave realizations with different significant wave heights are considered. The wave realizations are both calculated in the potential flow solver Ocean-Wave3D and in a coupled domain decomposed potential-flow CFD solver. The surface elevations of the calculated wave...
Efficient Error Calculation for Multiresolution Texture-Based Volume Visualization
Energy Technology Data Exchange (ETDEWEB)
LaMar, E; Hamann, B; Joy, K I
2001-10-16
Multiresolution texture-based volume visualization is an excellent technique to enable interactive rendering of massive data sets. Interactive manipulation of a transfer function is necessary for proper exploration of a data set. However, multiresolution techniques require assessing the accuracy of the resulting images, and re-computing the error after each change in a transfer function is very expensive. They extend their existing multiresolution volume visualization method by introducing a method for accelerating error calculations for multiresolution volume approximations. Computing the error for an approximation requires adding individual error terms. One error value must be computed once for each original voxel and its corresponding approximating voxel. For byte data, i.e., data sets where integer function values between 0 and 255 are given, they observe that the set of error pairs can be quite large, yet the set of unique error pairs is small. instead of evaluating the error function for each original voxel, they construct a table of the unique combinations and the number of their occurrences. To evaluate the error, they add the products of the error function for each unique error pair and the frequency of each error pair. This approach dramatically reduces the amount of computation time involved and allows them to re-compute the error associated with a new transfer function quickly.
Bagchi, Sabyasachi; Mandal, Debasish; Ghosh, Deepanwita; Das, Abhijit K.
2012-05-01
The structure, bonding, and energetics of the complexes obtained from the interaction between the most stable tautomeric forms of free DNA and RNA bases and Zn2+, Cd2+ and Hg2+ cations have been studied using density functional B3LYP method. The 6-311+G (2df, 2p) basis set along with LANL2DZ pseudopotentials for the cations are used in the calculations. The tautomerization paths of the nucleobases are investigated and transition states between the tautomeric forms of the free bases are located. The relative stability of the complexes and the tautomers of the free nucleobases are discussed referring to MIA and relative energy values. For uracil, thymine and adenine, interaction of the metal cations with the most stable tautomers form the least stable molecular complexes. For cytosine and guanine, the stability of the metalated complexes differs significantly. The enthalpy (ΔH), entropy (TΔS) and free energy (ΔG) of the complexes at 298 K have also been calculated.
[Cell-ELA-based determination of binding affinity of DNA aptamer against U87-EGFRvIII cell].
Tan, Yan; Liang, Huiyu; Wu, Xidong; Gao, Yubo; Zhang, Xingmei
2013-05-01
A15, a DNA aptamer with binding specificity for U87 glioma cells stably overexpressing the epidermal growth factor receptor variant III (U87-EGFRvIII), was generated by cell systematic evolution of ligands by exponential enrichment (cell-SELEX) using a random nucleotide library. Subsequently, we established a cell enzyme-linked assay (cell-ELA) to detect the affinity of A15 compared to an EGFR antibody. We used A15 as a detection probe and cultured U87-EGFRvIII cells as targets. Our data indicate that the equilibrium dissociation constants (K(d)) for A15 were below 100 nmol/L and had similar affinity compared to an EGFR antibody for U87-EGFRvIII. We demonstrated that the cell-ELA was a useful method to determine the equilibrium dissociation constants (K(d)) of aptamers generated by cell-SELEX.
Fan affinity laws from a collision model
International Nuclear Information System (INIS)
The performance of a fan is usually estimated using hydrodynamical considerations. The calculations are long and involved and the results are expressed in terms of three affinity laws. In this paper we use kinetic theory to attack this problem. A hard sphere collision model is used, and subsequently a correction to account for the flow behaviour of air is incorporated. Our calculations prove the affinity laws and provide numerical estimates of the air delivery, thrust and drag on a rotating fan. (paper)
Calculation of hydrodynamics for semi-submersibles based on NURBS
Institute of Scientific and Technical Information of China (English)
REN Hui-long; LIU Wen-xi
2008-01-01
Accurate hydrodynamic calculations for semi-submersibles are critical to support modern rapid exploration and extraction of ocean resources.In order to speed hydrodynamic calculations,lines modeling structures were separated into structural parts and then fitted to Non-uniform Rational B-spline(NURBS).In this way,the bow and stern section lines were generated.Modeling of the intersections of the parts was then done with the universal modeling tool MSC.Patran.Mesh was gererated on the model in order to obtain points of intersection on the joints,and then these points were fitted to NURBS.Next,the patch representation method was adopted to generate the meshes of wetted surfaces and interior free surfaces.Velocity potentials on the surfaces were calculated separately,on basis of which the irregular frequency effect was dealt with in the calculation of hydrodynamic coefficients.Finally,the motion response of the semi-submersible was calculated,and in order to improve calculations of vertical motion,a damping term was affixed in the vertical direction.The results show that the above methods cangenerate fine mesh accurately representing the wetted surface of a semi-submersible and thus improve the accuracy of hydrodynamic calculations.
Petros, Amy K; Reddi, Amit R; Kennedy, Michelle L; Hyslop, Alison G; Gibney, Brian R
2006-12-11
Metal-ligand interactions are critical components of metalloprotein assembly, folding, stability, electrochemistry, and catalytic function. Research over the past 3 decades on the interaction of metals with peptide and protein ligands has progressed from the characterization of amino acid-metal and polypeptide-metal complexes to the design of folded protein scaffolds containing multiple metal cofactors. De novo metalloprotein design has emerged as a valuable tool both for the modular synthesis of these complex metalloproteins and for revealing the fundamental tenets of metalloprotein structure-function relationships. Our research has focused on using the coordination chemistry of de novo designed metalloproteins to probe the interactions of metal cofactors with protein ligands relevant to biological phenomena. Herein, we present a detailed thermodynamic analysis of Fe(II), Co(II), Zn(II), and[4Fe-4S]2(+/+) binding to IGA, a 16 amino acid peptide ligand containing four cysteine residues, H2N-KLCEGG-CIGCGAC-GGW-CONH2. These studies were conducted to delineate the inherent metal-ion preferences of this unfolded tetrathiolate peptide ligand as well as to evaluate the role of the solution pH on metal-peptide complex speciation. The [4Fe-4S]2(+/+)-IGA complex is both an excellent peptide-based synthetic analogue for natural ferredoxins and is flexible enough to accommodate mononuclear metal-ion binding. Incorporation of a single ferrous ion provides the FeII-IGA complex, a spectroscopic model of a reduced rubredoxin active site that possesses limited stability in aqueous buffers. As expected based on the Irving-Williams series and hard-soft acid-base theory, the Co(II) and Zn(II) complexes of IGA are significantly more stable than the Fe(II) complex. Direct proton competition experiments, coupled with determinations of the conditional dissociation constants over a range of pH values, fully define the thermodynamic stabilities and speciation of each MII-IGA complex. The
Hybrid Electric Vehicle Control Strategy Based on Power Loss Calculations
Boyd, Steven J
2006-01-01
Defining an operation strategy for a Split Parallel Architecture (SPA) Hybrid Electric Vehicle (HEV) is accomplished through calculating powertrain component losses. The results of these calculations define how the vehicle can decrease fuel consumption while maintaining low vehicle emissions. For a HEV, simply operating the vehicle's engine in its regions of high efficiency does not guarantee the most efficient vehicle operation. The results presented are meant only to define a literal str...
Tasaki-Handa, Yuiko; Abe, Yukie; Ooi, Kenta; Tanaka, Mikiya; Wakisaka, Akihiro
2014-01-01
In this paper the exchange of lanthanide(III) ions (Ln(3+)) between a solution and a coordination polymer (CP) of di(2-ethylhexyl)phosphoric acid (Hdehp), [Ln(dehp)3], is studied. Kinetic and selectivity studies suggest that a polymeric network of [Ln(dehp)3] has different characteristics than the corresponding monomeric complex. The reaction rate is remarkably slow and requires over 600 h to reach in nearly equilibrium, and this can be explained by the polymeric crystalline structure and high valency of Ln(3+). The affinity of the exchange reaction reaches a maximum with the Ln(3+) possessing an ionic radius 7% smaller than that of the central Ln(3+), therefore, the affinity of the [Ln(dehp)3] is tunable based on the choice of the central metal ion. Such unique affinity, which differs from the monomeric complex, can be explained by two factors: the coordination preference and steric strain caused by the polymeric structure. The latter likely becomes predominant for Ln(3+) exchange when the ionic radius of the ion in solution is smaller than the original Ln(3+) by more than 7%. Structural studies suggest that the incoming Ln(3+) forms a new phase though an exchange reaction, and this could plausibly cause the structural strain.
Calculation of VPP basing on functional analyzing method
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
VPP can be used to deter mine the maxi mumvelocities of a sailboard at various sailing-routes,byestablishing the forces and moments balance-equa-tions on the sail and board in accordance with theprinciple of the maxi mal drive-force.Selectingroute is the most i mportant issue in upwind-sailing,and VPP calculations could provide the basis for de-ter mining the opti mal routes.VPP calculation of the sailboard perfor mance isa complex and difficult research task,and there arefew projects in this research-field...
Methods for Improving Aptamer Binding Affinity
Hijiri Hasegawa; Nasa Savory; Koichi Abe; Kazunori Ikebukuro
2016-01-01
Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of a...
3D transient calculations of PGV-1000 based on TRAC
Energy Technology Data Exchange (ETDEWEB)
Anatoly A Kazantsev; Andrey N Pozdnyakov [Simulation Systems Ltd., 133-208 Lenin str. 249030, Obninsk city, Kaluga reg. (Russian Federation); Vladimir V Sergeev; Valery A Evstifeev [Institute of Physics and Power Engineering (IPPE) 249020, Bondarenko square 1, Obninsk city, Kaluga reg., Russia, Government research center RF IPPE by A.I. Leipynski (Russian Federation)
2005-07-01
Full text of publication follows: During calculations of SAR accidents and transients it is necessary to perform steam generator simulation. Best accuracy is 3D transient calculations presented in report. Main outcomes of work was next: 1. There was shown by analysis the applicability of code TRAC (Los-Alamos laboratory) for thermal - hydraulic calculations of horizontal steam generator PGV-1000M. Special nodalization scheme was developed for it purposes. 2. Validation and selection of thermal-hydraulic correlations for improvement of using the code at calculation PGV-1000M were performed. As result Labuntsov formula is recommended for horizontal SG. 3. Calculations of nominal mode operation of PGV-1000M for cross-verification with code STEG (Electrogorsk Research and Engineering Center EREC) during its verification were performed. Solution by TRAC was obtained for transient problem after stabilization time. 4. Development of dynamic SG model as conjugate problem (thermal hydraulic of I and II circuits are calculated together) for research of the transient and accident processes stipulated by safety standards for NPP with VVER-1000 and VVER-1500. 5. Creating of calculation complex on the basis of code TRAC for the purposes of the analysis and optimization of a design. Development graphic pre- and post-processor for code TRAC. 6. The TRAC code allows to use correlation Zukauskas for friction factors in tube bundles through the initial data. Using postprocessing calculations and restart mode iterations allows to use Kolbasnikov's correlations for friction factors for biphasic mode in tube bundles. Developed nodalization model of PGV-1000M includes a conjugate hydrodynamical problem on I and to II circuits in view of thermal connection through packages of tubes. Thus primary circuit is considered in multichannel 1D approximation with hydraulic non-uniformity of flow rates between pre-settled groups of tubes. The hydrodynamics into shell of PG is presented as 3D
DEFF Research Database (Denmark)
Høholdt, Tom; Beelen, Peter; Ghorpade, Sudhir Ramakant
2010-01-01
We consider a new class of linear codes, called affine Grassmann codes. These can be viewed as a variant of generalized Reed-Muller codes and are closely related to Grassmann codes.We determine the length, dimension, and the minimum distance of any affine Grassmann code. Moreover, we show that...... affine Grassmann codes have a large automorphism group and determine the number of minimum weight codewords....
Inverse boundary element calculations based on structural modes
DEFF Research Database (Denmark)
Juhl, Peter Møller
2007-01-01
The inverse problem of calculating the flexural velocity of a radiating structure of a general shape from measurements in the field is often solved by combining a Boundary Element Method with the Singular Value Decomposition and a regularization technique. In their standard form these methods sol...
Institute of Scientific and Technical Information of China (English)
BO Chun-Miao; GONG Bo-Lin; HU Wen-Zhi
2008-01-01
Three hydrophilic immobilized metal affinity chromatographic packings for HPLC have been synthesized by chemical modification of 3.0 μm monodisperse non-porous poly(glycidyl methacrylate-co-ethylenedimethacrylate)(PGMMEDMA)beads.The retention behavior of proteins on the metal ion chelated columns loaded with copper(Ⅱ),nickel(Ⅱ)and zin(Ⅱ)ion was studied.The effect of pH on the protein retention Was investigated on both the naked and metal ion chelated columns in the range from 4.0 to 9.0.Four proteins were quickly separated in 3.0 min with linear gradient elution at a flow rate of 3.0 mL/min by using the synthesized Ni2+ -IDA(iminodiacetic acid)packings.The separation time was shorter than other immobilized metal affinity chromatography reported in the literature.Purification of lysozyme from egg white and trypsin on the commercially available trypsin was performed on the naked-IDA and Cu2+ -IDA columns,respectively.The purities of the purified trypsin and lysozyme were more than 92%and 95%,respectively.
Searching for Si-based spintronics by first principles calculations
International Nuclear Information System (INIS)
Density functional theory (DFT) calculations are used to study the epitaxial growth and the magnetic properties of thin films of MnSi on the Si(001) surface. For adsorption of a single Mn atom, we find that binding at the subsurface site below the Si surface dimers is the most stable adsorption site. There is an energy barrier of only 0.3 eV for adsorbed Mn to go subsurface, and an energy barrier of 1.3 eV for penetration to deeper layers. From the calculated potential-energy surface for the Mn adatom we conclude that the most stable site on the surface corresponds to the hollow site where Mn is placed between two Si surface dimers. Despite Si(001) geometrically being an anisotropic surface, the on-surface diffusion for both directions along and perpendicular to the Si dimer rows has almost the same diffusion barrier of 0.65 eV. For coverage above 1 ML, the lowest energy structure is a pure Mn subsurface layer, capped by a layer of Si adatoms. We conclude that the Mn-silicide films stabilize in an epitaxially CsCl-like (B2) crystal structure. Such MnSi films are found to have sizable magnetic moments at the Mn atoms near the surface and interface, and ferromagnetic coupling of the Mn clarify within the layers. Layer-resolved electronic densities-of-states are presented that show a high degree of spin polarization at the Fermi level, up to 30 and 50% for films with one or two MnSi films, respectively. In order to clarify the stability of ferromagnetism at finite temperatures we estimate the Curie temperature (Tc) of MnSi films using a multiple-sublattice Heisenberg model with first- and second-nearest neighbor interactions determined from DFT calculations for various collinear spin configurations. The Curie temperature is calculated both in the mean-field approximation (MFA) and in the random-phase approximation (RPA). In the latter case, we find a weak logarithmic dependence of Tc on the magnetic anisotropy parameter, which was calculated to be 0.4 meV. Large Curie
Calculation of VPP basing on functional analyzing method
Institute of Scientific and Technical Information of China (English)
Bai Kaixiang; Wang Dexun; Han Jiurui
2007-01-01
The establishment and realization of the VPP calucation's model for the functional analytic theory are discussed in this paper. Functional analyzing method is a theoretical model of the VPP calculation which can eliminate the influence of the sail and board's size skillfully, so it can be regarded as a brief standard of the sailboard's VPP results. As a brief watery dynamical model, resistance on board can be regarded as a direct proportion to the square of the boat-velocity. The boat-velocities at the state of six wind-velocities (3 m/s-8 m/s) with angles of 25°-180° are obtained by calculating, which provides an important gist of the sailing-route's selection in upwind-sailing.
Calculations of NMR chemical shifts with APW-based methods
Laskowski, Robert; Blaha, Peter
2012-01-01
We present a full potential, all electron augmented plane wave (APW) implementation of first-principles calculations of NMR chemical shifts. In order to obtain the induced current we follow a perturbation approach [Pickard and Mauri, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.63.245101 63, 245101 (2001)] and extended the common APW + local orbital (LO) basis by several LOs at higher energies. The calculated all-electron current is represented in traditional APW manner as Fourier series in the interstitial region and with a spherical harmonics representation inside the nonoverlapping atomic spheres. The current is integrated using a “pseudocharge” technique. The implementation is validated by comparison of the computed chemical shifts with some “exact” results for spherical atoms and for a set of solids and molecules with available published data.
Freeway Travel Speed Calculation Model Based on ETC Transaction Data
Jiancheng Weng; Rongliang Yuan; Ru Wang; Chang Wang
2014-01-01
Real-time traffic flow operation condition of freeway gradually becomes the critical information for the freeway users and managers. In fact, electronic toll collection (ETC) transaction data effectively records operational information of vehicles on freeway, which provides a new method to estimate the travel speed of freeway. First, the paper analyzed the structure of ETC transaction data and presented the data preprocess procedure. Then, a dual-level travel speed calculation model was estab...
International Nuclear Information System (INIS)
The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure–Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R2 = 0.55 and CCR = 0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R2 = 0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. - Highlights: • This is the largest curated dataset for ligand binding domain (LBD) of the THRβ. • We report the first QSAR model for antagonists of AF-2 domain of THRβ. • A combination of QSAR and docking enables prediction of both
Energy Technology Data Exchange (ETDEWEB)
Politi, Regina [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599 (United States); Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599 (United States); Rusyn, Ivan, E-mail: iir@unc.edu [Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599 (United States); Tropsha, Alexander, E-mail: alex_tropsha@unc.edu [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599 (United States)
2014-10-01
The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure–Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R{sup 2} = 0.55 and CCR = 0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R{sup 2} = 0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. - Highlights: • This is the largest curated dataset for ligand binding domain (LBD) of the THRβ. • We report the first QSAR model for antagonists of AF-2 domain of THRβ. • A combination of QSAR and docking enables
Institute of Scientific and Technical Information of China (English)
WANG Aijun; AO Qiang; HE Qing; GONG Xiaoming; GONG Kai; GONG Yandao; ZHAO Nanming; ZHANG Xiufang
2006-01-01
Neural stem cells (NSCs) are currently considered as powerful candidate seeding cells for regeneration of both spinal cords and peripheral nerves. In this study, NSCs derived from fetal rat cortices were co-cultured with chitosan to evaluate the cell affinity of this material. The results showed that NSCs grew and proliferated well on chitosan films and most of them differentiated into neuron-like cells after 4 days of culture. Then, molded and braided chitosan conduits were fabricated and characterized for their cytotoxicity, swelling, and mechanical properties. Both types of conduits had no cytotoxic effects on fibroblasts (L929 cells) or neuroblastoma (Neuro-2a) cells. The molded conduits are much softer and more flexible while the braided conduits possess much better mechanical properties, which suggests different potential applications.
Space resection model calculation based on Random Sample Consensus algorithm
Liu, Xinzhu; Kang, Zhizhong
2016-03-01
Resection has been one of the most important content in photogrammetry. It aims at the position and attitude information of camera at the shooting point. However in some cases, the observed values for calculating are with gross errors. This paper presents a robust algorithm that using RANSAC method with DLT model can effectually avoiding the difficulties to determine initial values when using co-linear equation. The results also show that our strategies can exclude crude handicap and lead to an accurate and efficient way to gain elements of exterior orientation.
Freeway travel speed calculation model based on ETC transaction data.
Weng, Jiancheng; Yuan, Rongliang; Wang, Ru; Wang, Chang
2014-01-01
Real-time traffic flow operation condition of freeway gradually becomes the critical information for the freeway users and managers. In fact, electronic toll collection (ETC) transaction data effectively records operational information of vehicles on freeway, which provides a new method to estimate the travel speed of freeway. First, the paper analyzed the structure of ETC transaction data and presented the data preprocess procedure. Then, a dual-level travel speed calculation model was established under different levels of sample sizes. In order to ensure a sufficient sample size, ETC data of different enter-leave toll plazas pairs which contain more than one road segment were used to calculate the travel speed of every road segment. The reduction coefficient α and reliable weight θ for sample vehicle speed were introduced in the model. Finally, the model was verified by the special designed field experiments which were conducted on several freeways in Beijing at different time periods. The experiments results demonstrated that the average relative error was about 6.5% which means that the freeway travel speed could be estimated by the proposed model accurately. The proposed model is helpful to promote the level of the freeway operation monitoring and the freeway management, as well as to provide useful information for the freeway travelers. PMID:25580107
Lectures on extended affine Lie algebras
Neher, Erhard
2010-01-01
We give an introduction to the structure theory of extended affine Lie algebras, which provide a common framework for finite-dimensional semisimple, affine and toroidal Lie algebras. The notes are based on a lecture series given during the Fields Institute summer school at the University of Ottawa in June 2009.
Shan Yang; Xiangqian Tong
2016-01-01
Power flow calculation and short circuit calculation are the basis of theoretical research for distribution network with inverter based distributed generation. The similarity of equivalent model for inverter based distributed generation during normal and fault conditions of distribution network and the differences between power flow and short circuit calculation are analyzed in this paper. Then an integrated power flow and short circuit calculation method for distribution network with inverte...
Ray-based calculations of laser backscatter in ICF targets
Strozzi, D J; Hinkel, D E; Froula, D H; London, R A; Callahan, D A
2008-01-01
A steady-state model for Brillouin and Raman backscatter along a laser ray path is presented. The daughter plasma waves are treated in the strong damping limit, and have amplitudes given by the (linear) kinetic response to the ponderomotive drive. Pump depletion, inverse-bremsstrahlung damping, bremsstrahlung emission, Thomson scattering off density fluctuations, and whole-beam focusing are included. The numerical code Deplete, which implements this model, is described. The model is compared with traditional linear gain calculations, as well as ``plane-wave'' simulations with the paraxial propagation code pF3D. Comparisons with Brillouin-scattering experiments at the Omega Laser Facility show that laser speckles greatly enhance the reflectivity over the Deplete results. An approximate upper bound on this enhancement is given by doubling the Deplete coupling coefficient. Analysis with Deplete of an ignition design for the National Ignition Facility (NIF), with a peak radiation temperature of 285 eV, shows enco...
Activity based models for countrywide electric vehicle power demand calculation
Knapen, Luk; Kochan, Bruno; BELLEMANS, Tom; JANSSENS, Davy; Wets, Geert
2011-01-01
Smart grid design depends on the availability of realistic data. In the near future, energy demand by electric vehicles will be a substantial component of the overall demand and peaks of required power could become critical in some regions. Transportation research has been using micro-simulation based activity-based models for trafﬁc forecasting. The resulting trip length distribution allows to estimate to what extent internal combustion engine vehicles can be substituted...
Indian Academy of Sciences (India)
Brijesh Kumar Sriwastava; Subhadip Basu; Ujjwal Maulik
2015-10-01
Protein–protein interaction (PPI) site prediction aids to ascertain the interface residues that participate in interaction processes. Fuzzy support vector machine (F-SVM) is proposed as an effective method to solve this problem, and we have shown that the performance of the classical SVM can be enhanced with the help of an interaction-affinity based fuzzy membership function. The performances of both SVM and F-SVM on the PPI databases of the Homo sapiens and E. coli organisms are evaluated and estimated the statistical significance of the developed method over classical SVM and other fuzzy membership-based SVM methods available in the literature. Our membership function uses the residue-level interaction affinity scores for each pair of positive and negative sequence fragments. The average AUC scores in the 10-fold cross-validation experiments are measured as 79.94% and 80.48% for the Homo sapiens and E. coli organisms respectively. On the independent test datasets, AUC scores are obtained as 76.59% and 80.17% respectively for the two organisms. In almost all cases, the developed F-SVM method improves the performances obtained by the corresponding classical SVM and the other classifiers, available in the literature.
Ray-Space Interpolation Based on Affine Projection%基于仿射投影的光线空间插值方法
Institute of Scientific and Technical Information of China (English)
孙季丰; 吴军政
2013-01-01
In order to effectively deal with the shape variation and noise pollution of the corresponding area in different views and, thereby, improve the quality and speed of viewpoint image synthesis, a ray-space interpolation method based on affine projection is proposed. In this method, first, the scale-invariant feature transform is applied to the feature detection and image matching for determining the affine transformation matrix among multi-viewpoint images. Then, ray-space interpolation is implemented via the projection through affine transformation matrix. Finally, a virtual viewpoint image is synthesized in the wavelet transform domain. Experimental results show that the proposed method is superior to the traditional block-matching interpolation and DDFI (Disparity Domain Filtering Interpolation) methods in terms of PSNR and computation time of the virtual viewpoint image.%为有效处理不同视点图像中对应区域的不同形变和噪声污染,提高所绘制的视点图像的质量和速度,提出了一种基于仿射投影的光线空间插值方法.该方法首先利用尺度不变特征变换进行特征检测和图像配准,计算出相应图像对之间的仿射变换矩阵,然后利用仿射变换投影进行光线空间插值,并在小波变换域绘制出虚拟视点图像.实验结果表明,采用文中方法绘制的虚拟视点图像的峰值信噪比和计算时间均优于传统的块匹配插值和视差域滤波插值方法.
Rauthu, Subhash R; Shiao, Tze Chieh; André, Sabine; Miller, Michelle C; Madej, Élodie; Mayo, Kevin H; Gabius, Hans-Joachim; Roy, René
2015-01-01
The emerging significance of lectins for pathophysiological processes provides incentive for the design of potent inhibitors. To this end, systematic assessment of contributions to affinity and selectivity by distinct types of synthetic tailoring of glycosides is a salient step, here taken for the aglyconic modifications of two disaccharide core structures. Firstly we report the synthesis of seven N-linked-lactosides and of eight O-linked N-acetyllactosamines, each substituted with a 1,2,3-triazole unit, prepared by copper-catalyzed azide-alkyne cycloaddition (CuAAC). The totally regioselective β-D-(1 → 4) galactosylation of a 6-O-TBDPSi-protected N-acetylglucosamine acceptor provided efficient access to the N-acetyllactosamine precursor. The resulting compounds were then systematically tested for lectin reactivity in two binding assays of increasing biorelevance (inhibition of lectin binding to a surface-presented glycoprotein and to cell surfaces). As well as a plant toxin, we also screened the relative inhibitory potential with adhesion/growth-regulatory galectins (total of eight proteins). This type of modification yielded up to 2.5-fold enhancement for prototype proteins, with further increases for galectins-3 and -4. Moreover, the availability of (15)N-labeled proteins and full assignments enabled (1)H, (15)N HSQC-based measurements for hu- man galectins-1, -3, and -7 against p-nitrophenyl lactopyranoside, a frequently tested standard inhibitor containing an aromatic aglycone. The measurements confirmed the highest affinity against galectin-3 and detected chemical shift differences in its hydrophobic core upon ligand binding, besides common alterations around the canonical contact site for the lactoside residue. What can be accomplished in terms of affinity/selectivity by this type of core extension having been determined, the applied combined strategy should be instrumental for proceeding with defining structure-activity correlations at other bioinspired
Minadakis, G; Nomicos, C; Eftaxias, K
2011-01-01
EM emissions in a wide frequency spectrum ranging from kHz to MHz are produced by opening cracks, which can be considered as precursors of general fracture. An important feature, observed on both laboratory and geophysical scale, is that the MHz radiation systematically precedes the kHz one. Yet, the link between an individual EM precursor and a distinctive stage of the EQ preparation comprises a crucial open question. A recently proposed two-stage model on preseismic EM activity suggests that the MHz EM emission is due to the fracture of the highly heterogeneous system that surrounds the fault. The finally emerged kHz EM emission is rooted in the final stage of EQ generation, namely, the fracture of entities sustaining the system. In this work we try to further penetrate and elucidate the link of the precursory kHz EM activity with the last stage of EQ generation building on two theoretical models for EQ dynamics. Firstly, the self-affine model states that an EQ is due to the slipping of two rough and rigid ...
QED Based Calculation of the Fine Structure Constant
Energy Technology Data Exchange (ETDEWEB)
Lestone, John Paul [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2016-10-13
Quantum electrodynamics is complex and its associated mathematics can appear overwhelming for those not trained in this field. Here, semi-classical approaches are used to obtain a more intuitive feel for what causes electrostatics, and the anomalous magnetic moment of the electron. These intuitive arguments lead to a possible answer to the question of the nature of charge. Virtual photons, with a reduced wavelength of λ, are assumed to interact with isolated electrons with a cross section of πλ^{2}. This interaction is assumed to generate time-reversed virtual photons that are capable of seeking out and interacting with other electrons. This exchange of virtual photons between particles is assumed to generate and define the strength of electromagnetism. With the inclusion of near-field effects the model presented here gives a fine structure constant of ~1/137 and an anomalous magnetic moment of the electron of ~0.00116. These calculations support the possibility that near-field corrections are the key to understanding the numerical value of the dimensionless fine structure constant.
Coupled-cluster based basis sets for valence correlation calculations
Claudino, Daniel; Gargano, Ricardo; Bartlett, Rodney J.
2016-03-01
Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These new sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via (-3 ≤ n ≤ 3) in atoms, correlation energies in diatomic molecules, and the quality of fitting potential energy curves as measured by spectroscopic constants. All energy calculations with ANO-VT-QZ have contraction errors within "chemical accuracy" of 1 kcal/mol, which is not true for cc-pVQZ, suggesting some improvement compared to the correlation consistent series of Dunning and co-workers.
Vertical emission profiles for Europe based on plume rise calculations
Bieser, J.; Aulinger, A.; Matthias, V.; Quante, M.; Denier Van Der Gon, H.A.C.
2011-01-01
The vertical allocation of emissions has a major impact on results of Chemistry Transport Models. However, in Europe it is still common to use fixed vertical profiles based on rough estimates to determine the emission height of point sources. This publication introduces a set of new vertical profile
A New Optimization Method for Centrifugal Compressors Based on 1D Calculations and Analyses
Pei-Yuan Li; Chu-Wei Gu; Yin Song
2015-01-01
This paper presents an optimization design method for centrifugal compressors based on one-dimensional calculations and analyses. It consists of two parts: (1) centrifugal compressor geometry optimization based on one-dimensional calculations and (2) matching optimization of the vaned diffuser with an impeller based on the required throat area. A low pressure stage centrifugal compressor in a MW level gas turbine is optimized by this method. One-dimensional calculation results show that D3/D...
UAV-based NDVI calculation over grassland: An alternative approach
Mejia-Aguilar, Abraham; Tomelleri, Enrico; Asam, Sarah; Zebisch, Marc
2016-04-01
The Normalised Difference Vegetation Index (NDVI) is one of the most widely used indicators for monitoring and assessing vegetation in remote sensing. The index relies on the reflectance difference between the near infrared (NIR) and red light and is thus able to track variations of structural, phenological, and biophysical parameters for seasonal and long-term monitoring. Conventionally, NDVI is inferred from space-borne spectroradiometers, such as MODIS, with moderate resolution up to 250 m ground resolution. In recent years, a new generation of miniaturized radiometers and integrated hyperspectral sensors with high resolution became available. Such small and light instruments are particularly adequate to be mounted on airborne unmanned aerial vehicles (UAV) used for monitoring services reaching ground sampling resolution in the order of centimetres. Nevertheless, such miniaturized radiometers and hyperspectral sensors are still very expensive and require high upfront capital costs. Therefore, we propose an alternative, mainly cheaper method to calculate NDVI using a camera constellation consisting of two conventional consumer-grade cameras: (i) a Ricoh GR modified camera that acquires the NIR spectrum by removing the internal infrared filter. A mounted optical filter additionally obstructs all wavelengths below 700 nm. (ii) A Ricoh GR in RGB configuration using two optical filters for blocking wavelengths below 600 nm as well as NIR and ultraviolet (UV) light. To assess the merit of the proposed method, we carry out two comparisons: First, reflectance maps generated by the consumer-grade camera constellation are compared to reflectance maps produced with a hyperspectral camera (Rikola). All imaging data and reflectance maps are processed using the PIX4D software. In the second test, the NDVI at specific points of interest (POI) generated by the consumer-grade camera constellation is compared to NDVI values obtained by ground spectral measurements using a
Olsson, H; Farde, L
2001-10-01
The D2 dopamine receptor density ranges from 0.2 to 40 nM among human brain regions. For high density regions radioligands like [(11)C]raclopride provide accurate and reliable estimates of the receptor density. In research on neuropsychiatric disorders there is, however, a growing need for quantitative approaches that accurately measure D2 dopamine receptor occupancy induced by drugs or endogenous dopamine in regions with low receptor density. The new high affinity radioligands [(11)C]FLB 457 and [(123)I]epidepride have been shown to provide a signal for extrasriatal D2 dopamine receptor populations in the human brain in vivo. Initial observations indicate, however, that the time required to reach equilibrium is dependent on receptor density. Ratio analyses may thus not be readily used for comparisons among different brain regions. The aim of the present simulation study was to examine commonly used approaches for calculation of drug induced D2 dopamine receptor occupancy among regions with widely different receptor density. The input functions and the rate constants of [(11)C]FLB 457 and the reference ligand [(11)C]raclopride were first used in a simulation estimating the effect of receptor density on equilibrium time. In a second step we examined how errors produced by inaccurate determination of the binding potential parameter propagate to calculations of drug induced receptor occupancy. The simulations showed a marked effect of receptor density on equilibrium time for [(11)C]FLB 457, but not for [(11)C]raclopride. For [(11)C]FLB 457, a receptor density above about 7 nM caused the time of equilibrium to fall beyond time of data acquisition (1 h). The use of preequilibrium data caused the peak equilibrium and the end time ratio approaches but not the simplified reference tissue model (SRTM) approach to underestimate the binding potential and thus also the drug occupancy calculated for high-density regions. The study supports the use of ratio and SRTM analyses in
Erol, Melek
Surface-enhanced Raman spectroscopy (SERS) in the presence of noble metal nanostructures holds significant promise for sensing and molecular fingerprinting down to single molecule level. This dissertation explores the effect of binding affinity and surface oxidation of Ag nanoparticles on SERS detection sensitivity of SO42-, CN-, SCN-, ClO4- and nitro-aromatic compounds in water. Specifically positively charged Ag nanoparticles (Ag [+]) were synthesized by UV-assisted reduction of silver nitrate using branched polyethyleneimine (BPEI) and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) solutions. Both primary amino and amide groups on the surface of Ag [+] allowed strong binding affinity with anions, critical for sensitive SERS measurements. For substrates with immobilized Ag [+] (30 nanoparticles/mum2), SERS sensitivity increased in the order of SO42- physiological conditions due to steric hindrance from the branched architecture of adsorbed polymer chains. BPEI coated surfaces were also effective for suppression of smaller positively charged proteins such as lysozyme and ribonuclease A at pH 7 and 0.15 M NaCl and of negatively charged proteins such as BSA and fibrinogen at pH 7 and 0.75 M NaCl. Furthermore, using PEI-modified protein-repellent surfaces, selective binding of avidin was achieved to surface-bound Ag nanoparticles, thus providing a promising strategy for SERS-based bio-detection.
CO2 Pipeline Cost Calculations, Based on Different Cost Models
Beáta Horánszky; Péter Forgács
2013-01-01
Carbon Capture and Storage (CCS) is considered to be a promising technology and an effective tool in the struggle against climate change. The method is based on the separation of air-polluting CO2 from fuel gases and its subsequent storage in different types of geological formations. The outlet points and formations used as CO2 storage sites are often very far from each other. According to certain recently announced, medium-term EU plans, a 20,000 km long pipeline system will be established f...
Affine and degenerate affine BMW algebras: Actions on tensor space
Daugherty, Zajj; Virk, Rahbar
2012-01-01
The affine and degenerate affine Birman-Murakami-Wenzl (BMW) algebras arise naturally in the context of Schur-Weyl duality for orthogonal and symplectic quantum groups and Lie algebras, respectively. Cyclotomic BMW algebras, affine and cyclotomic Hecke algebras, and their degenerate versions are quotients. In this paper we explain how the affine and degenerate affine BMW algebras are tantalizers (tensor power centralizer algebras) by defining actions of the affine braid group and the degenerate affine braid algebra on tensor space and showing that, in important cases, these actions induce actions of the affine and degenerate affine BMW algebras. We then exploit the connection to quantum groups and Lie algebras to determine universal parameters for the affine and degenerate affine BMW algebras. Finally, we show that the universal parameters are central elements--the higher Casimir elements for orthogonal and symplectic enveloping algebras and quantum groups.
Measuring an antibody affinity distribution molecule by molecule
Energy Technology Data Exchange (ETDEWEB)
Bradbury, Andrew M [Los Alamos National Laboratory; Werner, James H [Los Alamos National Laboratory; Temirov, Jamshid [INVITROGEN
2008-01-01
Single molecule fluorescence mIcroscopy was used to observe the binding and unbinding of hapten decorated quantum dots with individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.
Proton Affinity of Isomeric Dipeptides Containing Lysine and Non-Proteinogenic Lysine Homologues.
Batoon, Patrick; Ren, Jianhua
2016-08-18
Conformational effects on the proton affinity of oligopeptides have been studied using six alanine (A)-based acetylated dipeptides containing a basic probe that is placed closest to either the C- or the N-terminus. The basic probe includes Lysine (Lys) and two nonproteinogenic Lys-homologues, ornithine (Orn) and 2,3-diaminopropionic acid (Dap). The proton affinities of the peptides have been determined using the extended Cooks kinetic method in a triple quadrupole mass spectrometer. Computational studies have been carried out to search for the lowest energy conformers and to calculate theoretical proton affinities as well as various molecular properties using the density functional theory. The dipeptides containing a C-terminal probe, ALys, AOrn, and ADap, were determined to have a higher proton affinity by 1-4 kcal/mol than the corresponding dipeptides containing an N-terminal probe, LysA, OrnA, and DapA. For either the C-probe peptides or the N-probe peptides, the proton affinity reduces systematically as the side-chain of the probe residue is shortened. The difference in the proton affinities between isomeric peptides is largely associated with the variation of the conformations. The peptides with higher values of the proton affinity adopt a relatively compact conformation such that the protonated peptides can be stabilized through more efficient internal solvation. PMID:27459294
Backtracking Based Integer Factorisation, Primality Testing and Square Root Calculation
Directory of Open Access Journals (Sweden)
Mohammed Golam Kaosar
2014-02-01
Full Text Available Breaking a big integer into two factors is a famous problem in the field of Mathematics and Cryptography for years. Many crypto-systems use suc h a big number as their key or part of a key with the assumption - it is too big that the fa stest factorisation algorithms running on the fastest computers would take impractically long per iod of time to factorise. Hence, many efforts have been provided to break those crypto-systems by finding two factors of an integer for decades. In this paper, a new factorisation techniq ue is proposed which is based on the concept of backtracking. Binary bit by bit operations are p erformed to find two factors of a given integer. This proposed solution can be applied in c omputing square root, primality test, finding prime factors of integer numbers etc. If the propos ed solution is proven to be efficient enough, it may break the security of many crypto-systems. Impl ementation and performance comparison of the technique is kept for future research.
Statistical inference for discrete-time samples from affine stochastic delay differential equations
DEFF Research Database (Denmark)
Küchler, Uwe; Sørensen, Michael
2013-01-01
Statistical inference for discrete time observations of an affine stochastic delay differential equation is considered. The main focus is on maximum pseudo-likelihood estimators, which are easy to calculate in practice. A more general class of prediction-based estimating functions is investigated...
Bi, Xiaodong; Liu, Zhen
2014-01-01
Molecularly imprinted polymers (MIPs), as inexpensive and stable substitutes of antibodies, have shown great promise in immunoassays. Glycoproteins are of significant diagnostic value. To facilitate the application of MIPs in clinical diagnostics, a general and facile imprinting method toward glycoproteins oriented for an enzyme-linked immunosorbent assay (ELISA) in the form of a 96-well microplate is essential but has not been fully explored yet. In this study, a new method called boronate affinity-based oriented surface imprinting was proposed for facile preparation of glycoprotein-imprinted microplates. A template glycoprotein was first immobilized by a boronic acid-modified microplate through boronate affinity binding, and then, a thin layer of polyaniline was formed to cover the microplate surface via in-water self-copolymerization. After the template was removed by an acidic solution, 3D cavities that can rebind the template were fabricated on the microplate surface. Using horseradish peroxidase (HRP) as a model target, the effects of imprinting conditions as well as the properties and performance of the prepared MIPs were investigated. α-Fetoprotein (AFP)-imprinted microplate was then prepared, and thereby, a MIP-based ELISA method was established. The prepared MIPs exhibited several highly favorable features, including excellent specificity, widely applicable binding pH, superb tolerance for interference, high binding strength, fast equilibrium kinetics, and reusability. The MIP-based ELISA method was finally applied to the analysis of AFP in human serum. The result was in good agreement with that by radioimmunoassay, showing a promising prospect of the proposed method in clinical diagnostics.
The Calculation of Material Requirements Based on BOP in Assembly Production
Institute of Scientific and Technical Information of China (English)
ZENG Hong-xin; BIN Hong-zan
2005-01-01
A calculation method for material requirements which is based on BOP( Bill of Process) in assembly production is presented in this paper. Firstly, the BOP of assembly production is constructed.Then, the calculation method Based on the BOP is brought forward for material requirements planning.
Jung, Kwan Ho; Oh, Eun-Taex; Park, Heon Joo; Lee, Keun-Hyeung
2016-11-15
Developing fluorescent probes for monitoring intracellular Cu(+) is important for human health and disease, whereas a few types of their receptors showing a limited range of binding affinities for Cu(+) have been reported. In the present study, we first report a novel peptide receptor of a fluorescent probe for the detection of Cu(+). Dansyl-labeled tripeptide probe (Dns-LLC) formed a 1:1 complex with Cu(+) and showed a turn-on fluorescent response to Cu(+) in aqueous buffered solutions. The dissociation constant of Dns-LLC for Cu(+) was determined to be 12 fM, showing that Dns-LLC had more potent binding affinity for Cu(+) than those of previously reported chemical probes for Cu(+). The binding mode study showed that the thiol group of the peptide receptor plays a critical role in potent binding with Cu(+) and the sulfonamide and amide groups of the probe might cooperate to form a complex with Cu(+). Dns-LLC detected Cu(+) selectively by a turn-on response among various biologically relevant metal ions, including Cu(2+) and Zn(2+). The selectivity of the peptide-based probe for Cu(+) was strongly dependent on the position of the cysteine residue in the peptide receptor part. The fluorescent peptide-based probe penetrated the living RKO cells and successfully detected Cu(+) in the Golgi apparatus in live cells by a turn-on response. Given the growing interest in imaging Cu(+) in live cells, a novel peptide receptor of Cu(+) will offer the potential for developing a variety of fluorescent probes for Cu(+) in the field of copper biochemistry. PMID:27208475
Ab Initio Calculation on Self-Assembled Base-Functionalized Single-Walled Carbon Nanotubes
Institute of Scientific and Technical Information of China (English)
SONG Chen; XIA Yue-Yuan; ZHAO Ming-Wen; LIU Xiang-Dong; LI Ji-Ling; LI Li-Juan; LI Feng; HUANG Bo-Da
2006-01-01
@@ We perform ab initio calculations on the self-assembled base-functionalized single-walled carbon nanotubes (SWNTs) which exhibit the quasi-1D ‘ladder’ structure. The optimized configuration in the ab initio calculation is very similar to that obtainedfrom molecular dynamics simulation. We also calculate the electronic structures of the self-assembled base-functionalized SWNTs that exhibit distinct difference from the single-branch base-functionalized SWNT with a localized state lying just below the Fermi level, which may result from the coupling interaction between the bases accompanied by the self-assembly behaviour.
Institute of Scientific and Technical Information of China (English)
LIU Yuan-feng; ZHAO Mei
2005-01-01
An algorithm based on the data-adaptive filtering characteristics of singular spectrum analysis (SSA) is proposed to denoise chaotic data. Firstly, the empirical orthogonal functions ( EOFs ) and principal components ( PCs ) of the signal were calculated, reconstruct the signal using the EOFs and PCs, and choose the optimal reconstructing order based on sigular spectrum to obtain the denoised signal. The noise of the signal can influence the calculating precision of maximal Liapunov exponents. The proposed denoising algorithm was applied to the maximal Liapunov exponents calculations of two chaotic system, Henon map and Logistic map. Some numerical results show that this denoising algorithm could improve the calculating precision of maximal Liapunov exponent.
On purely transmitting defects in affine Toda field theory
Corrigan, E
2007-01-01
Affine Toda field theories with a purely transmitting integrable defect are considered and the model based on a_2 is analysed in detail. After providing a complete characterization of the problem in a classical framework, a suitable quantum transmission matrix, able to describe the interaction between an integrable defect and solitons, is found. Two independent paths are taken to reach the result. One is an investigation of the triangle equations using the S-matrix for the imaginary coupling bulk affine Toda field theories proposed by Hollowood, and the other uses a functional integral approach together with a bootstrap procedure. Evidence to support the results is collected in various ways: for instance, through the calculation of the transmission factors for the lightest breathers. While previous discoveries within the sine-Gordon model motivated this study, there are several new phenomena displayed in the a_2 model including intriguing disparities between the classical and the quantum pictures. For example...
Optimized Affinity Capture of Yeast Protein Complexes.
LaCava, John; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Rout, Michael P
2016-01-01
Here, we describe an affinity isolation protocol. It uses cryomilled yeast cell powder for producing cell extracts and antibody-conjugated paramagnetic beads for affinity capture. Guidelines for determining the optimal extraction solvent composition are provided. Captured proteins are eluted in a denaturing solvent (sodium dodecyl sulfate polyacrylamide gel electrophoresis sample buffer) for gel-based proteomic analyses. Although the procedures can be modified to use other sources of cell extract and other forms of affinity media, to date we have consistently obtained the best results with the method presented. PMID:27371596
International Nuclear Information System (INIS)
As an effort to achieve efficient yet accurate transport transient calculations for power reactors, the conditional transport update scheme in method of characteristics (MOC) based coarse mesh finite difference (CMFD) transient calculation is developed. In this scheme, the transport calculations serves as an online group constant generator for the 3-D CMFD transient calculation and the solution of 3-D transient problem is mainly obtained from the 3-D CMFD transient calculation. In order to reduce the computational burden of the intensive transport calculation, the transport updates is conditionally performed by monitoring change of composition and core condition. This efficient transient transport method is applied to 3x3 assembly rod ejection problem to examine the effectiveness and accuracy of the conditional transport calculation scheme. (author)
Altomare, Alessandra; Fasoli, Elisa; Colzani, Mara; Parra, Ximena Maria Paredes; Ferrari, Marina; Cilurzo, Francesco; Rumio, Cristiano; Cannizzaro, Luca; Carini, Marina; Righetti, Pier Giorgio; Aldini, Giancarlo
2016-03-20
Bovine colostrum (BC), the initial milk secreted by the mammary gland immediately after parturition, is widely used for several health applications. We here propose an off-target method based on proteomic analysis to explain at molecular level the potential health benefits of BC. The method is based on the set-up of an exhaustive protein data bank of bovine colostrum, including the minor protein components, followed by a bioinformatic functional analysis. The proteomic approach based on ProteoMiner technology combined to a highly selective affinity chromatography approach for the immunoglobulins depletion, identified 1786 proteins (medium confidence; 634 when setting high confidence), which were then clustered on the basis of their biological function. Protein networks were then created on the basis of the biological functions or health claims as input. A set of 93 proteins involved in the wound healing process was identified. Such an approach also permits the exploration of novel biological functions of BC by searching in the database the presence of proteins characterized by innovative functions. In conclusion an advanced approach based on an in depth proteomic analysis is reported which permits an explanation of the wound healing effect of bovine colostrum at molecular level and allows the search of novel potential beneficial effects. PMID:26809613
Altomare, Alessandra; Fasoli, Elisa; Colzani, Mara; Parra, Ximena Maria Paredes; Ferrari, Marina; Cilurzo, Francesco; Rumio, Cristiano; Cannizzaro, Luca; Carini, Marina; Righetti, Pier Giorgio; Aldini, Giancarlo
2016-03-20
Bovine colostrum (BC), the initial milk secreted by the mammary gland immediately after parturition, is widely used for several health applications. We here propose an off-target method based on proteomic analysis to explain at molecular level the potential health benefits of BC. The method is based on the set-up of an exhaustive protein data bank of bovine colostrum, including the minor protein components, followed by a bioinformatic functional analysis. The proteomic approach based on ProteoMiner technology combined to a highly selective affinity chromatography approach for the immunoglobulins depletion, identified 1786 proteins (medium confidence; 634 when setting high confidence), which were then clustered on the basis of their biological function. Protein networks were then created on the basis of the biological functions or health claims as input. A set of 93 proteins involved in the wound healing process was identified. Such an approach also permits the exploration of novel biological functions of BC by searching in the database the presence of proteins characterized by innovative functions. In conclusion an advanced approach based on an in depth proteomic analysis is reported which permits an explanation of the wound healing effect of bovine colostrum at molecular level and allows the search of novel potential beneficial effects.
Spectral affinity in protein networks
Directory of Open Access Journals (Sweden)
Teng Shang-Hua
2009-11-01
Full Text Available Abstract Background Protein-protein interaction (PPI networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network to find proteins with similar function. A spectral approach that considers random walks between nodes of interest is particularly useful in evaluating closeness in PPI networks. Spectral measures of closeness are more robust to noise in the data and are more precise than simpler methods based on edge density and shortest path length. Results We develop a novel affinity measure for pairs of proteins in PPI networks, which uses personalized PageRank, a random walk based method used in context-sensitive search on the Web. Our measure of closeness, which we call PageRank Affinity, is proportional to the number of times the smaller-degree protein is visited in a random walk that restarts at the larger-degree protein. PageRank considers paths of all lengths in a network, therefore PageRank Affinity is a precise measure that is robust to noise in the data. PageRank Affinity is also provably related to cluster co-membership, making it a meaningful measure. In our experiments on protein networks we find that our measure is better at predicting co-complex membership and finding functionally related proteins than other commonly used measures of closeness. Moreover, our experiments indicate that PageRank Affinity is very resilient to noise in the network. In addition, based on our method we build a tool that quickly finds nodes closest to a queried protein in any protein network, and easily scales to much larger biological networks. Conclusion We define a meaningful way to assess the closeness of two proteins in a PPI network, and show that our closeness measure is more biologically significant than other commonly used methods. We also develop a tool, accessible at http://xialab.bu.edu/resources/pnns, that allows the user to
Energy Technology Data Exchange (ETDEWEB)
Song, Chan-Ho; Park, Seung-Kook; Park, Hee-Seong; Moon, Jei-kwon [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)
2014-10-15
KAERI is performing research to calculate a coefficient for decommissioning work unit productivity to calculate the estimated time decommissioning work and estimated cost based on decommissioning activity experience data for KRR-2. KAERI used to calculate the decommissioning cost and manage decommissioning activity experience data through systems such as the decommissioning information management system (DECOMMIS), Decommissioning Facility Characterization DB System (DEFACS), decommissioning work-unit productivity calculation system (DEWOCS). In particular, KAERI used to based data for calculating the decommissioning cost with the form of a code work breakdown structure (WBS) based on decommissioning activity experience data for KRR-2.. Defined WBS code used to each system for calculate decommissioning cost. In this paper, we developed a program that can calculate the decommissioning cost using the decommissioning experience of KRR-2, UCP, and other countries through the mapping of a similar target facility between NPP and KRR-2. This paper is organized as follows. Chapter 2 discusses the decommissioning work productivity calculation method, and the mapping method of the decommissioning target facility will be described in the calculating program for decommissioning work productivity. At KAERI, research on various decommissioning methodologies of domestic NPPs will be conducted in the near future. In particular, It is difficult to determine the cost of decommissioning because such as NPP facility have the number of variables, such as the material of the target facility decommissioning, size, radiographic conditions exist.
Organ dose calculation in CT based on scout image data and automatic image registration
Energy Technology Data Exchange (ETDEWEB)
Kortesniemi, Mika; Salli, Eero; Seuri, Raija [HUS Helsinki Medical Imaging Center, Univ. of Helsinki, Helsinki (Finland)], E-mail: mika.kortesniemi@hus.fi
2012-10-15
Background Computed tomography (CT) has become the main contributor of the cumulative radiation exposure in radiology. Information on cumulative exposure history of the patient should be available for efficient management of radiation exposures and for radiological justification. Purpose To develop and evaluate automatic image registration for organ dose calculation in CT. Material and Methods Planning radiograph (scout) image data describing CT scan ranges from 15 thoracic CT examinations (9 men and 6 women) and 10 abdominal CT examinations (6 men and 4 women) were co-registered with the reference trunk CT scout image. 2-D affine transformation and normalized correlation metric was used for image registration. Longitudinal (z-axis) scan range coordinates on the reference scout image were converted into slice locations on the CT-Expo anthropomorphic male and female models, following organ and effective dose calculations. Results The average deviation of z-location of studied patient images from the corresponding location in the reference scout image was 6.2 mm. The ranges of organ and effective doses with constant exposure parameters were from 0 to 28.0 mGy and from 7.3 to 14.5 mSv, respectively. The mean deviation of the doses for fully irradiated organs (inside the scan range), partially irradiated organs and non-irradiated organs (outside the scan range) was 1%, 5%, and 22%, respectively, due to image registration. Conclusion The automated image processing method to registrate individual chest and abdominal CT scout radiograph with the reference scout radiograph is feasible. It can be used to determine the individual scan range coordinates in z-direction to calculate the organ dose values. The presented method could be utilized in automatic organ dose calculation in CT for radiation exposure tracking of the patients.
Directory of Open Access Journals (Sweden)
Shan Yang
2016-01-01
Full Text Available Power flow calculation and short circuit calculation are the basis of theoretical research for distribution network with inverter based distributed generation. The similarity of equivalent model for inverter based distributed generation during normal and fault conditions of distribution network and the differences between power flow and short circuit calculation are analyzed in this paper. Then an integrated power flow and short circuit calculation method for distribution network with inverter based distributed generation is proposed. The proposed method let the inverter based distributed generation be equivalent to Iθ bus, which makes it suitable to calculate the power flow of distribution network with a current limited inverter based distributed generation. And the low voltage ride through capability of inverter based distributed generation can be considered as well in this paper. Finally, some tests of power flow and short circuit current calculation are performed on a 33-bus distribution network. The calculated results from the proposed method in this paper are contrasted with those by the traditional method and the simulation method, whose results have verified the effectiveness of the integrated method suggested in this paper.
Fan Affinity Laws from a Collision Model
Bhattacharjee, Shayak
2012-01-01
The performance of a fan is usually estimated using hydrodynamical considerations. The calculations are long and involved and the results are expressed in terms of three affinity laws. In this paper we use kinetic theory to attack this problem. A hard sphere collision model is used, and subsequently a correction to account for the flow behaviour…
Study on the Cost Calculation of Local Fixed Telecom Network Based on Unbundled Network Elements
Institute of Scientific and Technical Information of China (English)
XU Liang; LIANG Xiong-jian; HUANG Xiu-qing
2005-01-01
In this paper, according to the practical condition of local fixed telecom network, based on the method of the realistic total element long-run incremental cost, the practical methods of dividing the network elements, calculating the cost of network elements and services are given, to provide reference for the cost calculation in telecom industry.
Assessing high affinity binding to HLA-DQ2.5 by a novel peptide library based approach
DEFF Research Database (Denmark)
Jüse, Ulrike; Arntzen, Magnus; Højrup, Peter;
2011-01-01
Here we report on a novel peptide library based method for HLA class II binding motif identification. The approach is based on water soluble HLA class II molecules and soluble dedicated peptide libraries. A high number of different synthetic peptides are competing to interact with a limited amount...... to HLA are then isolated by size exclusion chromatography and sequenced by tandem mass spectrometry online coupled to liquid chromatography. The MS/MS data are subsequently searched against a library defined database using a search engine such as Mascot, followed by manual inspection of the results. We...... library. The eluted sequences fit very well with the previously described HLA-DQ2.5 peptide binding motif. This novel method, limited by library complexity and sensitivity of mass spectrometry, allows the analysis of several thousand synthetic sequences concomitantly in a simple water soluble format....
Directory of Open Access Journals (Sweden)
Hosseininejad, M.
2012-11-01
Full Text Available Toxoplasma gondii is an apicomplexan parasite that infects human and almost all warm-blooded animals. The life cycle of the parasite includes an asexual reproduction in intermediate hosts (Mammals and birds and a sexual reproduction in definitive hosts (Felidae. Cats are both the intermediate and the definitive host for T. gondii. The aim of this study was to investigate anti-T. gondii antibodies in cats by using an immunoblot method based on a major surface antigen; SAG1. Six sero-negative kittens were infected intra-peritoneally by Rh strain of T. gondii. Serum samples were collected and evaluated for the presence of IgG antibodies by using two techniques; immunoblotting and indirect fluorescent antibody test (IFAT.SAG1 based immunoblotting was able to detect anti-T. gondii antibodies at least eight days after infection. Comparative evaluation showed that this method is as sensitive as IFAT to diagnose T. gondii infection in cats.
A MEMS Dielectric Affinity Glucose Biosensor
Xian HUANG; Li, SiQi; Davis, Erin; Li, Dachao; Wang, Qian; Lin, Qiao
2013-01-01
Continuous glucose monitoring (CGM) sensors based on affinity detection are desirable for long-term and stable glucose management. However, most affinity sensors contain mechanical moving structures and complex design in sensor actuation and signal readout, limiting their reliability in subcutaneously implantable glucose detection. We have previously demonstrated a proof-of-concept dielectric glucose sensor that measured pre-mixed glucose-sensitive polymer solutions at various glucose concent...
Jeraj, Robert; Keall, Paul
2000-12-01
The effect of the statistical uncertainty, or noise, in inverse treatment planning for intensity modulated radiotherapy (IMRT) based on Monte Carlo dose calculation was studied. Sets of Monte Carlo beamlets were calculated to give uncertainties at Dmax ranging from 0.2% to 4% for a lung tumour plan. The weights of these beamlets were optimized using a previously described procedure based on a simulated annealing optimization algorithm. Several different objective functions were used. It was determined that the use of Monte Carlo dose calculation in inverse treatment planning introduces two errors in the calculated plan. In addition to the statistical error due to the statistical uncertainty of the Monte Carlo calculation, a noise convergence error also appears. For the statistical error it was determined that apparently successfully optimized plans with a noisy dose calculation (3% 1σ at Dmax ), which satisfied the required uniformity of the dose within the tumour, showed as much as 7% underdose when recalculated with a noise-free dose calculation. The statistical error is larger towards the tumour and is only weakly dependent on the choice of objective function. The noise convergence error appears because the optimum weights are determined using a noisy calculation, which is different from the optimum weights determined for a noise-free calculation. Unlike the statistical error, the noise convergence error is generally larger outside the tumour, is case dependent and strongly depends on the required objectives.
Short Circuit Calculation in Networks with a High Share of Inverter Based Distributed Generation
Margossian, Harag; Deconinck, Geert; Sachau, Jürgen
2014-01-01
Conventional short circuit calculation programs do not consider the actual behavior of inverter based distributed generation (DG). Several techniques to consider them have been suggested in literature and are briefly described in this paper. A tool is developed with the combination of these techniques. The approach uses standard short circuit calculation tools and accommodates inverter based DG with different fault responses. The approach is evaluated and compared against other techniques usi...
International Nuclear Information System (INIS)
The introduction of macros in try calculation sheets allows the automatic application of various dating models using unsupported ''210 Pb data from a data base. The calculation books the contain the models have been modified to permit the implementation of these macros. The Marine and Aquatic Radioecology group of CIEMAT (MARG) will be involved in new European Projects, thus new models have been developed. This report contains a detailed description of: a) the new implement macros b) the design of a dating Menu in the calculation sheet and c) organization and structure of the data base. (Author) 4 refs
Sun, L; Meng, S
2016-08-01
The human proton-coupled peptide transporter (hPEPT1) with broad substrates is an important route for improving the pharmacokinetic performance of drugs. Thus, it is essential to predict the affinity constant between drug molecule and hPEPT1 for rapid virtual screening of hPEPT1's substrate during lead optimization, candidate selection and hPEPT1 prodrug design. Here, a structure-based in silico model for 114 compounds was constructed based on eight structural parameters. This model was built by the multiple linear regression method and satisfied all the prerequisites of the regression models. For the entire data set, the r(2) and adjusted r(2) values were 0.74 and 0.72, respectively. Then, this model was used to perform substrate/non-substrate classification. For 29 drugs from DrugBank database, all were correctly classified as substrates of hPEPT1. This model was also used to perform substrate/non-substrate classification for 18 drugs and their prodrugs; this QSAR model also can distinguish between the substrate and non-substrate. In conclusion, the QSAR model in this paper was validated by a large external data set, and all results indicated that the developed model was robust, stable, and can be used for rapid virtual screening of hPEPT1's substrate in the early stage of drug discovery. PMID:27586363
Affine and degenerate affine BMW algebras: The center
Daugherty, Zajj; Virk, Rahbar
2011-01-01
The degenerate affine and affine BMW algebras arise naturally in the context of Schur-Weyl duality for orthogonal and symplectic Lie algebras and quantum groups, respectively. Cyclotomic BMW algebras, affine Hecke algebras, cyclotomic Hecke algebras, and their degenerate versions are quotients. In this paper the theory is unified by treating the orthogonal and symplectic cases simultaneously; we make an exact parallel between the degenerate affine and affine cases via a new algebra which takes the role of the affine braid group for the degenerate setting. A main result of this paper is an identification of the centers of the affine and degenerate affine BMW algebras in terms of rings of symmetric functions which satisfy a "cancellation property" or "wheel condition" (in the degenerate case, a reformulation of a result of Nazarov). Miraculously, these same rings also arise in Schubert calculus, as the cohomology and K-theory of isotropic Grassmanians and symplectic loop Grassmanians. We also establish new inte...
Periodic cyclic homology of affine Hecke algebras
Solleveld, Maarten
2009-01-01
This is the author's PhD-thesis, which was written in 2006. The version posted here is identical to the printed one. Instead of an abstract, the short list of contents: Preface 5 1 Introduction 9 2 K-theory and cyclic type homology theories 13 3 Affine Hecke algebras 61 4 Reductive p-adic groups 103 5 Parameter deformations in affine Hecke algebras 129 6 Examples and calculations 169 A Crossed products 223 Bibliography 227 Index 237 Samenvatting 245 Curriculum vitae 253
Directory of Open Access Journals (Sweden)
Nicholas Allen Kinney
Full Text Available Three dimensional nuclear architecture is important for genome function, but is still poorly understood. In particular, little is known about the role of the "boundary conditions"--points of attachment between chromosomes and the nuclear envelope. We describe a method for modeling the 3D organization of the interphase nucleus, and its application to analysis of chromosome-nuclear envelope (Chr-NE attachments of polytene (giant chromosomes in Drosophila melanogaster salivary glands. The model represents chromosomes as self-avoiding polymer chains confined within the nucleus; parameters of the model are taken directly from experiment, no fitting parameters are introduced. Methods are developed to objectively quantify chromosome territories and intertwining, which are discussed in the context of corresponding experimental observations. In particular, a mathematically rigorous definition of a territory based on convex hull is proposed. The self-avoiding polymer model is used to re-analyze previous experimental data; the analysis suggests 33 additional Chr-NE attachments in addition to the 15 already explored Chr-NE attachments. Most of these new Chr-NE attachments correspond to intercalary heterochromatin--gene poor, dark staining, late replicating regions of the genome; however, three correspond to euchromatin--gene rich, light staining, early replicating regions of the genome. The analysis also suggests 5 regions of anti-contact, characterized by aversion for the NE, only two of these correspond to euchromatin. This composition of chromatin suggests that heterochromatin may not be necessary or sufficient for the formation of a Chr-NE attachment. To the extent that the proposed model represents reality, the confinement of the polytene chromosomes in a spherical nucleus alone does not favor the positioning of specific chromosome regions at the NE as seen in experiment; consequently, the 15 experimentally known Chr-NE attachment positions do not
BRST Cohomology in Quantum Affine Algebra $U_q(\\widehat{sl_2})$
Konno, H
1994-01-01
Using free field representation of quantum affine algebra $U_q(\\widehat{sl_2})$, we investigate the structure of the Fock modules over $U_q(\\widehat{sl_2})$. The analisys is based on a $q$-analog of the BRST formalism given by Bernard and Felder in the affine Kac-Moody algebra $\\widehat {sl_2}$. We give an explicit construction of the singular vectors using the BRST charge. By the same cohomology analysis as the classical case ($q=1$), we obtain the irreducible highest weight representation space as a nontrivial cohomology group. This enables us to calculate a trace of the $q$-vertex operators over this space.
Affinity driven social networks
Ruyú, B.; Kuperman, M. N.
2007-04-01
In this work we present a model for evolving networks, where the driven force is related to the social affinity between individuals of a population. In the model, a set of individuals initially arranged on a regular ordered network and thus linked with their closest neighbors are allowed to rearrange their connections according to a dynamics closely related to that of the stable marriage problem. We show that the behavior of some topological properties of the resulting networks follows a non trivial pattern.
Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.
Wickstrom, Lauren; Deng, Nanjie; He, Peng; Mentes, Ahmet; Nguyen, Crystal; Gilson, Michael K; Kurtzman, Tom; Gallicchio, Emilio; Levy, Ronald M
2016-01-01
Force field accuracy is still one of the "stalemates" in biomolecular modeling. Model systems with high quality experimental data are valuable instruments for the validation and improvement of effective potentials. With respect to protein-ligand binding, organic host-guest complexes have long served as models for both experimental and computational studies because of the abundance of binding affinity data available for such systems. Binding affinity data collected for cyclodextrin (CD) inclusion complexes, a popular model for molecular recognition, is potentially a more reliable resource for tuning energy parameters than hydration free energy measurements. Convergence of binding free energy calculations on CD host-guest systems can also be obtained rapidly, thus offering the opportunity to assess the robustness of these parameters. In this work, we demonstrate how implicit solvent parameters can be developed using binding affinity experimental data and the binding energy distribution analysis method (BEDAM) and validated using the Grid Inhomogeneous Solvation Theory analysis. These new solvation parameters were used to study protein-ligand binding in two drug targets against the HIV-1 virus and improved the agreement between the calculated and the experimental binding affinities. This work illustrates how benchmark sets of high quality experimental binding affinity data and physics-based binding free energy models can be used to evaluate and optimize force fields for protein-ligand systems. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26256816
Affine morphisms at zero level
Das, Paramita; Gupta, Ved Prakash
2010-01-01
Given a finite index subfactor, we show that the {\\em affine morphisms at zero level} in the affine category over the planar algebra associated to the subfactor is isomorphic to the fusion algebra of the subfactor as a *-algebra.
On the Affine Isoperimetric Inequalities
Indian Academy of Sciences (India)
Wuyang Yu; Gangsong Leng
2011-11-01
We obtain an isoperimetric inequality which estimate the affine invariant -surface area measure on convex bodies. We also establish the reverse version of -Petty projection inequality and an affine isoperimetric inequality of $_{-p}K$.
Directory of Open Access Journals (Sweden)
Pirrello Julien
2012-10-01
Full Text Available Abstract Background The phytohormone ethylene is involved in a wide range of developmental processes and in mediating plant responses to biotic and abiotic stresses. Ethylene signalling acts via a linear transduction pathway leading to the activation of Ethylene Response Factor genes (ERF which represent one of the largest gene families of plant transcription factors. How an apparently simple signalling pathway can account for the complex and widely diverse plant responses to ethylene remains yet an unanswered question. Building on the recent release of the complete tomato genome sequence, the present study aims at gaining better insight on distinctive features among ERF proteins. Results A set of 28 cDNA clones encoding ERFs in the tomato (Solanum lycopersicon were isolated and shown to fall into nine distinct subclasses characterised by specific conserved motifs most of which with unknown function. In addition of being able to regulate the transcriptional activity of GCC-box containing promoters, tomato ERFs are also shown to be active on promoters lacking this canonical ethylene-responsive-element. Moreover, the data reveal that ERF affinity to the GCC-box depends on the nucleotide environment surrounding this cis-acting element. Site-directed mutagenesis revealed that the nature of the flanking nucleotides can either enhance or reduce the binding affinity, thus conferring the binding specificity of various ERFs to target promoters. Based on their expression pattern, ERF genes can be clustered in two main clades given their preferential expression in reproductive or vegetative tissues. The regulation of several tomato ERF genes by both ethylene and auxin, suggests their potential contribution to the convergence mechanism between the signalling pathways of the two hormones. Conclusions The data reveal that regions flanking the core GCC-box sequence are part of the discrimination mechanism by which ERFs selectively bind to their target
Directory of Open Access Journals (Sweden)
Wensheng Lan
2012-06-01
Full Text Available We have developed a novel optical biosensor device using recombinant methyl parathion hydrolase (MPH enzyme immobilized on agarose by metal-chelate affinity to detect organophosphorus (OP compounds with a nitrophenyl group. The biosensor principle is based on the optical measurement of the product of OP catalysis by MPH (p-nitrophenol. Briefly, MPH containing six sequential histidines (6× His tag at its N-terminal was bound to nitrilotriacetic acid (NTA agarose with Ni ions, resulting in the flexible immobilization of the bio-reaction platform. The optical biosensing system consisted of two light-emitting diodes (LEDs and one photodiode. The LED that emitted light at the wavelength of the maximum absorption for p-nitrophenol served as the signal light, while the other LED that showed no absorbance served as the reference light. The optical sensing system detected absorbance that was linearly correlated to methyl parathion (MP concentration and the detection limit was estimated to be 4 μM. Sensor hysteresis was investigated and the results showed that at lower concentration range of MP the difference got from the opposite process curves was very small. With its easy immobilization of enzymes and simple design in structure, the system has the potential for development into a practical portable detector for field applications.
Rucci, Michael; Hardie, Russell C; Barnard, Kenneth J
2014-05-01
In this paper, we present a computationally efficient video restoration algorithm to address both blur and noise for a Nyquist sampled imaging system. The proposed method utilizes a temporal Kalman filter followed by a correlation-model based spatial adaptive Wiener filter (AWF). The Kalman filter employs an affine background motion model and novel process-noise variance estimate. We also propose and demonstrate a new multidelay temporal Kalman filter designed to more robustly treat local motion. The AWF is a spatial operation that performs deconvolution and adapts to the spatially varying residual noise left in the Kalman filter stage. In image areas where the temporal Kalman filter is able to provide significant noise reduction, the AWF can be aggressive in its deconvolution. In other areas, where less noise reduction is achieved with the Kalman filter, the AWF balances the deconvolution with spatial noise reduction. In this way, the Kalman filter and AWF work together effectively, but without the computational burden of full joint spatiotemporal processing. We also propose a novel hybrid system that combines a temporal Kalman filter and BM3D processing. To illustrate the efficacy of the proposed methods, we test the algorithms on both simulated imagery and video collected with a visible camera.
Kutilek, Victoria D; Andrews, Christine L; Richards, Matthew P; Xu, Zangwei; Sun, Tianxiao; Chen, Yiping; Hashke, Andrew; Smotrov, Nadya; Fernandez, Rafael; Nickbarg, Elliott B; Chamberlin, Chad; Sauvagnat, Berengere; Curran, Patrick J; Boinay, Ryan; Saradjian, Peter; Allen, Samantha J; Byrne, Noel; Elsen, Nathaniel L; Ford, Rachael E; Hall, Dawn L; Kornienko, Maria; Rickert, Keith W; Sharma, Sujata; Shipman, Jennifer M; Lumb, Kevin J; Coleman, Kevin; Dandliker, Peter J; Kariv, Ilona; Beutel, Bruce
2016-07-01
The primary objective of early drug discovery is to associate druggable target space with a desired phenotype. The inability to efficiently associate these often leads to failure early in the drug discovery process. In this proof-of-concept study, the most tractable starting points for drug discovery within the NF-κB pathway model system were identified by integrating affinity selection-mass spectrometry (AS-MS) with functional cellular assays. The AS-MS platform Automated Ligand Identification System (ALIS) was used to rapidly screen 15 NF-κB proteins in parallel against large-compound libraries. ALIS identified 382 target-selective compounds binding to 14 of the 15 proteins. Without any chemical optimization, 22 of the 382 target-selective compounds exhibited a cellular phenotype consistent with the respective target associated in ALIS. Further studies on structurally related compounds distinguished two chemical series that exhibited a preliminary structure-activity relationship and confirmed target-driven cellular activity to NF-κB1/p105 and TRAF5, respectively. These two series represent new drug discovery opportunities for chemical optimization. The results described herein demonstrate the power of combining ALIS with cell functional assays in a high-throughput, target-based approach to determine the most tractable drug discovery opportunities within a pathway. PMID:26969322
Fujimura, Nobuyuki; Ohta, Akio; Makihara, Katsunori; Miyazaki, Seiichi
2016-08-01
An evaluation method for the energy level of the valence band (VB) top from the vacuum level (VL) for metals, dielectrics, and semiconductors from the results of X-ray photoelectron spectroscopy (XPS) is presented for the accurate determination of the energy band diagram for materials of interest. In this method, the VB top can be determined by the energy difference between the onset of VB signals and the cut-off energy for secondary photoelectrons by considering the X-ray excitation energy (hν). The energy level of the VB top for three kinds of Si-based materials (H-terminated Si, wet-cleaned 4H-SiC, and thermally grown SiO2) has been investigated by XPS under monochromatized Al Kα radiation (hν = 1486.6 eV). We have also demonstrated the determination of the electron affinity for the samples by this measurement technique in combination with the measured and reported energy bandgaps (E g).
Adjoint affine fusion and tadpoles
Urichuk, Andrew; Walton, Mark A.
2016-01-01
We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-pol...
Affine Patches on Positroid Varieties and Affine Pipe Dreams (Thesis)
Snider, Michelle
2010-01-01
The objects of interest in this thesis are positroid varieties in the Grassmannian, which are indexed by juggling patterns. In particular, we study affine patches on these positroid varieties. Our main result corresponds these affine patches to Kazhdan-Lusztig varieties in the affine Grassmannian. We develop a new term order and study how these spaces are related to subword complexes and Stanley-Reisner ideals. We define an extension of pipe dreams to the affine case and conclude by showing how our affine pipe dreams are generalizations of Cauchon and Le diagrams.
Affine and quasi-affine frames for rational dilations
DEFF Research Database (Denmark)
Bownik, Marcin; Lemvig, Jakob
2011-01-01
, the corresponding family of quasi-affine systems are frames with uniform frame bounds. We also prove a similar equivalence result between pairs of dual affine frames and dual quasi-affine frames. Finally, we uncover some fundamental differences between the integer and rational settings by exhibiting an example......In this paper we extend the investigation of quasi-affine systems, which were originally introduced by Ron and Shen [J. Funct. Anal. 148 (1997), 408-447] for integer, expansive dilations, to the class of rational, expansive dilations. We show that an affine system is a frame if, and only if...
Affinity purification of aprotinin from bovine lung.
Xin, Yu; Liu, Lanhua; Chen, Beizhan; Zhang, Ling; Tong, Yanjun
2015-05-01
An affinity protocol for the purification of aprotinin from bovine lung was developed. To simulate the structure of sucrose octasulfate, a natural specific probe for aprotinin, the affinity ligand was composed of an acidic head and a hydrophobic stick, and was then linked with Sepharose. The sorbent was then subjected to adsorption analysis with pure aprotinin. The purification process consisted of one step of affinity chromatography and another step of ultrafiltration. Then purified aprotinin was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis, trypsin inhibitor activity, gel-filtration, and thin-layer chromatography analysis. As calculated, the theoretical maximum adsorption (Qmax ) of the affinity sorbent was 25,476.0 ± 184.8 kallikrein inactivator unit/g wet gel; the dissociation constant of the complex "immobilized ligand-aprotinin" (Kd ) was 4.6 ± 0.1 kallikrein inactivator unit/mL. After the affinity separation of bovine lung aprotinin, reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis and gel-filtration chromatography revealed that the protein was a single polypeptide, and the purities were ∼ 97 and 100%, respectively; the purified peptide was also confirmed with aprotinin standard by gel-filtration chromatography and thin-layer chromatography. After the whole purification process, protein, and bioactivity recoveries were 2.2 and 92.6%, respectively; and the specific activity was up to 15,907.1 ± 10.2 kallikrein inactivator unit/mg. PMID:25677462
A New Optimization Method for Centrifugal Compressors Based on 1D Calculations and Analyses
Directory of Open Access Journals (Sweden)
Pei-Yuan Li
2015-05-01
Full Text Available This paper presents an optimization design method for centrifugal compressors based on one-dimensional calculations and analyses. It consists of two parts: (1 centrifugal compressor geometry optimization based on one-dimensional calculations and (2 matching optimization of the vaned diffuser with an impeller based on the required throat area. A low pressure stage centrifugal compressor in a MW level gas turbine is optimized by this method. One-dimensional calculation results show that D3/D2 is too large in the original design, resulting in the low efficiency of the entire stage. Based on the one-dimensional optimization results, the geometry of the diffuser has been redesigned. The outlet diameter of the vaneless diffuser has been reduced, and the original single stage diffuser has been replaced by a tandem vaned diffuser. After optimization, the entire stage pressure ratio is increased by approximately 4%, and the efficiency is increased by approximately 2%.
Hagedorn, Linda Serra
1998-01-01
A study explored two distinct methods of calculating a precise measure of gender-based wage differentials among college faculty. The first estimation considered wage differences using a formula based on human capital; the second included compensation for past discriminatory practices. Both measures were used to predict three specific aspects of…
Calculation Model for Current-voltage Relation of Silicon Quantum-dots-based Nano-memory
Institute of Scientific and Technical Information of China (English)
YANG Hong-guan; DAI Da-kang; YU Biao; SHANG Lin-lin; GUO You-hong
2007-01-01
Based on the capacitive coupling formalism, an analytic model for calculating the drain currents of the quantum-dots floating-gate memory cell is proposed. Using this model, one can calculate numerically the drain currents of linear, saturation and subthreshold regions of the device with/without charges stored on the floating dots. The read operation process of an n-channel Si quantum-dots floating-gate nano-memory cell is discussed after calculating the drain currents versus the drain to source voltages and control gate voltages in both high and low threshold states respectively.
Simple atmospheric transmittance calculation based on a Fourier-transformed Voigt profile.
Kobayashi, Hirokazu
2002-11-20
A method of line-by-line transmission calculation for a homogeneous atmospheric layer that uses the Fourier-transformed Voigt profile is presented. The method is based on a pure Voigt function with no approximation and an interference term that takes into account the line-mixing effect. One can use the method to calculate transmittance, considering each line shape as it is affected by temperature and pressure, with a line database with an arbitrary wave-number range and resolution. To show that the method is feasible for practical model development, we compared the calculated transmittance with that obtained with a conventional model, and good consistency was observed. PMID:12463237
Calculation of response of Chinese hamster cells to ions based on track structure theory
Institute of Scientific and Technical Information of China (English)
LiuXiao－Wei; ZhangChun－Xiang
1997-01-01
Considering biological cells as single target two-hit detectors,an analytic formula to calculate the response of cells to ions is developed based on track structure theory.In the calculation,the splitting deposition energy between ion kill mode and γ kill mode is not used.The results of calculation are in agreement with the experimental data for response of Chinese hamster cells,whose response to γ rays can be described by the response function of single target two hit detector to ions.
A GIS extension model to calculate urban heat island intensity based on urban geometry
Nakata, C. M.; Souza, Léa Cristina Lucas; Rodrigues, Daniel Souto
2015-01-01
This paper presents a simulation model, which was incorporated into a Geographic Information System (GIS), in order to calculate the maximum intensity of urban heat islands based on urban geometry data. The method-ology of this study stands on a theoretical-numerical basis (Okeâ s model), followed by the study and selection of existing GIS tools, the design of the calculation model, the incorporation of the resulting algorithm into the GIS platform and the application of the tool, developed ...
Aptamer Affinity Maturation by Resampling and Microarray Selection.
Kinghorn, Andrew B; Dirkzwager, Roderick M; Liang, Shaolin; Cheung, Yee-Wai; Fraser, Lewis A; Shiu, Simon Chi-Chin; Tang, Marco S L; Tanner, Julian A
2016-07-19
Aptamers have significant potential as affinity reagents, but better approaches are critically needed to discover higher affinity nucleic acids to widen the scope for their diagnostic, therapeutic, and proteomic application. Here, we report aptamer affinity maturation, a novel aptamer enhancement technique, which combines bioinformatic resampling of aptamer sequence data and microarray selection to navigate the combinatorial chemistry binding landscape. Aptamer affinity maturation is shown to improve aptamer affinity by an order of magnitude in a single round. The novel aptamers exhibited significant adaptation, the complexity of which precludes discovery by other microarray based methods. Honing aptamer sequences using aptamer affinity maturation could help optimize a next generation of nucleic acid affinity reagents. PMID:27346322
Bie, Zijun; Chen, Yang; Li, Hengye; Wu, Ronghu; Liu, Zhen
2014-06-27
Boronate affinity materials have attracted increasing attentions as sample enrichment platforms for glycoproteomic analysis in recent years. However, most of the boronate affinity materials that have already employed for proteomic analysis are suffering from apparent disadvantages, such as alkaline pH for binding, weak affinity, and relatively poor selectivity. Benzoboroxoles are a unique class of boronic acids which have showed excellent binding properties for the recognition of cis-diol-containing compounds. Recently, a 3-carboxy-benzoboroxole-functionalized monolithic column had been reported and it had exhibited the best selectivity and affinity as well as the lowest binding pH among all reported boronate affinity monolithic columns. In this study, an off-line hyphenation of this boronate affinity monolithic column-based extraction with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was developed and the powerfulness of this hyphenated approach in the analysis of glycoproteins and glycopeptides in complex samples was investigated. The approach was first applied to the analysis of glycopeptides in the tryptic digest of horseradish peroxidase (HRP). Totally 22 glycopeptides were identified. To the best of our knowledge, this is the best performance among all the boronic acid-functionalized materials. We further employed this approach to the analysis of intact proteins in human saliva. Totally 6 intact glycoproteins were successfully identified. As comparison, when the samples were analyzed without extraction, only a few glycopeptides were identified from the tryptic digest of HRP while no glycoproteins were found from the saliva samples. PMID:24928239
Rudra, Suparna; Dasmandal, Somnath; Patra, Chiranjit; Kundu, Arjama; Mahapatra, Ambikesh
2016-09-01
The binding interaction of a synthesized Schiff base Fe(II) complex with biological macromolecules viz., bovine serum albumin (BSA) and calf thymus(ct)-DNA have been investigated using different spectroscopic techniques coupled with viscosity measurements at physiological pH and 298 K. Regular amendments in emission intensities of BSA upon the action of the complex indicate significant interaction between them, and the binding interaction have been characterized by Stern Volmer plots and thermodynamic binding parameters. On the basis of this quenching technique one binding site with binding constant (Kb = (7.6 ± 0.21) × 105) between complex and protein have been obtained at 298 K. Time-resolved fluorescence studies have also been encountered to understand the mechanism of quenching induced by the complex. Binding affinities of the complex to the fluorophores of BSA namely tryptophan (Trp) and tyrosine (Tyr) have been judged by synchronous fluorescence studies. Secondary structural changes of BSA rooted by the complex has been revealed by CD spectra. On the other hand, hypochromicity of absorption spectra of the complex with the addition of ct-DNA and the gradual reduction in emission intensities of ethidium bromide bound ct-DNA in presence of the complex indicate noticeable interaction between ct-DNA and the complex with the binding constant (4.2 ± 0.11) × 106 M- 1. Life-time measurements have been studied to determine the relative amplitude of binding of the complex to ct-DNA base pairs. Mode of binding interaction of the complex with ct-DNA has been deciphered by viscosity measurements. CD spectra have also been used to understand the changes in ct-DNA structure upon binding with the metal complex. Density functional theory (DFT) and molecular docking analysis have been employed in highlighting the interactive phenomenon and binding location of the complex with the macromolecules.
Rudra, Suparna; Dasmandal, Somnath; Patra, Chiranjit; Kundu, Arjama; Mahapatra, Ambikesh
2016-09-01
The binding interaction of a synthesized Schiff base Fe(II) complex with biological macromolecules viz., bovine serum albumin (BSA) and calf thymus(ct)-DNA have been investigated using different spectroscopic techniques coupled with viscosity measurements at physiological pH and 298K. Regular amendments in emission intensities of BSA upon the action of the complex indicate significant interaction between them, and the binding interaction have been characterized by Stern Volmer plots and thermodynamic binding parameters. On the basis of this quenching technique one binding site with binding constant (Kb=(7.6±0.21)×10(5)) between complex and protein have been obtained at 298K. Time-resolved fluorescence studies have also been encountered to understand the mechanism of quenching induced by the complex. Binding affinities of the complex to the fluorophores of BSA namely tryptophan (Trp) and tyrosine (Tyr) have been judged by synchronous fluorescence studies. Secondary structural changes of BSA rooted by the complex has been revealed by CD spectra. On the other hand, hypochromicity of absorption spectra of the complex with the addition of ct-DNA and the gradual reduction in emission intensities of ethidium bromide bound ct-DNA in presence of the complex indicate noticeable interaction between ct-DNA and the complex with the binding constant (4.2±0.11)×10(6)M(-1). Life-time measurements have been studied to determine the relative amplitude of binding of the complex to ct-DNA base pairs. Mode of binding interaction of the complex with ct-DNA has been deciphered by viscosity measurements. CD spectra have also been used to understand the changes in ct-DNA structure upon binding with the metal complex. Density functional theory (DFT) and molecular docking analysis have been employed in highlighting the interactive phenomenon and binding location of the complex with the macromolecules.
Directory of Open Access Journals (Sweden)
Young Ah Goo
2008-01-01
Full Text Available Recently, several research groups have published methods for the determination of proteomic expression profiling by mass spectrometry without the use of exogenously added stable isotopes or stable isotope dilution theory. These so-called label-free, methods have the advantage of allowing data on each sample to be acquired independently from all other samples to which they can later be compared in silico for the purpose of measuring changes in protein expression between various biological states. We developed label free software based on direct measurement of peptide ion current area (PICA and compared it to two other methods, a simpler label free method known as spectral counting and the isotope coded affinity tag (ICAT method. Data analysis by these methods of a standard mixture containing proteins of known, but varying, concentrations showed that they performed similarly with a mean squared error of 0.09. Additionally, complex bacterial protein mixtures spiked with known concentrations of standard proteins were analyzed using the PICA label-free method. These results indicated that the PICA method detected all levels of standard spiked proteins at the 90% confidence level in this complex biological sample. This finding confirms that label-free methods, based on direct measurement of the area under a single ion current trace, performed as well as the standard ICAT method. Given the fact that the label-free methods provide ease in experimental design well beyond pair-wise comparison, label-free methods such as our PICA method are well suited for proteomic expression profiling of large numbers of samples as is needed in clinical analysis.
Institute of Scientific and Technical Information of China (English)
仪晓斌; 陈莹
2016-01-01
针对目前正面人脸合成算法运算量大或合成图像失真较大的问题，提出一种基于分段仿射变换和泊松融合的正面人脸图像合成算法，将多幅输入图像用分段仿射变换（Piecewise Affine Warp，PAW）映射到正面人脸模板，并根据映射时产生的非刚性形变求得其对应的权重矩阵，进而获取每幅映射图像对应的变形掩膜，依次以这些映射图像为前景图像，以其对应的变形掩膜为泊松掩膜，并以上一次的融合图像为背景图像进行泊松融合，生成一幅平滑自然的正面人脸图像。实验结果表明，相比现有算法，该算法生成的正面人脸图像更加逼近真实正面人脸图像，而且很好地保留了输入人脸的个体信息。%In this paper, a frontal face synthesizing strategy based on Poisson image fusion and Piecewise Affine Warp (PAW)is proposed to solve the problem of large-scale computation cost or transformation distortion in general synthesizing methods. The multiple non-frontal input images are mapped to the frontal face template with PAW. The corresponding weight matrices are calculated according to the magnitude of deformation which can be used to obtain the foreground mask for Poisson fusion. Iterative fusion strategy is designed to synthesize one frontal image from multiple non-frontal images. In each step, the PAW image is used as foreground image. The deformation mask is used as foreground mask, and the fusion image of the previous step is used as background. Experiments show that the synthesized frontal image can per-fectly preserve personal facial details and outperforms others in both subjective and objective evaluations.
Inverse treatment planning for radiation therapy based on fast Monte Carlo dose calculation
International Nuclear Information System (INIS)
An inverse treatment planning system based on fast Monte Carlo (MC) dose calculation is presented. It allows optimisation of intensity modulated dose distributions in 15 to 60 minutes on present day personal computers. If a multi-processor machine is available, parallel simulation of particle histories is also possible, leading to further calculation time reductions. The optimisation process is divided into two stages. The first stage results influence profiles based on pencil beam (PB) dose calculation. The second stage starts with MC verification and post-optimisation of the PB dose and fluence distributions. Because of the potential to accurately model beam modifiers, MC based inverse planning systems are able to optimise compensator thicknesses and leaf trajectories instead of intensity profiles only. The corresponding techniques, whose implementation is the subject for future work, are also presented here. (orig.)
The Calculation of Collision Risk on Air-Routes Based on Variable Nominal Separation
Institute of Scientific and Technical Information of China (English)
QU Yu-ling; HAN Song-chen
2010-01-01
In this paper, a new method to calculate collision risk of air-routes, based on variable nominal separation, is proposed. The collision risk model of air-routes, based on the time variable and initial time interval variable, is given. Because the distance and the collision probability vary with time when the nominal relative speed between aircraft is not zero for a fixed initial time interval, the distance, the variable nominal separation, and the collision probability at any time can be expressed as functions of time and initial time interval. By the probabilistic theory, a model for calculating collision risk is acquired based on initial time interval distribution, flow rates, and the proportion of aircraft type. From the results of calculations, the collision risk can be characterized by the model when the nominal separation changes with time. As well the roles of parameters can be shown more readily.
Li, Shuyi; Niklasson, Gunnar A.; Granqvist, Claes-Göran
2011-01-01
Composites including VO2-based thermochromic nanoparticles are able to combine high luminous transmittance T-lum with a significant modulation of the solar energy transmittance Delta T-sol at a "critical" temperature in the vicinity of room temperature. Thus nanothermochromics is of much interest for energy efficient fenestration and offers advantages over thermochromic VO2-based thin films. This paper presents calculations based on effective medium theory applied to dilute suspensions of cor...
Case-Based Reasoning Topological Complexity Calculation of Design for Components
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
Directly calculating the topological and geometric complexity from the STEP (standard for the exchange of product model data, ISO 10303) file is a huge task. So, a case-based reasoning approach is presented, which is based on the similarity between the new component and the old one, to calculate the topological and geometric complexity of new components. In order to index, retrieve in historical component database, a new way of component representation is brought forth. And then an algorithm is given to extract topological graph from its STEP files. A mathematical model, which describes how to compare the similarity, is discussed. Finally, an example is given to show the result.
DEFF Research Database (Denmark)
Mattsson, T.R.; Wahnström, G.; Bengtsson, L.;
1997-01-01
First-principles density-functional calculations of hydrogen adsorption on the Ni (001) surface have been performed in order to get a better understanding of adsorption and diffusion of hydrogen on metal surfaces. We find good agreement with experiments for the adsorption energy, binding distance...
Directory of Open Access Journals (Sweden)
Yan Zhenzhen
2016-01-01
Full Text Available In order to obtain the Required Safety Egress Time (RSET accurately, traditional engineering calculation method of evacuation time has been optimized in this paper. Several principles and fact situations were used to optimize the method, such as detecting principle of the fire detecting system, reaction characteristics of staff being in urgent situation, evacuating queuing theory, building structure and the plugging at the porthole. Taking a three-storey KTV as an example, two methods are used to illustrate the reliability and scientific reasonability of the calculation result. The result is deduced by comparing the error (less than 2% at an allowable range between two results. One result is calculated by a modified method of engineering calculation method, and the other one is given based on a Steering model of Pathfinder evacuation simulation software. The optimized RSET has a good feasibility and Accuracy.
Huang, Yuanshen; Li, Ting; Xu, Banglian; Hong, Ruijin; Tao, Chunxian; Ling, Jinzhong; Li, Baicheng; Zhang, Dawei; Ni, Zhengji; Zhuang, Songlin
2013-02-10
Fraunhofer diffraction formula cannot be applied to calculate the diffraction wave energy distribution of concave gratings like plane gratings because their grooves are distributed on a concave spherical surface. In this paper, a method based on the Kirchhoff diffraction theory is proposed to calculate the diffraction efficiency on concave gratings by considering the curvature of the whole concave spherical surface. According to this approach, each groove surface is divided into several limited small planes, on which the Kirchhoff diffraction field distribution is calculated, and then the diffraction field of whole concave grating can be obtained by superimposition. Formulas to calculate the diffraction efficiency of Rowland-type and flat-field concave gratings are deduced from practical applications. Experimental results showed strong agreement with theoretical computations. With the proposed method, light energy can be optimized to the expected diffraction wave range while implementing aberration-corrected design of concave gratings, particularly for the concave blazed gratings.
Institute of Scientific and Technical Information of China (English)
ZHANG Zhi-jie; LIU Yu-hua; L(U) Zhong-yuan; LI Ze-sheng
2009-01-01
The rotational isomeric state(RIS) model was constructed for poly(vinylidene chloride)(PVDC) based on quantum chemistry calculations. The statistical weighted parameters were obtained from RIS representations and ab initio energies of conformers for model molecules 2,2,4,4-tetrachloropentane(TCP) and 2,2,4,4,6, 6-hexachlorohep-tane(HCH). By employing the RIS method, the characteristic ratio C∞ was calculated for PVDC. The calculated cha-racteristic ratio for PVDC is in good agreement with experiment result. Additionally, we studied the influence of the statistical weighted parameters on C∞ by calculating δC∞/δlnw. According to the values of δC∞/δlnw, the effects of second-order Cl-CH2 pentane type interaction and Cl-Cl long range interaction on C∞ were found to be important. In contrast, first-order interaction is unimportant.
The effects of calculator-based laboratories on standardized test scores
Stevens, Charlotte Bethany Rains
Nationwide, the goal of providing a productive science and math education to our youth in today's educational institutions is centering itself around the technology being utilized in these classrooms. In this age of digital technology, educational software and calculator-based laboratories (CBL) have become significant devices in the teaching of science and math for many states across the United States. Among the technology, the Texas Instruments graphing calculator and Vernier Labpro interface, are among some of the calculator-based laboratories becoming increasingly popular among middle and high school science and math teachers in many school districts across this country. In Tennessee, however, it is reported that this type of technology is not regularly utilized at the student level in most high school science classrooms, especially in the area of Physical Science (Vernier, 2006). This research explored the effect of calculator based laboratory instruction on standardized test scores. The purpose of this study was to determine the effect of traditional teaching methods versus graphing calculator teaching methods on the state mandated End-of-Course (EOC) Physical Science exam based on ability, gender, and ethnicity. The sample included 187 total tenth and eleventh grade physical science students, 101 of which belonged to a control group and 87 of which belonged to the experimental group. Physical Science End-of-Course scores obtained from the Tennessee Department of Education during the spring of 2005 and the spring of 2006 were used to examine the hypotheses. The findings of this research study suggested the type of teaching method, traditional or calculator based, did not have an effect on standardized test scores. However, the students' ability level, as demonstrated on the End-of-Course test, had a significant effect on End-of-Course test scores. This study focused on a limited population of high school physical science students in the middle Tennessee
Applying Activity Based Costing (ABC Method to Calculate Cost Price in Hospital and Remedy Services
Directory of Open Access Journals (Sweden)
A Dabiri
2012-04-01
Full Text Available Background: Activity Based Costing (ABC is one of the new methods began appearing as a costing methodology in the 1990. It calculates cost price by determining the usage of resources. In this study, ABC method was used for calculating cost price of remedial services in hospitals.Methods: To apply ABC method, Shahid Faghihi Hospital was selected. First, hospital units were divided into three main departments: administrative, diagnostic, and hospitalized. Second, activity centers were defined by the activity analysis method. Third, costs of administrative activity centers were allocated into diagnostic and operational departments based on the cost driver. Finally, with regard to the usage of cost objectives from services of activity centers, the cost price of medical services was calculated.Results: The cost price from ABC method significantly differs from tariff method. In addition, high amount of indirect costs in the hospital indicates that capacities of resources are not used properly.Conclusion: Cost price of remedial services with tariff method is not properly calculated when compared with ABC method. ABC calculates cost price by applying suitable mechanisms but tariff method is based on the fixed price. In addition, ABC represents useful information about the amount and combination of cost price services.
The Utility of Affine Variables and Affine Coherent States
Klauder, John R
2011-01-01
Affine coherent states are generated by affine kinematical variables much like canonical coherent states are generated by canonical kinematical variables. Although all classical and quantum formalisms normally entail canonical variables, it is shown that affine variables can serve equally well for many classical and quantum studies. This general purpose analysis provides tools to discuss two major applications: (1) the completely successful quantization of a nonrenormalizable scalar quantum field theory by affine techniques, in complete contrast to canonical techniques which only offer triviality; and (2) a formulation of the kinematical portion of quantum gravity that favors affine kinematical variables over canonical kinematical variables, and which generates a framework in which a favorable analysis of the constrained dynamical issues can take place. All this is possible because of the close connection between the affine and the canonical stories, while the few distinctions can be used to advantage when ap...
Classification of neocortical interneurons using affinity propagation
Santana, Roberto; McGarry, Laura M.; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael
2013-01-01
In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339
Calculation of thermal expansion coefficient of glasses based on topological constraint theory
Zeng, Huidan; Ye, Feng; Li, Xiang; Wang, Ling; Yang, Bin; Chen, Jianding; Zhang, Xianghua; Sun, Luyi
2016-10-01
In this work, the thermal expansion behavior and the structure configuration evolution of glasses were studied. Degree of freedom based on the topological constraint theory is correlated with configuration evolution; considering the chemical composition and the configuration change, the analytical equation for calculating the thermal expansion coefficient of glasses from degree of freedom was derived. The thermal expansion of typical silicate and chalcogenide glasses was examined by calculating their thermal expansion coefficients (TEC) using the approach stated above. The results showed that this approach was energetically favorable for glass materials and revealed the corresponding underlying essence from viewpoint of configuration entropy. This work establishes a configuration-based methodology to calculate the thermal expansion coefficient of glasses that, lack periodic order.
Optimization Method for Indoor Thermal Comfort Based on Interactive Numerical Calculation
Institute of Scientific and Technical Information of China (English)
无
2008-01-01
In order to implement the optimal design of the indoor thermal comfort based on the numerical modeling method, the numerical calculation platform is combined seamlessly with the data-processing platform, and an interactive numerical calculation platform which includes the functions of numerical simulation and optimization is established. The artificial neural network (ANN) and the greedy strategy are introduced into the hill-climbing pattern heuristic search process, and the optimizing search direction can be predicted by using small samples; when searching along the direction using the greedy strategy, the optimal values can be quickly approached. Therefore, excessive external calling of the numerical modeling process can be avoided,and the optimization time is decreased obviously. The experimental results indicate that the satisfied output parameters of air conditioning can be quickly given out based on the interactive numerical calculation platform and the improved search method, and the optimization for indoor thermal comfort can be completed.
Jacobi Structures on Affine Bundles
Institute of Scientific and Technical Information of China (English)
J. GRABOWSKI; D. IGLESIAS; J. C. MARRERO; E. PADR(O)N; P. URBA(N)SKI
2007-01-01
We study affine Jacobi structures (brackets) on an affine bundle π: A→M, i.e. Jacobi brackets that close on affine functions. We prove that if the rank of A is non-zero, there is a one-to- one correspondence between affine Jacobi structures on A and Lie algebroid structures on the vector bundle A+=∪p∈M Aff(Ap, R) of affine functionals. In the case rank A = 0, it is shown that there is a one-to-one correspondence between affins Jacobi structures on A and local Lie algebras on A+. Some examples and applications, also for the linear case, are discussed. For a special type of affine Jacobi structures which are canonically exhibited (strongly-affine or affine-homogeneous Jacobi structures) over a real vector space of finite dimension, we describe the leaves of its characteristic foliation as the orbits of an affine representation. These afline Jacobi structures can be viewed as an analog of the Kostant-Arnold-LiouviUe linear Poisson structure on the dual space of a real finite-dimensional Lie algebra.
Effects of van der Waals interaction for first-principles calculations on iron-based superconductors
International Nuclear Information System (INIS)
Highlights: •van der Waals density functional calculations for iron-based superconductors. •Optimized structures are evaluated. •van der Waals density functional reproduce lattice constants of FeSe. •Except for FeSe, van der Waals interaction hardly affects crystal structures. -- Abstract: We investigate effects of van der Waals (vdW) interaction on various iron-based superconductors by first-principles calculations based on the van der Waals density functional (vdW-DF) taking account of non-local and long range interaction. vdW-DF reproduces well the lattice constants of FeSe, while the crystal structure of other iron-based superconductors are not so sensitive to vdW interaction. These results suggest that the effects of vdW interaction on layered superconductors are often essential although they depend on the characters of the interlayer couplings
Amadei, A; Apol, MEF; DiNola, A; Berendsen, HJC
1996-01-01
A new theory is presented for calculating the Helmholtz free energy based on the potential energy distribution function. The usual expressions of free energy, internal energy and entropy involving the partition function are rephrased in terms of the potential energy distribution function, which must
An initio calculations for defects in silicon-based amorphous semiconductors
Ishii, Nobuhiko; Shimizu, Tatsuo
1992-01-01
We have calclulated the ESR hyperfine parameters of threefold-coordinated Si atoms and twofold-coordinated P and N atoms in Si-based amorphous semiconductors using the density functional theory with a local-spin-density approximation. These calculated results have been compared with the observed ESR results.
Shetty, Dinesh; Khedkar, Jayshree K; Park, Kyeng Min; Kim, Kimoon
2015-12-01
The design of synthetic, monovalent host-guest molecular recognition pairs is still challenging and of particular interest to inquire into the limits of the affinity that can be achieved with designed systems. In this regard, cucurbit[7]uril (CB[7]), an important member of the host family cucurbit[n]uril (CB[n], n = 5-8, 10, 14), has attracted much attention because of its ability to form ultra-stable complexes with multiple guests. The strong hydrophobic effect between the host cavity and guests, ion-dipole and dipole-dipole interactions of guests with CB portals helps in cooperative and multiple noncovalent interactions that are essential for realizing such strong complexations. These highly selective, strong yet dynamic interactions can be exploited in many applications including affinity chromatography, biomolecule immobilization, protein isolation, biological catalysis, and sensor technologies. In this review, we summarize the progress in the development of high affinity guests for CB[7], factors affecting the stability of complexes, theoretical insights, and the utility of these high affinity pairs in different challenging applications. PMID:26434388
Rubagotti, Sara; Croci, Stefania; Ferrari, Erika; Iori, Michele; Capponi, Pier C.; Lorenzini, Luca; Calzà, Laura; Versari, Annibale; Asti, Mattia
2016-01-01
Curcumin derivatives labelled with fluorine-18 or technetium-99m have recently shown their potential as diagnostic tools for Alzheimer’s disease. Nevertheless, no study by exploiting the labelling with gallium-68 has been performed so far, in spite of its suitable properties (positron emitter, generator produced radionuclide). Herein, an evaluation of the affinity for synthetic β-amyloid fibrils and for amyloid plaques of three nat/68Ga-labelled curcumin analogues, namely curcumin curcumin (CUR), bis-dehydroxy-curcumin (bDHC) and diacetyl-curcumin (DAC), was performed. Affinity and specificity were tested in vitro on amyloid synthetic fibrils by using gallium-68 labelled compounds. Post-mortem brain cryosections from Tg2576 mice were used for the ex vivo visualization of amyloid plaques. The affinity of 68Ga(CUR)2+, 68Ga(DAC)2+, and 68Ga(bDHC)2+ for synthetic β-amyloid fibrils was moderate and their uptake could be observed in vitro. On the other hand, amyloid plaques could not be visualized on brain sections of Tg2576 mice after injection, probably due to the low stability of the complexes in vivo and of a hampered passage through the blood–brain barrier. Like curcumin, all nat/68Ga-curcuminoid complexes maintain a high affinity for β-amyloid plaques. However, structural modifications are still needed to improve their applicability as radiotracers in vivo. PMID:27608011
Rubagotti, Sara; Croci, Stefania; Ferrari, Erika; Iori, Michele; Capponi, Pier C; Lorenzini, Luca; Calzà, Laura; Versari, Annibale; Asti, Mattia
2016-01-01
Curcumin derivatives labelled with fluorine-18 or technetium-99m have recently shown their potential as diagnostic tools for Alzheimer's disease. Nevertheless, no study by exploiting the labelling with gallium-68 has been performed so far, in spite of its suitable properties (positron emitter, generator produced radionuclide). Herein, an evaluation of the affinity for synthetic β-amyloid fibrils and for amyloid plaques of three (nat/68)Ga-labelled curcumin analogues, namely curcumin curcumin (CUR), bis-dehydroxy-curcumin (bDHC) and diacetyl-curcumin (DAC), was performed. Affinity and specificity were tested in vitro on amyloid synthetic fibrils by using gallium-68 labelled compounds. Post-mortem brain cryosections from Tg2576 mice were used for the ex vivo visualization of amyloid plaques. The affinity of (68)Ga(CUR)₂⁺, (68)Ga(DAC)₂⁺, and (68)Ga(bDHC)₂⁺ for synthetic β-amyloid fibrils was moderate and their uptake could be observed in vitro. On the other hand, amyloid plaques could not be visualized on brain sections of Tg2576 mice after injection, probably due to the low stability of the complexes in vivo and of a hampered passage through the blood-brain barrier. Like curcumin, all (nat/68)Ga-curcuminoid complexes maintain a high affinity for β-amyloid plaques. However, structural modifications are still needed to improve their applicability as radiotracers in vivo. PMID:27608011
Directory of Open Access Journals (Sweden)
Chao Hu
2015-04-01
Full Text Available Slope excavation is one of the most crucial steps in the construction of a hydraulic project. Excavation project quality assessment and excavated volume calculation are critical in construction management. The positioning of excavation projects using traditional instruments is inefficient and may cause error. To improve the efficiency and precision of calculation and assessment, three-dimensional laser scanning technology was used for slope excavation quality assessment. An efficient data acquisition, processing, and management workflow was presented in this study. Based on the quality control indices, including the average gradient, slope toe elevation, and overbreak and underbreak, cross-sectional quality assessment and holistic quality assessment methods were proposed to assess the slope excavation quality with laser-scanned data. An algorithm was also presented to calculate the excavated volume with laser-scanned data. A field application and a laboratory experiment were carried out to verify the feasibility of these methods for excavation quality assessment and excavated volume calculation. The results show that the quality assessment indices can be obtained rapidly and accurately with design parameters and scanned data, and the results of holistic quality assessment are consistent with those of cross-sectional quality assessment. In addition, the time consumption in excavation project quality assessment with the laser scanning technology can be reduced by 70%−90%, as compared with the traditional method. The excavated volume calculated with the scanned data only slightly differs from measured data, demonstrating the applicability of the excavated volume calculation method presented in this study.
CCSD(T)/CBS fragment-based calculations of lattice energy of molecular crystals
Červinka, Ctirad; Fulem, Michal; Růžička, Květoslav
2016-02-01
A comparative study of the lattice energy calculations for a data set of 25 molecular crystals is performed using an additive scheme based on the individual energies of up to four-body interactions calculated using the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)) with an estimated complete basis set (CBS) description. The CCSD(T)/CBS values on lattice energies are used to estimate sublimation enthalpies which are compared with critically assessed and thermodynamically consistent experimental values. The average absolute percentage deviation of calculated sublimation enthalpies from experimental values amounts to 13% (corresponding to 4.8 kJ mol-1 on absolute scale) with unbiased distribution of positive to negative deviations. As pair interaction energies present a dominant contribution to the lattice energy and CCSD(T)/CBS calculations still remain computationally costly, benchmark calculations of pair interaction energies defined by crystal parameters involving 17 levels of theory, including recently developed methods with local and explicit treatment of electronic correlation, such as LCC and LCC-F12, are also presented. Locally and explicitly correlated methods are found to be computationally effective and reliable methods enabling the application of fragment-based methods for larger systems.
Institute of Scientific and Technical Information of China (English)
魏喜换; 王春娟; 赵梅; 李剑芳; 邬敏辰
2014-01-01
β-mannanase sequences , respectively , forming a series of mutant enzymes . Lastly , binding free energies (ΔGbind ) of various β-mannanases with mannobiose were calculated by using the molecular mechanics Poisson-Boltzmann surface area ( MM-PBSA) method , respectively . The ΔGbind of AuMan5AY111F was -237.7 kJ/mol , lower than those of other enzymes .Based on the rational design ,an AuMan5AY111F-encoding gene , Auman5AY111F , was constructed by mutating a Tyr111-encoding codon ( TAC) of the Auman5A into a Phe111-encoding TTC by megaprimer PCR . Then , the Auman5AY111F and Auman5A were expressed in Pichia pastoris GS115 , and kinetic parameters of the purified recombinant AuMan5AY111F and AuMan5A ( reAuMan5AY111F and reAuMan5A ) were determined , respectively . The results displayed that the Km value of reAuMan5AY111F , towards guar gum , dropped to 2 .5 mg/mL from 3 .9 mg/mL of reAuMan5A , indicating the substrate affinity of reAuMan5A increased correspondingly . While , the Vmax value of reAuMan5A kept almost unchanged after site-directed mutagenesis . The directed modification of AuMan5A based on the rational design for enhancing its substrate affinity was firstly predicted by using various bioinformatics softwares , and then was confirmed by site-directed mutagenesis . This work provides a novel technology strategy for the directed modification of substrate affinities of β-mannanases and other enzymes .%以宇佐美曲霉(Aspergillus usamii)YL-01-78的5家族β-甘露聚糖酶(AuMan5A)为研究对象，对其底物亲和力的定向改造进行理性设计及定点突变以获取米氏常数 Km 值较低的突变酶AuMan5AY111F .首先采用同源建模和分子对接模拟等方法预测AuMan5A与甘露二糖对接复合物的空间结构；在此结构上使用PyMol软件统计到距甘露二糖8Å以内的38个氨基酸位点.其次对不同来源的、与AuMan5A一级结构序列全同率大于50％的β-甘露聚糖酶进行多序列比对；排除21个
Thermodynamic calculations in the development of high-temperature Co–Re-based alloys
Energy Technology Data Exchange (ETDEWEB)
Gorr, Bronislava, E-mail: gorr@ifwt.mb.uni-siegen.de [University of Siegen, Institut für Werkstofftechnik, Siegen (Germany); Christ, Hans-Jürgen [University of Siegen, Institut für Werkstofftechnik, Siegen (Germany); Mukherji, Debashis; Rösler, Joachim [TU Braunschweig, Institut für Werkstoffe, Braunschweig (Germany)
2014-01-05
Highlights: • Phase diagram as a starting point for alloy development. • Design of pre-oxidation treatments by means of thermodynamic assessment. • Contribution of thermodynamic calculations to the general understanding of materials chemistry. -- Abstract: The experimental Co–Re-based alloys are being developed for high-temperature applications for service temperatures beyond 1100 °C. One of the main tasks of this research is to find the optimal chemical composition. Thermodynamic calculations are very helpful for composition selection and optimization. In this study, thermodynamic calculations were used to identify potential alloying elements and to determine suitable concentration ranges to improve properties, such as strength and oxidation resistance that are essential for high-temperature structural materials. The calculated ternary phase diagram of the Co–Re–Cr system was used to design the reference model alloy. Corrosion products formed under different atmospheric conditions were reliably predicted for a number of model Co–Re-based alloys. Pre-oxidation treatment, a common method used to improve the oxidation resistance of alloys in aggressive atmosphere, was successfully designed based on thermodynamic considerations.
Li, Junchang; Tu, Han-Yen; Yeh, Wei-Chieh; Gui, Jinbin; Cheng, Chau-Jern
2014-09-20
Based on scalar diffraction theory and the geometric structure of liquid crystal on silicon (LCoS), we study the impulse responses and image depth of focus in a holographic three-dimensional (3D) display system. Theoretical expressions of the impulse response and the depth of focus of reconstructed 3D images are obtained, and experimental verifications of the imaging properties are performed. The results indicated that the images formed by holographic display based on the LCoS device were periodic image fields surrounding optical axes. The widths of the image fields were directly proportional to the wavelength and diffraction distance, and inversely proportional to the pixel size of the LCoS device. Based on the features of holographic 3D imaging and focal depth, we enhance currently popular hologram calculation methods of 3D objects to improve the computing speed of hologram calculation.
Adsorption affinity of anions on metal oxyhydroxides
Pechenyuk, S. I.; Semushina, Yu. P.; Kuz'mich, L. F.
2013-03-01
The dependences of anion (phosphate, carbonate, sulfate, chromate, oxalate, tartrate, and citrate) adsorption affinity anions from geometric characteristics, acid-base properties, and complex forming ability are generalized. It is shown that adsorption depends on the nature of both the anions and the ionic medium and adsorbent. It is established that anions are generally grouped into the following series of adsorption affinity reduction: PO{4/3-}, CO{3/2-} > C2O{4/2-}, C(OH)(CH2)2(COO){3/3-}, (CHOH)2(COO){2/2-} > CrO{4/2-} ≫ SO{4/2-}.
Nonlinear Predictor Feedback for Input-Affine Systems with Distributed Input Delays
Ponomarev, Anton
2016-01-01
Prediction-based transformation is applied to control-affine systems with distributed input delays. Transformed system state is calculated as a prediction of the system's future response to the past input with future input set to zero. Stabilization of the new system leads to Lyapunov-Krasovskii proven stabilization of the original one. Conditions on the original system are: smooth linearly bounded open-loop vector field and smooth uniformly bounded input vectors. About the transformed system...
[Risk factor calculator for medical underwriting of life insurers based on the PROCAM study].
Geritse, A; Müller, G; Trompetter, T; Schulte, H; Assmann, G
2008-06-01
For its electronic manual GEM, used to perform medical risk assessment in life insurance, SCOR Global Life Germany has developed an innovative and evidence-based calculator of the mortality risk depending on cardiovascular risk factors. The calculator contains several new findings regarding medical underwriting, which were gained from the analysis of the PROCAM (Prospective Cardiovascular Münster) study. For instance, in the overall consideration of all risk factors of a medically examined applicant, BMI is not an independent risk factor. Further, given sufficient information, the total extra mortality of a person no longer results from adding up the ratings for the single risk factors. In fact, this new approach of risk assessment considers the interdependencies between the different risk factors. The new calculator is expected to improve risk selection and standard acceptances will probably increase.
Calculation Scheme Based on a Weighted Primitive: Application to Image Processing Transforms
Directory of Open Access Journals (Sweden)
Gregorio de Miguel Casado
2007-01-01
Full Text Available This paper presents a method to improve the calculation of functions which specially demand a great amount of computing resources. The method is based on the choice of a weighted primitive which enables the calculation of function values under the scope of a recursive operation. When tackling the design level, the method shows suitable for developing a processor which achieves a satisfying trade-off between time delay, area costs, and stability. The method is particularly suitable for the mathematical transforms used in signal processing applications. A generic calculation scheme is developed for the discrete fast Fourier transform (DFT and then applied to other integral transforms such as the discrete Hartley transform (DHT, the discrete cosine transform (DCT, and the discrete sine transform (DST. Some comparisons with other well-known proposals are also provided.
FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations
Steinmann, Casper; Hansen, Anne S; Jensen, Jan H
2012-01-01
Near linear scaling fragment based quantum chemical calculations are becoming increasingly popular for treating large systems with high accuracy and is an active field of research. However, it remains difficult to set up these calculations without expert knowledge. To facilitate the use of such methods, software tools need to be available for support, setup and lower the barrier of entry for usage by non-experts. We present a fragmentation methodology and accompanying tools called FragIt to help setup these calculations. It uses the SMARTS language to find chemically appropriate substructures in structures and is used to prepare input files for the fragment molecular orbital method in the GAMESS program package. We present patterns of fragmentation for proteins and polysaccharides, specifically D-galactopyranose for use in cyclodextrins.
GPU-based acceleration of free energy calculations in solid state physics
Januszewski, Michał; Ptok, Andrzej; Crivelli, Dawid; Gardas, Bartłomiej
2015-07-01
Obtaining a thermodynamically accurate phase diagram through numerical calculations is a computationally expensive problem that is crucially important to understanding the complex phenomena of solid state physics, such as superconductivity. In this work we show how this type of analysis can be significantly accelerated through the use of modern GPUs. We illustrate this with a concrete example of free energy calculation in multi-band iron-based superconductors, known to exhibit a superconducting state with oscillating order parameter (OP). Our approach can also be used for classical BCS-type superconductors. With a customized algorithm and compiler tuning we are able to achieve a 19×speedup compared to the CPU (119×compared to a single CPU core), reducing calculation time from minutes to mere seconds, enabling the analysis of larger systems and the elimination of finite size effects.
Roca-Maza, X; Centelles, M; Ring, P; Schuck, P
2011-01-01
Although ab-initio calculations of relativistic Brueckner theory lead to large scalar isovector fields in nuclear matter, at present, successful versions of covariant density functional theory neglect the interactions in this channel. A new high precision density functional DD-ME$\\delta$ is presented which includes four mesons $\\sigma$, $\\omega$, $\\delta$, and $\\rho$ with density dependent meson-nucleon couplings. It is based to a large extent on microscopic ab-initio calculations in nuclear matter. Only four of its parameters are determined by adjusting to binding energies and charge radii of finite nuclei. The other parameters, in particular the density dependence of the meson-nucleon vertices, are adjusted to non-relativistic and relativistic Brueckner calculations of symmetric and asymmetric nuclear matter. The isovector effective mass $m_{p}^{\\ast}-m_{n}^{\\ast}$ derived from relativistic Brueckner theory is used to determine the coupling strength of the $\\delta$-meson and its density dependence.
Specification of materials Data for Fire Safety Calculations based on ENV 1992-1-2
DEFF Research Database (Denmark)
Hertz, Kristian Dahl
1997-01-01
of constructions of any concrete exposed to any time of any fire exposure can be calculated.Chapter 4.4 provides information on what should be observed if more general calculation methods are used.Annex A provides some additional information on materials data. This chapter is not a part of the code......The part 1-2 of the Eurocode on Concrete deals with Structural Fire Design.In chapter 3, which is partly written by the author of this paper, some data are given for the development of a few material parameters at high temperatures. These data are intended to represent the worst possible concrete...... to experience form tests on structural specimens based on German siliceous concrete subjected to Standard fire exposure until the time of maximum gas temperature.Chapter 4.3, which is written by the author of this paper, provides a simplified calculation method by means of which the load bearing capacity...
Fontanot, Fabio; Silva, Laura; Monaco, Pierluigi; Skibba, Ramin; 10.1111/j.1365-2966.2008.14126.x
2009-01-01
The treatment of dust attenuation is crucial in order to compare the predictions of galaxy formation models with multiwavelength observations. Most past studies have either used simple analytic prescriptions or else full radiative transfer (RT) calculations. Here, we couple star formation histories and morphologies predicted by the semi-analytic galaxy formation model MORGANA with RT calculations from the spectrophotometric and dust code GRASIL to create a library of galaxy SEDs from the UV/optical through the far Infrared, and compare the predictions of the RT calculations with analytic prescriptions. We consider a low and high redshift sample, as well as an additional library constructed with empirical, non-cosmological star formation histories and simple (pure bulge or disc) morphologies. Based on these libraries, we derive fitting formulae for the effective dust optical depth as a function of galaxy physical properties such as metallicity, gas mass, and radius. We show that such fitting formulae can predi...
An automated Monte-Carlo based method for the calculation of cascade summing factors
Jackson, M. J.; Britton, R.; Davies, A. V.; McLarty, J. L.; Goodwin, M.
2016-10-01
A versatile method has been developed to calculate cascade summing factors for use in quantitative gamma-spectrometry analysis procedures. The proposed method is based solely on Evaluated Nuclear Structure Data File (ENSDF) nuclear data, an X-ray energy library, and accurate efficiency characterisations for single detector counting geometries. The algorithm, which accounts for γ-γ, γ-X, γ-511 and γ-e- coincidences, can be applied to any design of gamma spectrometer and can be expanded to incorporate any number of nuclides. Efficiency characterisations can be derived from measured or mathematically modelled functions, and can accommodate both point and volumetric source types. The calculated results are shown to be consistent with an industry standard gamma-spectrometry software package. Additional benefits including calculation of cascade summing factors for all gamma and X-ray emissions, not just the major emission lines, are also highlighted.
Hafiz, Hasnain; Barbiellini, B.; Jia, Q.; Tylus, U.; Strickland, K.; Bansil, A.; Mukerjee, S.
2015-03-01
Catalysts based on Fe/N/C clusters can support the oxygen-reduction reaction (ORR) without the use of expensive metals such as platinum. These systems can also prevent some poisonous species to block the active sites from the reactant. We have performed spin-polarized calculations on various Fe/N/C fragments using the Vienna Ab initio Simulation Package (VASP) code. Some results are compared to similar calculations obtained with the Gaussian code. We investigate the partial density of states (PDOS) of the 3d orbitals near the Fermi level and calculate the binding energies of several ligands. Correlations of the binding energies with the 3d electronic PDOS's are used to propose electronic descriptors of the ORR associated with the 3d states of Fe. We also suggest a structural model for the most active site with a ferrous ion (Fe2+) in the high spin state or the so-called Doublet 3 (D3).
Energy Technology Data Exchange (ETDEWEB)
Murata, Isao [Osaka Univ., Suita (Japan); Mori, Takamasa; Nakagawa, Masayuki; Itakura, Hirofumi
1996-03-01
The method to calculate neutronics parameters of a core composed of randomly distributed spherical fuels has been developed based on a statistical geometry model with a continuous energy Monte Carlo method. This method was implemented in a general purpose Monte Carlo code MCNP, and a new code MCNP-CFP had been developed. This paper describes the model and method how to use it and the validation results. In the Monte Carlo calculation, the location of a spherical fuel is sampled probabilistically along the particle flight path from the spatial probability distribution of spherical fuels, called nearest neighbor distribution (NND). This sampling method was validated through the following two comparisons: (1) Calculations of inventory of coated fuel particles (CFPs) in a fuel compact by both track length estimator and direct evaluation method, and (2) Criticality calculations for ordered packed geometries. This method was also confined by applying to an analysis of the critical assembly experiment at VHTRC. The method established in the present study is quite unique so as to a probabilistic model of the geometry with a great number of spherical fuels distributed randomly. Realizing the speed-up by vector or parallel computations in future, it is expected to be widely used in calculation of a nuclear reactor core, especially HTGR cores. (author).
International Nuclear Information System (INIS)
After an accidental release of radionuclides to the inhabited environment the external gamma irradiation from deposited radioactivity contributes significantly to the radiation exposure of the population for extended periods. For evaluating this exposure pathway, three main model requirements are needed: (i) to calculate the air kerma value per photon emitted per unit source area, based on Monte Carlo (MC) simulations; (ii) to describe the distribution and dynamics of radionuclides on the diverse urban surfaces; and (iii) to combine all these elements in a relevant urban model to calculate the resulting doses according to the actual scenario. This paper provides an overview about the different approaches to calculate photon transport in urban areas and about several dose calculation codes published. Two types of Monte Carlo simulations are presented using the global and the local approaches of photon transport. Moreover, two different philosophies of the dose calculation, the 'location factor method' and a combination of relative contamination of surfaces with air kerma values are described. The main features of six codes (ECOSYS, EDEM2M, EXPURT, PARATI, TEMAS, URGENT) are highlighted together with a short model-model features intercomparison
Heavy Ion SEU Cross Section Calculation Based on Proton Experimental Data, and Vice Versa
Wrobel, F; Pouget, V; Dilillo, L; Ecoffet, R; Lorfèvre, E; Bezerra, F; Brugger, M; Saigné, F
2014-01-01
The aim of this work is to provide a method to calculate single event upset (SEU) cross sections by using experimental data. Valuable tools such as PROFIT and SIMPA already focus on the calculation of the proton cross section by using heavy ions cross-section experiments. However, there is no available tool that calculates heavy ion cross sections based on measured proton cross sections with no knowledge of the technology. We based our approach on the diffusion-collection model with the aim of analyzing the characteristics of transient currents that trigger SEUs. We show that experimental cross sections could be used to characterize the pulses that trigger an SEU. Experimental results allow yet defining an empirical rule to identify the transient current that are responsible for an SEU. Then, the SEU cross section can be calculated for any kind of particle and any energy with no need to know the Spice model of the cell. We applied our method to some technologies (250 nm, 90 nm and 65 nm bulk SRAMs) and we sho...
LWR decay heat calculations using a GRS improved ENDF/B-6 based ORIGEN data library
Energy Technology Data Exchange (ETDEWEB)
Hesse, U.; Hummelsheim, K.I.; Kilger, R.; Moser, F.E.; Langenbuch, S. [Gesellschaft fur Anlagen- und Reaktorsicherheit (GRS) mbH, Forschungsinstitute, Garching (Germany)
2008-07-01
The known ORNL ORIGEN code is widely spread over the world for inventory, activity and decay heat tasks and is used stand-alone or implemented in activation, shielding or burn-up systems. More than 1000 isotopes with more than six coupled neutron capture and radioactive decay channels are handled simultaneously by the code. The characteristics of the calculated inventories, e.g., masses, activities, neutron and photon source terms or the decay heat during short or long decay time steps are achieved by summing over all isotopes, characterized in the ORIGEN libraries. An extended nuclear GRS-ORIGENX data library is now developed for practical appliance. The library was checked for activation tasks of structure material isotopes and for actinide and fission product burn-up calculations compared with experiments and standard methods. The paper is directed to the LWR decay heat calculation features of the new library and shows the differences of dynamical and time integrated results of Endf/B-6 based and older Endf/B-5 based libraries for decay heat tasks compared to fission burst experiments, ANS curves and some other published data. A multi-group time exponential evaluation is given for the fission burst power of {sup 235}U, {sup 238}U, {sup 239}Pu and {sup 241}Pu, to be used in quick LWR reactor accident decay heat calculation tools. (authors)
Frandoloso, Rafael; Martínez, Sonia; Rodríguez-Ferri, Elías F.; García-Iglesias, María José; Pérez-Martínez, Claudia; Martínez-Fernández, Beatriz; Gutiérrez-Martín, César B.
2010-01-01
Haemophilus parasuis is the agent responsible for causing Glässer's disease, which is characterized by fibrinous polyserositis, polyarthritis, and meningitis in pigs. In this study, we have characterized native outer membrane proteins with affinity to porcine transferrin (NPAPT) from H. parasuis serovar 5, Nagasaki strain. This pool of proteins was used as antigen to developed two vaccine formulations: one was adjuvanted with a mineral oil (Montanide IMS 2215 VG PR), while the other was poten...
Modelling lateral beam quality variations in pencil kernel based photon dose calculations
Nyholm, T.; Olofsson, J.; Ahnesjö, A.; Karlsson, M.
2006-08-01
Standard treatment machines for external radiotherapy are designed to yield flat dose distributions at a representative treatment depth. The common method to reach this goal is to use a flattening filter to decrease the fluence in the centre of the beam. A side effect of this filtering is that the average energy of the beam is generally lower at a distance from the central axis, a phenomenon commonly referred to as off-axis softening. The off-axis softening results in a relative change in beam quality that is almost independent of machine brand and model. Central axis dose calculations using pencil beam kernels show no drastic loss in accuracy when the off-axis beam quality variations are neglected. However, for dose calculated at off-axis positions the effect should be considered, otherwise errors of several per cent can be introduced. This work proposes a method to explicitly include the effect of off-axis softening in pencil kernel based photon dose calculations for arbitrary positions in a radiation field. Variations of pencil kernel values are modelled through a generic relation between half value layer (HVL) thickness and off-axis position for standard treatment machines. The pencil kernel integration for dose calculation is performed through sampling of energy fluence and beam quality in sectors of concentric circles around the calculation point. The method is fully based on generic data and therefore does not require any specific measurements for characterization of the off-axis softening effect, provided that the machine performance is in agreement with the assumed HVL variations. The model is verified versus profile measurements at different depths and through a model self-consistency check, using the dose calculation model to estimate HVL values at off-axis positions. A comparison between calculated and measured profiles at different depths showed a maximum relative error of 4% without explicit modelling of off-axis softening. The maximum relative error
A CT-based analytical dose calculation method for HDR 192Ir brachytherapy
International Nuclear Information System (INIS)
% for both calculation methods. Conclusions: A correction-based dose calculation method has been validated for HDR 192Ir brachytherapy. Its high calculation efficiency makes it feasible for use in treatment planning. Because tissue inhomogeneity effects are small and primary dose predominates in the near-source region, TG-43 is adequate for target dose estimation provided shielding and contrast solution are not used.
Tian, Pu
2015-01-01
Free energy is arguably the most important thermodynamic property for physical systems. Despite the fact that free energy is a state function, presently available rigorous methodologies, such as those based on thermodynamic integration (TI) or non-equilibrium work (NEW) analysis, involve energetic calculations on path(s) connecting the starting and the end macrostates. Meanwhile, presently widely utilized approximate end-point free energy methods lack rigorous treatment of conformational variation within end macrostates, and are consequently not sufficiently reliable. Here we present an alternative and rigorous end point free energy calculation formulation based on microscopic configurational space coarse graining, where the configurational space of a high dimensional system is divided into a large number of sufficiently fine and uniform elements, which were termed conformers. It was found that change of free energy is essentially decided by change of the number of conformers, with an error term that accounts...
Dose calculation from a D-D-reaction-based BSA for boron neutron capture synovectomy
International Nuclear Information System (INIS)
Monte Carlo simulations were carried out to calculate dose in a knee phantom from a D-D-reaction-based Beam Shaping Assembly (BSA) for Boron Neutron Capture Synovectomy (BNCS). The BSA consists of a D(d,n)-reaction-based neutron source enclosed inside a polyethylene moderator and graphite reflector. The polyethylene moderator and graphite reflector sizes were optimized to deliver the highest ratio of thermal to fast neutron yield at the knee phantom. Then neutron dose was calculated at various depths in a knee phantom loaded with boron and therapeutic ratios of synovium dose/skin dose and synovium dose/bone dose were determined. Normalized to same boron loading in synovium, the values of the therapeutic ratios obtained in the present study are 12-30 times higher than the published values.
Dose calculation from a D-D-reaction-based BSA for boron neutron capture synovectomy
Energy Technology Data Exchange (ETDEWEB)
Abdalla, Khalid [Department of Physics, Hail University, Hail (Saudi Arabia)], E-mail: khalidafnan@uoh.edu.sa; Naqvi, A.A. [Department of Physics, King Fahd University of Petroleum and Minerals and Center for Applied Physical Sciences, Box No. 1815, Dhahran 31261 (Saudi Arabia)], E-mail: aanaqvi@kfupm.edu.sa; Maalej, N.; Elshahat, B. [Department of Physics, King Fahd University of Petroleum and Minerals and Center for Applied Physical Sciences, Box No. 1815, Dhahran 31261 (Saudi Arabia)
2010-04-15
Monte Carlo simulations were carried out to calculate dose in a knee phantom from a D-D-reaction-based Beam Shaping Assembly (BSA) for Boron Neutron Capture Synovectomy (BNCS). The BSA consists of a D(d,n)-reaction-based neutron source enclosed inside a polyethylene moderator and graphite reflector. The polyethylene moderator and graphite reflector sizes were optimized to deliver the highest ratio of thermal to fast neutron yield at the knee phantom. Then neutron dose was calculated at various depths in a knee phantom loaded with boron and therapeutic ratios of synovium dose/skin dose and synovium dose/bone dose were determined. Normalized to same boron loading in synovium, the values of the therapeutic ratios obtained in the present study are 12-30 times higher than the published values.
Stiffness of Diphenylalanine-Based Molecular Solids from First Principles Calculations
Azuri, Ido; Hod, Oded; Gazit, Ehud; Kronik, Leeor
2013-03-01
Diphenylalanine-based peptide nanotubes were found to be unexpectedly stiff, with a Young modulus of 19 GPa. Here, we calculate the Young modulus from first principles, using density functional theory with dispersive corrections. This allows us to show that at least half of the stiffness of the material comes from dispersive interactions and to identify the nature of the interactions that contribute most to the stiffness. This presents a general strategy for the analysis of bioinspired functional materials.
A Cultural Study of a Science Classroom and Graphing Calculator-based Technology
Casey, Dennis Alan
2001-01-01
Social, political, and technological events of the past two decades have had considerable bearing on science education. While sociological studies of scientists at work have seriously questioned traditional histories of science, national and state educational systemic reform initiatives have been enacted, stressing standards and accountability. Recently, powerful instructional technologies have become part of the landscape of the classroom. One example, graphing calculator-based technology...
A CAD based automatic modeling method for primitive solid based Monte Carlo calculation geometry
International Nuclear Information System (INIS)
The Multi-Physics Coupling Analysis Modeling Program (MCAM), developed by FDS Team, China, is an advanced modeling tool aiming to solve the modeling challenges for multi-physics coupling simulation. The automatic modeling method for SuperMC, the Super Monte Carlo Calculation Program for Nuclear and Radiation Process, was recently developed and integrated in MCAM5.2. This method could bi-convert between CAD model and SuperMC input file. While converting from CAD model to SuperMC model, the CAD model was decomposed into several convex solids set, and then corresponding SuperMC convex basic solids were generated and output. While inverting from SuperMC model to CAD model, the basic primitive solids was created and related operation was done to according the SuperMC model. This method was benchmarked with ITER Benchmark model. The results showed that the method was correct and effective. (author)
An AIS-based approach to calculate atmospheric emissions from the UK fishing fleet
Coello, Jonathan; Williams, Ian; Hudson, Dominic A.; Kemp, Simon
2015-08-01
The fishing industry is heavily reliant on the use of fossil fuel and emits large quantities of greenhouse gases and other atmospheric pollutants. Methods used to calculate fishing vessel emissions inventories have traditionally utilised estimates of fuel efficiency per unit of catch. These methods have weaknesses because they do not easily allow temporal and geographical allocation of emissions. A large proportion of fishing and other small commercial vessels are also omitted from global shipping emissions inventories such as the International Maritime Organisation's Greenhouse Gas Studies. This paper demonstrates an activity-based methodology for the production of temporally- and spatially-resolved emissions inventories using data produced by Automatic Identification Systems (AIS). The methodology addresses the issue of how to use AIS data for fleets where not all vessels use AIS technology and how to assign engine load when vessels are towing trawling or dredging gear. The results of this are compared to a fuel-based methodology using publicly available European Commission fisheries data on fuel efficiency and annual catch. The results show relatively good agreement between the two methodologies, with an estimate of 295.7 kilotons of fuel used and 914.4 kilotons of carbon dioxide emitted between May 2012 and May 2013 using the activity-based methodology. Different methods of calculating speed using AIS data are also compared. The results indicate that using the speed data contained directly in the AIS data is preferable to calculating speed from the distance and time interval between consecutive AIS data points.
International Nuclear Information System (INIS)
This work is concerning a methodology of Ni-base superalloy development for a very high temperature gas-cooled reactor(VHTR) using design of experiments(DOE) and thermodynamic calculations. Total 32 sets of the Ni-base superalloys with various chemical compositions were formulated based on a fractional factorial design of DOE, and the thermodynamic stability of topologically close-packed(TCP) phases of those alloys was calculated by using the THERMO-CALC software. From the statistical evaluation of the effect of the chemical composition on the formation of TCP phase up to a temperature of 950 .deg. C, which should be suppressed for prolonged service life when it used as the structural components of VHTR, 16 sets were selected for further calculation of the mechanical properties. Considering the yield and ultimate tensile strengths of the selected alloys estimated by using the JMATPRO software, the optimized chemical composition of the alloys for VHTR application, especially intermediate heat exchanger, was proposed for a succeeding experimental study
Theoretical and Experimental Determination of the Proton Affinity of (CF3CH2)2O
Zehe, Michael J.; Ball, David W.
1998-01-01
We report the experimental determination of the proton affinity of the molecule (CF3CH2)2O using chemical ionization mass spectrometry, and we compare it to the theoretical value obtained for protonation at the oxygen atom using the calculational methodology (MP2/6-31G**//MP2/3-21G). The proton affinity for this molecule as measured by bracketing experiments was between 724 kJ/mole and 741 kJ/mole. Ab initio (MP2/6-31G**//MP2/3-21G) calculations yield a value of about 729 kJ/mole, in agreement with the chemical ionization experiments. The results of these and related calculations suggest that the (MP2/6-31G**//MP2/3-21G) methodology is acceptable for estimating the proton affinities of partially-and fully-fluorinated methyl and ethyl ethers. We submit that any conclusions about the chemistry of fluoroether polymer lubricants based on their basicity can also be predicted reliably with such calculations.
European and international collaboration in affinity proteomics.
Stoevesandt, Oda; Taussig, Michael J
2012-06-15
In affinity proteomics, specific protein-binding molecules (a.k.a. binders), principally antibodies, are applied as reagents in proteome analysis. In recent years, advances in binder technologies have created the potential for an unprecedented view on protein expression and distribution patterns in plasma, cells and tissues and increasingly on protein function. Particular strengths of affinity proteomics methods include detecting proteins in their natural environments of cell or tissue, high sensitivity and selectivity for detection of low abundance proteins and exploiting binding actions such as functional interference in living cells. To maximise the use and impact of affinity reagents, it will be essential to create comprehensive, standardised binder collections. With this in mind, the EU FP7 programme AFFINOMICS (http://www.affinomics.org), together with the preceding EU programmes ProteomeBinders and AffinityProteome, aims to extend affinity proteomics research by generating a large-scale resource of validated protein-binding molecules for characterisation of the human proteome. Activity is directed at producing binders to about 1000 protein targets, primarily in signal transduction and cancer, by establishing a high throughput, coordinated production pipeline. An important aspect of AFFINOMICS is the development of highly efficient recombinant selection methods, based on phage, cell and ribosome display, capable of producing high quality binders at greater throughput and lower cost than hitherto. The programme also involves development of innovative and sensitive technologies for specific detection of target proteins and their interactions, and deployment of binders in proteomics studies of clinical relevance. The need for such binder generation programmes is now recognised internationally, with parallel initiatives in the USA for cancer (NCI) and transcription factors (NIH) and within the Human Proteome Organisation (HUPO). The papers in this volume of New
Assessment of Calculation Procedures for Piles in Clay Based on Static Loading Tests
DEFF Research Database (Denmark)
Augustesen, Anders; Andersen, Lars
2008-01-01
College in London. The calculation procedures are assessed based on an established database of static loading tests. To make a consistent evaluation of the design methods, corrections related to undrained shear strength and time between pile driving and testing have been employed. The study indicates...... that the interpretation of the field tests is of paramount importance, both with regard to the soil profile and the loading conditions. Based on analyses of 253 static pile loading tests distributed on 111 sites, API-RP2A provides the better description of the data. However, it should be emphasised that some input...
Striving for Empathy: Affinities, Alliances and Peer Sexuality Educators
Fields, Jessica; Copp, Martha
2015-01-01
Peer sexuality educators' accounts of their work reveal two approaches to empathy with their students: affinity and alliance. "Affinity-based empathy" rests on the idea that the more commonalities sexuality educators and students share (or perceive they share), the more they will be able to empathise with one another, while…
High affinity retinoic acid receptor antagonists: analogs of AGN 193109.
Johnson, A T; Wang, L; Gillett, S J; Chandraratna, R A
1999-02-22
A series of high affinity retinoic acid receptor (RAR) antagonists were prepared based upon the known antagonist AGN 193109 (2). Introduction of various phenyl groups revealed a preference for substitution at the para-position relative to the meta-site. Antagonists with the highest affinities for the RARs possessed hydrophobic groups, however, the presence of polar functionality was also well tolerated.
Calculator: A Hardware Design, Math and Software Programming Project Base Learning
Directory of Open Access Journals (Sweden)
F. Criado
2015-03-01
Full Text Available This paper presents the implementation by the students of a complex calculator in hardware. This project meets hardware design goals, and also highly motivates them to use competences learned in others subjects. The learning process, associated to System Design, is hard enough because the students have to deal with parallel execution, signal delay, synchronization … Then, to strengthen the knowledge of hardware design a methodology as project based learning (PBL is proposed. Moreover, it is also used to reinforce cross subjects like math and software programming. This methodology creates a course dynamics that is closer to a professional environment where they will work with software and mathematics to resolve the hardware design problems. The students design from zero the functionality of the calculator. They are who make the decisions about the math operations that it is able to resolve it, and also the operands format or how to introduce a complex equation into the calculator. This will increase the student intrinsic motivation. In addition, since the choices may have consequences on the reliability of the calculator, students are encouraged to program in software the decisions about how implement the selected mathematical algorithm. Although math and hardware design are two tough subjects for students, the perception that they get at the end of the course is quite positive.
A GIS-based method for flooded area calculation and damage evaluation
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
Using geographic information system to study flooded area and damage evaluation has been a hotspot in environmental disaster research for years. In this paper, a model for flooded area calculation and damage evaluation is presented. Flooding is divided into two types:‘source flood' and ‘non-source flood'. The source-flood area calculation is based on seed spread algorithm. The flood damage evaluation is calculated by overlaying the flooded area range with thematic maps and relating the result to other social and economic data. To raise the operational efficiency of the model, a skipping approach is used to speed seed spread algorithm and all thematic maps are converted to raster format before overlay analysis. The accuracy of flooded area calculation and damage evaluation is mainly dependent upon the resolution and precision of the digital elevation model (DEM) data, upon the accuracy of registering all raster layers, and upon the quality of economic information. This model has been successfully used in the Zhejiang Province Comprehensive Water Management Information System developed by the authors. The applications show that this model is especially useful for most counties of China and other developing countries.
Shielding calculations for a 250 MeV hospital-based proton accelerator
Energy Technology Data Exchange (ETDEWEB)
Agosteo, S. [Politecnico di Milano (Italy). Ist. di Ingegneria Nucleare; Arduini, G. [Fondazione Italiana Ricerca sul Cancro, via Corridoni 7, 20122 Milano (Italy); Bodei, G. [Politecnico di Milano (Italy). Ist. di Ingegneria Nucleare; Monti, S. [ENEA, ERG-FISS-FIRE, via Martiri di Monte Sole 4, 40129 Bologna (Italy); Padoani, F. [ENEA, ERG-FISS-FIRE, via Martiri di Monte Sole 4, 40129 Bologna (Italy); Silari, M. [Consiglio Nazionale delle Ricerche, Istituto Tecnologie Biomediche Avanzate, via Ampere 56, I-20131, Milano (Italy); Tinti, R. [ENEA, ERG-FISS-FIRE, via Martiri di Monte Sole 4, 40129 Bologna (Italy); Tromba, G. [Sincrotrone (``ELETTRA``) Trieste, Padriciano 99, 34012 Trieste (Italy)
1996-05-21
The accelerator shields (250 MeV protons, 400 MeV/u {sup 16}O{sup 8+} ions) and treatment rooms of the Hadrontherapy Centre, a hospital-based facility under design in Italy, were determined by means of Monte Carlo calculations. The LCS and FLUKA codes were employed, together with analytical estimates carried out by making use of empirical formulas from the literature, and the results compared. In the case of 250 MeV protons a 250 cm thick concrete wall ensures an annual dose equivalent lower than 2 mSv in the environments adjacent to the accelerator room. The best ceiling thickness was found to be 200 cm for a unitary occupancy factor. The photon dose equivalent beyond the concrete shield was also estimated using the LCS code. In the case of ions the shield thickness was calculated using empirical formulas from the literature; the concrete thicknesses calculated for protons should ensure the required dose equivalent when some local shields are added. Monte Carlo calculations of the treatment room shielding were also carried out using the FLUKA code. (orig.).
Yano, Masato; Hirose, Kenji; Yoshikawa, Minoru; Thermal management technology Team
Facile property calculation model for adsorption chillers was developed based on equilibrium adsorption cycles. Adsorption chillers are one of promising systems that can use heat energy efficiently because adsorption chillers can generate cooling energy using relatively low temperature heat energy. Properties of adsorption chillers are determined by heat source temperatures, adsorption/desorption properties of adsorbent, and kinetics such as heat transfer rate and adsorption/desorption rate etc. In our model, dependence of adsorption chiller properties on heat source temperatures was represented using approximated equilibrium adsorption cycles instead of solving conventional time-dependent differential equations for temperature changes. In addition to equilibrium cycle calculations, we calculated time constants for temperature changes as functions of heat source temperatures, which represent differences between equilibrium cycles and real cycles that stemmed from kinetic adsorption processes. We found that the present approximated equilibrium model could calculate properties of adsorption chillers (driving energies, cooling energies, and COP etc.) under various driving conditions quickly and accurately within average errors of 6% compared to experimental data.
Pennec, Fabienne; Alzina, Arnaud; Tessier-Doyen, Nicolas; Naitali, Benoit; Smith, David S.
2012-11-01
This work is about the calculation of thermal conductivity of insulating building materials made from plant particles. To determine the type of raw materials, the particle sizes or the volume fractions of plant and binder, a tool dedicated to calculate the thermal conductivity of heterogeneous materials has been developped, using the discrete element method to generate the volume element and the finite element method to calculate the homogenized properties. A 3D optical scanner has been used to capture plant particle shapes and convert them into a cluster of discret elements. These aggregates are initially randomly distributed but without any overlap, and then fall down in a container due to the gravity force and collide with neighbour particles according to a velocity Verlet algorithm. Once the RVE is built, the geometry is exported in the open-source Salome-Meca platform to be meshed. The calculation of the effective thermal conductivity of the heterogeneous volume is then performed using a homogenization technique, based on an energy method. To validate the numerical tool, thermal conductivity measurements have been performed on sunflower pith aggregates and on packed beds of the same particles. The experimental values have been compared satisfactorily with a batch of numerical simulations.
International Nuclear Information System (INIS)
This work is about the calculation of thermal conductivity of insulating building materials made from plant particles. To determine the type of raw materials, the particle sizes or the volume fractions of plant and binder, a tool dedicated to calculate the thermal conductivity of heterogeneous materials has been developped, using the discrete element method to generate the volume element and the finite element method to calculate the homogenized properties. A 3D optical scanner has been used to capture plant particle shapes and convert them into a cluster of discret elements. These aggregates are initially randomly distributed but without any overlap, and then fall down in a container due to the gravity force and collide with neighbour particles according to a velocity Verlet algorithm. Once the RVE is built, the geometry is exported in the open-source Salome-Meca platform to be meshed. The calculation of the effective thermal conductivity of the heterogeneous volume is then performed using a homogenization technique, based on an energy method. To validate the numerical tool, thermal conductivity measurements have been performed on sunflower pith aggregates and on packed beds of the same particles. The experimental values have been compared satisfactorily with a batch of numerical simulations.
Energy Technology Data Exchange (ETDEWEB)
Park, Peter C. [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Schreibmann, Eduard; Roper, Justin; Elder, Eric; Crocker, Ian [Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia (United States); Fox, Tim [Varian Medical Systems, Palo Alto, California (United States); Zhu, X. Ronald [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Dong, Lei [Scripps Proton Therapy Center, San Diego, California (United States); Dhabaan, Anees, E-mail: anees.dhabaan@emory.edu [Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia (United States)
2015-03-15
Purpose: Computed tomography (CT) artifacts can severely degrade dose calculation accuracy in proton therapy. Prompted by the recently increased popularity of magnetic resonance imaging (MRI) in the radiation therapy clinic, we developed an MRI-based CT artifact correction method for improving the accuracy of proton range calculations. Methods and Materials: The proposed method replaces corrupted CT data by mapping CT Hounsfield units (HU number) from a nearby artifact-free slice, using a coregistered MRI. MRI and CT volumetric images were registered with use of 3-dimensional (3D) deformable image registration (DIR). The registration was fine-tuned on a slice-by-slice basis by using 2D DIR. Based on the intensity of paired MRI pixel values and HU from an artifact-free slice, we performed a comprehensive analysis to predict the correct HU for the corrupted region. For a proof-of-concept validation, metal artifacts were simulated on a reference data set. Proton range was calculated using reference, artifactual, and corrected images to quantify the reduction in proton range error. The correction method was applied to 4 unique clinical cases. Results: The correction method resulted in substantial artifact reduction, both quantitatively and qualitatively. On respective simulated brain and head and neck CT images, the mean error was reduced from 495 and 370 HU to 108 and 92 HU after correction. Correspondingly, the absolute mean proton range errors of 2.4 cm and 1.7 cm were reduced to less than 2 mm in both cases. Conclusions: Our MRI-based CT artifact correction method can improve CT image quality and proton range calculation accuracy for patients with severe CT artifacts.
Wang, Junmei; Hou, Tingjun
2012-05-25
It is of great interest in modern drug design to accurately calculate the free energies of protein-ligand or nucleic acid-ligand binding. MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) and MM-GBSA (molecular mechanics generalized Born surface area) have gained popularity in this field. For both methods, the conformational entropy, which is usually calculated through normal-mode analysis (NMA), is needed to calculate the absolute binding free energies. Unfortunately, NMA is computationally demanding and becomes a bottleneck of the MM-PB/GBSA-NMA methods. In this work, we have developed a fast approach to estimate the conformational entropy based upon solvent accessible surface area calculations. In our approach, the conformational entropy of a molecule, S, can be obtained by summing up the contributions of all atoms, no matter they are buried or exposed. Each atom has two types of surface areas, solvent accessible surface area (SAS) and buried SAS (BSAS). The two types of surface areas are weighted to estimate the contribution of an atom to S. Atoms having the same atom type share the same weight and a general parameter k is applied to balance the contributions of the two types of surface areas. This entropy model was parametrized using a large set of small molecules for which their conformational entropies were calculated at the B3LYP/6-31G* level taking the solvent effect into account. The weighted solvent accessible surface area (WSAS) model was extensively evaluated in three tests. For convenience, TS values, the product of temperature T and conformational entropy S, were calculated in those tests. T was always set to 298.15 K through the text. First of all, good correlations were achieved between WSAS TS and NMA TS for 44 protein or nucleic acid systems sampled with molecular dynamics simulations (10 snapshots were collected for postentropy calculations): the mean correlation coefficient squares (R²) was 0.56. As to the 20 complexes, the TS
Classification of neocortical interneurons using affinity propagation
Directory of Open Access Journals (Sweden)
Roberto eSantana
2013-12-01
Full Text Available In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. Neuronal classification has been a difficult problem because it is unclear what a neuronal cell class actually is and what are the best characteristics are to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological or molecular characteristics, when applied to selected datasets, have provided quantitative and unbiased identification of distinct neuronal subtypes. However, better and more robust classification methods are needed for increasingly complex and larger datasets. We explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. In fact, using a combined anatomical/physiological dataset, our algorithm differentiated parvalbumin from somatostatin interneurons in 49 out of 50 cases. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits.
Miliordos, Evangelos; Xantheas, Sotiris S
2013-08-15
We propose a general procedure for the numerical calculation of the harmonic vibrational frequencies that is based on internal coordinates and Wilson's GF methodology via double differentiation of the energy. The internal coordinates are defined as the geometrical parameters of a Z-matrix structure, thus avoiding issues related to their redundancy. Linear arrangements of atoms are described using a dummy atom of infinite mass. The procedure has been automated in FORTRAN90 and its main advantage lies in the nontrivial reduction of the number of single-point energy calculations needed for the construction of the Hessian matrix when compared to the corresponding number using double differentiation in Cartesian coordinates. For molecules of C1 symmetry the computational savings in the energy calculations amount to 36N - 30, where N is the number of atoms, with additional savings when symmetry is present. Typical applications for small and medium size molecules in their minimum and transition state geometries as well as hydrogen bonded clusters (water dimer and trimer) are presented. In all cases the frequencies based on internal coordinates differ on average by coordinates.
Performance of IRI-based ionospheric critical frequency calculations with reference to forecasting
ÜNal, Ä.°Brahim; ŞEnalp, Erdem Türker; YeşIl, Ali; Tulunay, Ersin; Tulunay, Yurdanur
2011-02-01
Ionospheric critical frequency (foF2) is an important ionospheric parameter in telecommunication. Ionospheric processes are highly nonlinear and time varying. Thus, mathematical modeling based on physical principles is extremely difficult if not impossible. The authors forecast foF2 values by using neural networks and, in parallel, they calculate foF2 values based on the IRI model. The foF2 values were forecast 1 h in advance by using the Middle East Technical University Neural Network model (METU-NN) and the work was reported previously. Since then, the METU-NN has been improved. In this paper, 1 h in advance forecast foF2 values and the calculated foF2 values have been compared with the observed values considering the Slough (51.5°N, 0.6°W), Uppsala (59.8°N, 17.6°E), and Rome (41.8°N, 12.5°E) station foF2 data. The authors have considered the models alternative to each other. The performance results of the models are promising. The METU-NN foF2 forecast errors are smaller than the calculated foF2 errors. The models may be used in parallel employing the METU-NN as the primary source for the foF2 forecasting.
Energy Technology Data Exchange (ETDEWEB)
McGee, K P; Lake, D; Mariappan, Y; Manduca, A; Ehman, R L [Department of Radiology, Mayo Clinic College of Medicine, 200 First Street, SW, Rochester, MN 55905 (United States); Hubmayr, R D [Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic College of Medicine, 200 First Street, SW, Rochester, MN 55905 (United States); Ansell, K, E-mail: mcgee.kiaran@mayo.edu [Schaeffer Academy, 2700 Schaeffer Lane NE, Rochester, MN 55906 (United States)
2011-07-21
Magnetic resonance elastography (MRE) is a non-invasive phase-contrast-based method for quantifying the shear stiffness of biological tissues. Synchronous application of a shear wave source and motion encoding gradient waveforms within the MRE pulse sequence enable visualization of the propagating shear wave throughout the medium under investigation. Encoded shear wave-induced displacements are then processed to calculate the local shear stiffness of each voxel. An important consideration in local shear stiffness estimates is that the algorithms employed typically calculate shear stiffness using relatively high signal-to-noise ratio (SNR) MRE images and have difficulties at an extremely low SNR. A new method of estimating shear stiffness based on the principal spatial frequency of the shear wave displacement map is presented. Finite element simulations were performed to assess the relative insensitivity of this approach to decreases in SNR. Additionally, ex vivo experiments were conducted on normal rat lungs to assess the robustness of this approach in low SNR biological tissue. Simulation and experimental results indicate that calculation of shear stiffness by the principal frequency method is less sensitive to extremely low SNR than previously reported MRE inversion methods but at the expense of loss of spatial information within the region of interest from which the principal frequency estimate is derived.
SU-E-T-161: Evaluation of Dose Calculation Based On Cone-Beam CT
Energy Technology Data Exchange (ETDEWEB)
Abe, T; Nakazawa, T; Saitou, Y; Nakata, A; Yano, M [Graduate School of Medicine, Sapporo Medical University, Sapporo, Hokkaido (Japan); Tateoka, K [Graduate School of Medicine, Sapporo Medical University, Sapporo, Hokkaido (Japan); Radiation Therapy Research Institute, Social Medical Corporation Teishinkai, Sapporo, Hokkaido (Japan); Fujimoto, K [Radiation Therapy Research Institute, Social Medical Corporation Teishinkai, Sapporo, Hokkaido (Japan); Sakata, K [Graduate School of Medicine, Sapporo Medical University, Sapporo, Hokkaido (Japan); Sapporo Medical University, Sapporo, Hokkaido (Japan)
2014-06-01
Purpose: The purpose of this study is to convert pixel values in cone-beam CT (CBCT) using histograms of pixel values in the simulation CT (sim-CT) and the CBCT images and to evaluate the accuracy of dose calculation based on the CBCT. Methods: The sim-CT and CBCT images immediately before the treatment of 10 prostate cancer patients were acquired. Because of insufficient calibration of the pixel values in the CBCT, it is difficult to be directly used for dose calculation. The pixel values in the CBCT images were converted using an in-house program. A 7 fields treatment plans (original plan) created on the sim-CT images were applied to the CBCT images and the dose distributions were re-calculated with same monitor units (MUs). These prescription doses were compared with those of original plans. Results: In the results of the pixel values conversion in the CBCT images,the mean differences of pixel values for the prostate,subcutaneous adipose, muscle and right-femur were −10.78±34.60, 11.78±41.06, 29.49±36.99 and 0.14±31.15 respectively. In the results of the calculated doses, the mean differences of prescription doses for 7 fields were 4.13±0.95%, 0.34±0.86%, −0.05±0.55%, 1.35±0.98%, 1.77±0.56%, 0.89±0.69% and 1.69±0.71% respectively and as a whole, the difference of prescription dose was 1.54±0.4%. Conclusion: The dose calculation on the CBCT images achieve an accuracy of <2% by using this pixel values conversion program. This may enable implementation of efficient adaptive radiotherapy.
Phase-only stereoscopic hologram calculation based on Gerchberg-Saxton iterative algorithm
Xia, Xinyi; Xia, Jun
2016-09-01
A phase-only computer-generated holography (CGH) calculation method for stereoscopic holography is proposed in this paper. The two-dimensional (2D) perspective projection views of the three-dimensional (3D) object are generated by the computer graphics rendering techniques. Based on these views, a phase-only hologram is calculated by using the Gerchberg-Saxton (GS) iterative algorithm. Comparing with the non-iterative algorithm in the conventional stereoscopic holography, the proposed method improves the holographic image quality, especially for the phase-only hologram encoded from the complex distribution. Both simulation and optical experiment results demonstrate that our proposed method can give higher quality reconstruction comparing with the traditional method. Project supported by the National Basic Research Program of China (Grant No. 2013CB328803) and the National High Technology Research and Development Program of China (Grant Nos. 2013AA013904 and 2015AA016301).
Hypothesis testing and power calculations for taxonomic-based human microbiome data.
Directory of Open Access Journals (Sweden)
Patricio S La Rosa
Full Text Available This paper presents new biostatistical methods for the analysis of microbiome data based on a fully parametric approach using all the data. The Dirichlet-multinomial distribution allows the analyst to calculate power and sample sizes for experimental design, perform tests of hypotheses (e.g., compare microbiomes across groups, and to estimate parameters describing microbiome properties. The use of a fully parametric model for these data has the benefit over alternative non-parametric approaches such as bootstrapping and permutation testing, in that this model is able to retain more information contained in the data. This paper details the statistical approaches for several tests of hypothesis and power/sample size calculations, and applies them for illustration to taxonomic abundance distribution and rank abundance distribution data using HMP Jumpstart data on 24 subjects for saliva, subgingival, and supragingival samples. Software for running these analyses is available.
A Force-Based Grid Manipulator for ALE Calculations in a Lobe Pump
Institute of Scientific and Technical Information of China (English)
John Vande Voorde; Jan Vierendeels; Erik Dick
2003-01-01
In this paper, a time-dependant calculation of flow in a lobe pump is presented. Calculations are performed using the arbitrary Lagrangean Eulerean (ALE) method. A grid manipulator is needed to move the nodes between time steps. The used grid manipulator is based on the pseudo-force idea. This means that each node is fictitiously connected with its 8 neighbours via fictitious springs. The equilibrium of the resulting pseudo spring forces defines the altered position of the nodes. The grid manipulator was coupled with a commercial flow solver and the whole was tested on the flow through a three-lobe lobe pump. Results were obtained for a rotational speed of 460 rpm and incompressible silicon oil as fluid.
Calculation and analysis of heat source of PWR assemblies based on Monte Carlo method
International Nuclear Information System (INIS)
When fission occurs in nuclear fuel in reactor core, it releases numerous neutron and γ radiation, which takes energy deposition in fuel components and yields many factors such as thermal stressing and radiation damage influencing the safe operation of a reactor. Using the three-dimensional Monte Carlo transport calculation program MCNP and continuous cross-section database based on ENDF/B series to calculate the heat rate of the heat source on reference assemblies of a PWR when loading with 18-month short refueling cycle mode, and get the precise values of the control rod, thimble plug and new burnable poison rod within Gd, so as to provide basis for reactor design and safety verification. (authors)
GPU-based fast Monte Carlo simulation for radiotherapy dose calculation
Jia, Xun; Graves, Yan Jiang; Folkerts, Michael; Jiang, Steve B
2011-01-01
Monte Carlo (MC) simulation is commonly considered to be the most accurate dose calculation method in radiotherapy. However, its efficiency still requires improvement for many routine clinical applications. In this paper, we present our recent progress towards the development a GPU-based MC dose calculation package, gDPM v2.0. It utilizes the parallel computation ability of a GPU to achieve high efficiency, while maintaining the same particle transport physics as in the original DPM code and hence the same level of simulation accuracy. In GPU computing, divergence of execution paths between threads can considerably reduce the efficiency. Since photons and electrons undergo different physics and hence attain different execution paths, we use a simulation scheme where photon transport and electron transport are separated to partially relieve the thread divergence issue. High performance random number generator and hardware linear interpolation are also utilized. We have also developed various components to hand...
Institute of Scientific and Technical Information of China (English)
蒋亚虎
2015-01-01
To solve the problem caused by fluctuation of received signal strength indicator and large computing capacity in on‐line measurement ,an indoor localization algorithm based on singularity detection and affinity propagation clustering was proposed . Taking advantage of Hampel filter and KDE ,a method of singularity detection was proposed ,then affinity propagation clustering algorithm was used to cluster received signal strength indicator .Rough and meticulous localization method was used to locate the consumer .The algorithm proposed can improve localization accuracy and reduce computing capacity Comparing with the tradi‐tional method .%为克服基于无线局域网指纹定位算法中接收信号值波动和在线检测时计算量大的问题，提出一种基于奇异值检测和A P聚类的无线局域网指纹定位算法。分析 H am pel滤波器和核概率密度估计在接收信号强度值中奇异值检测的不足，结合Hampel滤波器和核概率密度估计两种方法在奇异值检测中的优势，给出一种奇异值检测算法；利用 AP聚类算法，对离线训练系统中的信号强度测量值进行聚类；通过AP聚类粗检测和基于加权 k近邻算法的细检测评估得到用户位置，完成定位。对比传统方法，该定位算法能够提高定位的准确性，降低算法的计算复杂度。
Espel, Federico Puente
The main objective of this PhD research is to develop a high accuracy modeling tool using a Monte Carlo based coupled system. The presented research comprises the development of models to include the thermal-hydraulic feedback to the Monte Carlo method and speed-up mechanisms to accelerate the Monte Carlo criticality calculation. Presently, deterministic codes based on the diffusion approximation of the Boltzmann transport equation, coupled with channel-based (or sub-channel based) thermal-hydraulic codes, carry out the three-dimensional (3-D) reactor core calculations of the Light Water Reactors (LWRs). These deterministic codes utilize nuclear homogenized data (normally over large spatial zones, consisting of fuel assembly or parts of fuel assembly, and in the best case, over small spatial zones, consisting of pin cell), which is functionalized in terms of thermal-hydraulic feedback parameters (in the form of off-line pre-generated cross-section libraries). High accuracy modeling is required for advanced nuclear reactor core designs that present increased geometry complexity and material heterogeneity. Such high-fidelity methods take advantage of the recent progress in computation technology and coupled neutron transport solutions with thermal-hydraulic feedback models on pin or even on sub-pin level (in terms of spatial scale). The continuous energy Monte Carlo method is well suited for solving such core environments with the detailed representation of the complicated 3-D problem. The major advantages of the Monte Carlo method over the deterministic methods are the continuous energy treatment and the exact 3-D geometry modeling. However, the Monte Carlo method involves vast computational time. The interest in Monte Carlo methods has increased thanks to the improvements of the capabilities of high performance computers. Coupled Monte-Carlo calculations can serve as reference solutions for verifying high-fidelity coupled deterministic neutron transport methods
Effects of CT based Voxel Phantoms on Dose Distribution Calculated with Monte Carlo Method
Chen, Chaobin; Huang, Qunying; Wu, Yican
2005-04-01
A few CT-based voxel phantoms were produced to investigate the sensitivity of Monte Carlo simulations of x-ray beam and electron beam to the proportions of elements and the mass densities of the materials used to express the patient's anatomical structure. The human body can be well outlined by air, lung, adipose, muscle, soft bone and hard bone to calculate the dose distribution with Monte Carlo method. The effects of the calibration curves established by using various CT scanners are not clinically significant based on our investigation. The deviation from the values of cumulative dose volume histogram derived from CT-based voxel phantoms is less than 1% for the given target.
Effects of CT based Voxel Phantoms on Dose Distribution Calculated with Monte Carlo Method
Institute of Scientific and Technical Information of China (English)
Chen Chaobin; Huang Qunying; Wu Yican
2005-01-01
A few CT-based voxel phantoms were produced to investigate the sensitivity of Monte Carlo simulations of X-ray beam and electron beam to the proportions of elements and the mass densities of the materials used to express the patient's anatomical structure. The human body can be well outlined by air, lung, adipose, muscle, soft bone and hard bone to calculate the dose distribution with Monte Carlo method. The effects of the calibration curves established by using various CT scanners are not clinically significant based on our investigation. The deviation from the values of cumulative dose volume histogram derived from CT-based voxel phantoms is less than 1% for the given target.
Energy Technology Data Exchange (ETDEWEB)
Davydov, N.G.; Kiselevskiy, Yu.N.
1983-01-01
A computer (EVM) and an ASOI-VSP-SK program complex are used to analyze data from seismic exploration and acoustical logging with interval by interval calculation of the velocity every four meters. Vertical seismic profilling (VSP) results are used to identify all the upper layers as reference layers. The basic reference level, the third, which corresponds to the floor of the carbonate middle to upper Visean series, is not sustained due to the thin layered state of the terrigeneous section. Based on data from vertical seismic profilling, the reflected wave method (MOV) and the common depth point method (MOGT), the reference 3-a and 6-a levels are identified. Deep reflections of the seventh, 7-a and Rf, approximately confined to the roof and floor of the lower Paleozoic deposits and the upper part of the upper reef series, are noted in the series of the Caledonian cap of the Prebaykal massifs based on vertical seismic profilling. Collector levels are noted on the basis of the frequency of the wave spectra and from the absorption coefficient in the Testas structure and in other low amplitude structures. The insufficiency of the depth capability of the common depth point method and the poor knowledge level of seismic exploration of the section of the lower Paleozoa and the upper Proterozoa of the Chu Sarysuyskiy depresion are noted.
Yang, Xiaoting; Hu, Yufei; Li, Gongke
2014-05-16
Quantification of monoamine neurotransmitters is very important in diagnosing and monitoring of patients with neurological disorders. We developed an online analytical method to selectively determine urinary monoamine neurotransmitters, which coupled the boronate affinity monolithic column micro-solid-phase extraction with high-performance liquid chromatography (HPLC). The boronate affinity monolithic column was prepared by in situ polymerization of vinylphenylboronic acid (VPBA) and N,N'-methylenebisacrylamide (MBAA) in a stainless capillary column. The prepared monolithic column showed good permeability, high extraction selectivity and capacity. The column-to-column reproducibility was satisfactory and the enrichment factors were 17-243 for four monoamine neurotransmitters. Parameters that influence the online extraction efficiency, including pH of sample solution, flow rate of extraction and desorption, extraction volume and desorption volume were investigated. Under the optimized conditions, the developed method exhibited low limit of detection (0.06-0.80μg/L), good linearity (with R(2) between 0.9979 and 0.9993). The recoveries in urine samples were 81.0-105.5% for four monoamine neurotransmitters with intra- and inter-day RSDs of 2.1-8.2% and 3.7-10.6%, respectively. The online analytical method was sensitive, accurate, selective, reliable and applicable to analysis of trace monoamine neurotransmitters in human urine sample.
Directory of Open Access Journals (Sweden)
Junfeng Gu
2015-10-01
Full Text Available Binding affinity prediction of protein–ligand complexes has attracted widespread interest. In this study, a self-adaptive steered molecular dynamics (SMD method is proposed to reveal the binding affinity of protein–ligand complexes. The SMD method is executed through adjusting pulling direction to find an optimum trajectory of ligand dissociation, which is realized by minimizing the stretching force automatically. The SMD method is then used to simulate the dissociations of 19 common protein–ligand complexes which are derived from two homology families, and the binding free energy values are gained through experimental techniques. Results show that the proposed SMD method follows a different dissociation pathway with lower a rupture force and energy barrier when compared with the conventional SMD method, and further analysis indicates the rupture forces of the complexes in the same protein family correlate well with their binding free energy, which reveals the possibility of using the proposed SMD method to identify the active ligand.
GPU-based Monte Carlo radiotherapy dose calculation using phase-space sources
Townson, Reid; Tian, Zhen; Graves, Yan Jiang; Zavgorodni, Sergei; Jiang, Steve B
2013-01-01
A novel phase-space source implementation has been designed for GPU-based Monte Carlo dose calculation engines. Due to the parallelized nature of GPU hardware, it is essential to simultaneously transport particles of the same type and similar energies but separated spatially to yield a high efficiency. We present three methods for phase-space implementation that have been integrated into the most recent version of the GPU-based Monte Carlo radiotherapy dose calculation package gDPM v3.0. The first method is to sequentially read particles from a patient-dependent phase-space and sort them on-the-fly based on particle type and energy. The second method supplements this with a simple secondary collimator model and fluence map implementation so that patient-independent phase-space sources can be used. Finally, as the third method (called the phase-space-let, or PSL, method) we introduce a novel strategy to pre-process patient-independent phase-spaces and bin particles by type, energy and position. Position bins l...
Realization of Fractal Affine Transformation
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
This paper gives the definition of fractal affine transformation and presents a specific method for its realization and its cor responding mathematical equations which are essential in fractal image construction.
Infinite transitivity on affine varieties
Arzhantsev, Ivan; Flenner, Hubert; Kaliman, Shulim; Kutzschebauch, Frank; ZAIDENBERG, MIKHAIL
2012-01-01
In this note we survey recent results on automorphisms of affine algebraic varieties, infinitely transitive group actions and flexibility. We present related constructions and examples, and discuss geometric applications and open problems.
Kühn, M.; John, W.; Weigel, R.
2014-11-01
This contribution contains the mechanisms for calculation of magnetic shielding effectiveness from material samples, based on measured electrical parameters. For this, measurement systems for the electrical conductivity of high and low conductive material samples with respect to the direction of current flow are presented and discussed. Also a definition of isotropic and anisotropic materials with electrical circuit diagrams is given. For prediction of shielding effectiveness for isotropic and anisotropic materials, several analytical models are presented. Also adaptions to gain a near field solution are part of this contribution. All analytical models will also be validated with an adequate measurement system.
Fast calculation of computer-generated hologram using run-length encoding based recurrence relation.
Nishitsuji, Takashi; Shimobaba, Tomoyoshi; Kakue, Takashi; Ito, Tomoyoshi
2015-04-20
Computer-Generated Holograms (CGHs) can be generated by superimposing zoneplates. A zoneplate is a grating that can concentrate an incident light into a point. Since a zoneplate has a circular symmetry, we reported an algorithm that rapidly generates a zoneplate by drawing concentric circles using computer graphic techniques. However, random memory access was required in the algorithm and resulted in degradation of the computational efficiency. In this study, we propose a fast CGH generation algorithm without random memory access using run-length encoding (RLE) based recurrence relation. As a result, we succeeded in improving the calculation time by 88%, compared with that of the previous work.
The Calculation Model for Operation Cost of Coal Resources Development Based on ANN
Institute of Scientific and Technical Information of China (English)
刘海滨
2004-01-01
On the basis of analysis and selection of factors influencing operation cost of coal resources development, fuzzy set method and artificial neural network (ANN) were adopted to set up the classification analysis model of coal resources. The collected samples were classified by using this model. Meanwhile, the pattern recognition model for classifying of the coal resources was built according to the factors influencing operation cost. Based on the results achieved above, in the light of the theory of information diffusion, the calculation model for operation cost of coal resources development has been presented and applied in practice, showing that these models are reasonable.
Institute of Scientific and Technical Information of China (English)
王学滨
2004-01-01
A method for calculation of temperature distribution in adiabatic shear band is proposed in terms of gradient-dependent plasticity where the characteristic length describes the interactions and interplaying among microstructures. First, the increment of the plastic shear strain distribution in adiabatic shear band is obtained based on gradient-dependent plasticity. Then, the plastic work distribution is derived according to the current flow shear stress and the obtained increment of plastic shear strain distribution. In the light of the well-known assumption that 90% of plastic work is converted into the heat resulting in increase in temperature in adiabatic shear band, the increment of the temperature distribution is presented. Next, the average temperature increment in the shear band is calculated to compute the change in flow shear stress due to the thermal softening effect. After the actual flow shear stress considering the thermal softening effect is obtained according to the Johnson-Cook constitutive relation, the increment of the plastic shear strain distribution, the plastic work and the temperature in the next time step are recalculated until the total time is consumed. Summing the temperature distribution leads to rise in the total temperature distribution. The present calculated maximum temperature in adiabatic shear band in titanium agrees with the experimental observations. Moreover, the temperature profiles for different flow shear stresses are qualitatively consistent with experimental and numerical results. Effects of some related parameters on the temperature distribution are also predicted.
GPU-based ultra fast dose calculation using a finite pencil beam model
Gu, Xuejun; Men, Chunhua; Pan, Hubert; Majumdar, Amitava; Jiang, Steve B
2009-01-01
Online adaptive radiation therapy (ART) is an attractive concept that promises the ability to deliver an optimal treatment in response to the inter-fraction variability in patient anatomy. However, it has yet to be realized due to technical limitations. Fast dose deposit coefficient calculation is a critical component of the online planning process that is required for plan optimization of intensity modulated radiation therapy (IMRT). Computer graphics processing units (GPUs) are well-suited to provide the requisite fast performance for the data-parallel nature of dose calculation. In this work, we develop a dose calculation engine based on a finite-size pencil beam (FSPB) algorithm and a GPU parallel computing framework. The developed framework can accommodate any FSPB model. We test our implementation on a case of a water phantom and a case of a prostate cancer patient with varying beamlet and voxel sizes. All testing scenarios achieved speedup ranging from 200~400 times when using a NVIDIA Tesla C1060 card...
Excel pour l'ingénieur bases, graphiques, calculs, macros, VBA
Bellan, Philippe
2010-01-01
Excel, utilisé par tout possesseur d'un ordinateur personnel pour effectuer des manipulations élémentaires de tableaux et de chiffres, est en réalité un outil beaucoup plus puissant, aux potentialités souvent ignorées. A tous ceux, étudiants scientifiques, élèves-ingénieurs ou ingénieurs en exercice qui pensaient le calcul numérique seulement possible à travers des logiciels lourds et coûteux, ce livre montrera qu'un grand nombre de problèmes mathématiques courants de l'ingénieur peuvent être résolus numériquement en utilisant les outils de calcul et la capacité graphique d'Excel. A cet effet, après avoir introduit les notions de base, l'ouvrage décrit les fonctions disponibles avec Excel, puis quelques méthodes numériques simples permettant de calculer des intégrales, de résoudre des équations différentielles, d'obtenir les solutions de systèmes linéaires ou non, de traiter des problèmes d'optimisation... Les méthodes numériques présentées, qui sont très simples, peuvent...
a Novel Sub-Pixel Matching Algorithm Based on Phase Correlation Using Peak Calculation
Xie, Junfeng; Mo, Fan; Yang, Chao; Li, Pin; Tian, Shiqiang
2016-06-01
The matching accuracy of homonymy points of stereo images is a key point in the development of photogrammetry, which influences the geometrical accuracy of the image products. This paper presents a novel sub-pixel matching method phase correlation using peak calculation to improve the matching accuracy. The peak theoretic centre that means to sub-pixel deviation can be acquired by Peak Calculation (PC) according to inherent geometrical relationship, which is generated by inverse normalized cross-power spectrum, and the mismatching points are rejected by two strategies: window constraint, which is designed by matching window and geometric constraint, and correlation coefficient, which is effective for satellite images used for mismatching points removing. After above, a lot of high-precise homonymy points can be left. Lastly, three experiments are taken to verify the accuracy and efficiency of the presented method. Excellent results show that the presented method is better than traditional phase correlation matching methods based on surface fitting in these aspects of accuracy and efficiency, and the accuracy of the proposed phase correlation matching algorithm can reach 0.1 pixel with a higher calculation efficiency.
International Nuclear Information System (INIS)
This is the first report to provide radiation doses, arising from inhalation of radon itself, in mice and rats. To quantify absorbed doses to organs and tissues in mice, rats, and humans, we computed the behavior of inhaled radon in their bodies on the basis of a physiologically based pharmacokinetic (PBPK) model. It was assumed that radon dissolved in blood entering the gas exchange compartment is transported to any tissue by the blood circulation to be instantaneously distributed according to a tissue/blood partition coefficient. The calculated concentrations of radon in the adipose tissue and red bone marrow following its inhalation were much higher than those in the others, because of the higher partition coefficients. Compared with a previous experimental data for rats and model calculation for humans, the present calculation was proved to be valid. Absorbed dose rates to organs and tissues were estimated to be within the range of 0.04-1.4 nGy (Bqm-3)-1 day-1 for all the species. Although the dose rates are not so high, it may be better to pay attention to the dose to the red bone marrow from the perspective of radiation protection. For more accurate dose assessment, it is necessary to update tissue/blood partition coefficients of radon that strongly govern the result of the PBPK modeling. (author)
Dual-energy CT-based material extraction for tissue segmentation in Monte Carlo dose calculations
Bazalova, Magdalena; Carrier, Jean-François; Beaulieu, Luc; Verhaegen, Frank
2008-05-01
Monte Carlo (MC) dose calculations are performed on patient geometries derived from computed tomography (CT) images. For most available MC codes, the Hounsfield units (HU) in each voxel of a CT image have to be converted into mass density (ρ) and material type. This is typically done with a (HU; ρ) calibration curve which may lead to mis-assignment of media. In this work, an improved material segmentation using dual-energy CT-based material extraction is presented. For this purpose, the differences in extracted effective atomic numbers Z and the relative electron densities ρe of each voxel are used. Dual-energy CT material extraction based on parametrization of the linear attenuation coefficient for 17 tissue-equivalent inserts inside a solid water phantom was done. Scans of the phantom were acquired at 100 kVp and 140 kVp from which Z and ρe values of each insert were derived. The mean errors on Z and ρe extraction were 2.8% and 1.8%, respectively. Phantom dose calculations were performed for 250 kVp and 18 MV photon beams and an 18 MeV electron beam in the EGSnrc/DOSXYZnrc code. Two material assignments were used: the conventional (HU; ρ) and the novel (HU; ρ, Z) dual-energy CT tissue segmentation. The dose calculation errors using the conventional tissue segmentation were as high as 17% in a mis-assigned soft bone tissue-equivalent material for the 250 kVp photon beam. Similarly, the errors for the 18 MeV electron beam and the 18 MV photon beam were up to 6% and 3% in some mis-assigned media. The assignment of all tissue-equivalent inserts was accurate using the novel dual-energy CT material assignment. As a result, the dose calculation errors were below 1% in all beam arrangements. Comparable improvement in dose calculation accuracy is expected for human tissues. The dual-energy tissue segmentation offers a significantly higher accuracy compared to the conventional single-energy segmentation.
GPU-based fast Monte Carlo dose calculation for proton therapy
Jia, Xun; Schümann, Jan; Paganetti, Harald; Jiang, Steve B.
2012-12-01
Accurate radiation dose calculation is essential for successful proton radiotherapy. Monte Carlo (MC) simulation is considered to be the most accurate method. However, the long computation time limits it from routine clinical applications. Recently, graphics processing units (GPUs) have been widely used to accelerate computationally intensive tasks in radiotherapy. We have developed a fast MC dose calculation package, gPMC, for proton dose calculation on a GPU. In gPMC, proton transport is modeled by the class II condensed history simulation scheme with a continuous slowing down approximation. Ionization, elastic and inelastic proton nucleus interactions are considered. Energy straggling and multiple scattering are modeled. Secondary electrons are not transported and their energies are locally deposited. After an inelastic nuclear interaction event, a variety of products are generated using an empirical model. Among them, charged nuclear fragments are terminated with energy locally deposited. Secondary protons are stored in a stack and transported after finishing transport of the primary protons, while secondary neutral particles are neglected. gPMC is implemented on the GPU under the CUDA platform. We have validated gPMC using the TOPAS/Geant4 MC code as the gold standard. For various cases including homogeneous and inhomogeneous phantoms as well as a patient case, good agreements between gPMC and TOPAS/Geant4 are observed. The gamma passing rate for the 2%/2 mm criterion is over 98.7% in the region with dose greater than 10% maximum dose in all cases, excluding low-density air regions. With gPMC it takes only 6-22 s to simulate 10 million source protons to achieve ˜1% relative statistical uncertainty, depending on the phantoms and energy. This is an extremely high efficiency compared to the computational time of tens of CPU hours for TOPAS/Geant4. Our fast GPU-based code can thus facilitate the routine use of MC dose calculation in proton therapy.
The sodium ion affinities of asparagine, glutamine, histidine and arginine
Wang, Ping; Ohanessian, Gilles; Wesdemiotis, Chrys
2008-01-01
The sodium ion affinities of the amino acids Asn, Gln, His and Arg have been determined by experimental and computational approaches (for Asn, His and Arg). Na+-bound heterodimers with amino acid and peptide ligands (Pep1, Pep2) were produced by electrospray ionization. From the dissociation kinetics of these Pep1-Na+-Pep2 ions to Pep1-Na+ and Pep2-Na+, determined by collisionally activated dissociation, a ladder of relative affinities was constructed and subsequently converted to absolute affinities by anchoring the relative values to known Na+ affinities. The Na+ affinities of Asn, His and Arg, were calculated at the MP2(full)/6-311+G(2d,2p)//MP2/6-31G(d) level of ab initio theory. The resulting experimental and computed Na+ affinities are in excellent agreement with one another. These results, combined with those of our previous studies, yield the sodium ion affinities of 18 out of the 20 [alpha]-amino acids naturally occurring in peptides and proteins of living systems.
Evaluation of on-board kV cone beam CT (CBCT)-based dose calculation
Yang, Yong; Schreibmann, Eduard; Li, Tianfang; Wang, Chuang; Xing, Lei
2007-02-01
On-board CBCT images are used to generate patient geometric models to assist patient setup. The image data can also, potentially, be used for dose reconstruction in combination with the fluence maps from treatment plan. Here we evaluate the achievable accuracy in using a kV CBCT for dose calculation. Relative electron density as a function of HU was obtained for both planning CT (pCT) and CBCT using a Catphan-600 calibration phantom. The CBCT calibration stability was monitored weekly for 8 consecutive weeks. A clinical treatment planning system was employed for pCT- and CBCT-based dose calculations and subsequent comparisons. Phantom and patient studies were carried out. In the former study, both Catphan-600 and pelvic phantoms were employed to evaluate the dosimetric performance of the full-fan and half-fan scanning modes. To evaluate the dosimetric influence of motion artefacts commonly seen in CBCT images, the Catphan-600 phantom was scanned with and without cyclic motion using the pCT and CBCT scanners. The doses computed based on the four sets of CT images (pCT and CBCT with/without motion) were compared quantitatively. The patient studies included a lung case and three prostate cases. The lung case was employed to further assess the adverse effect of intra-scan organ motion. Unlike the phantom study, the pCT of a patient is generally acquired at the time of simulation and the anatomy may be different from that of CBCT acquired at the time of treatment delivery because of organ deformation. To tackle the problem, we introduced a set of modified CBCT images (mCBCT) for each patient, which possesses the geometric information of the CBCT but the electronic density distribution mapped from the pCT with the help of a BSpline deformable image registration software. In the patient study, the dose computed with the mCBCT was used as a surrogate of the 'ground truth'. We found that the CBCT electron density calibration curve differs moderately from that of pCT. No
SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.
Directory of Open Access Journals (Sweden)
Brejnev Muhizi Muhire
Full Text Available The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV. There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT, a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms.
Directory of Open Access Journals (Sweden)
Lintong Jia
2016-01-01
Full Text Available Aircraft combat survivability is defined as the capability of an aircraft to avoid or withstand a man-made hostile environment, which has been increasingly important. In order to give a rational calculation of aircraft combat survivability, an integrated method based on combination weighting and multiattribute intelligent grey target decision model is proposed. Firstly, an evaluation index system containing susceptibility index and vulnerability index as well as their subindexes is established. Then a multiattribute intelligent grey target decision model is introduced. A combination weighting method is brought up based on a modified AHP (analytic hierarchy process method and the entropy method, offering a rational weight for various indexes. Finally, utilize the multiattribute intelligent grey target decision model to assess the aircraft combat survivability of aircraft, verified by a practical case of five aircraft. The results show that the proposed method is effective and has a great value in engineering application, which will provide useful references for other projects’ evaluation.
Tadano, Shigeru; Takeda, Ryo; Miyagawa, Hiroaki
2013-01-01
This paper proposes a method for three dimensional gait analysis using wearable sensors and quaternion calculations. Seven sensor units consisting of a tri-axial acceleration and gyro sensors, were fixed to the lower limbs. The acceleration and angular velocity data of each sensor unit were measured during level walking. The initial orientations of the sensor units were estimated using acceleration data during upright standing position and the angular displacements were estimated afterwards using angular velocity data during gait. Here, an algorithm based on quaternion calculation was implemented for orientation estimation of the sensor units. The orientations of the sensor units were converted to the orientations of the body segments by a rotation matrix obtained from a calibration trial. Body segment orientations were then used for constructing a three dimensional wire frame animation of the volunteers during the gait. Gait analysis was conducted on five volunteers, and results were compared with those from a camera-based motion analysis system. Comparisons were made for the joint trajectory in the horizontal and sagittal plane. The average RMSE and correlation coefficient (CC) were 10.14 deg and 0.98, 7.88 deg and 0.97, 9.75 deg and 0.78 for the hip, knee and ankle flexion angles, respectively. PMID:23877128
Calculations of helium separation via uniform pores of stanene-based membranes
Directory of Open Access Journals (Sweden)
Guoping Gao
2015-12-01
Full Text Available The development of low energy cost membranes to separate He from noble gas mixtures is highly desired. In this work, we studied He purification using recently experimentally realized, two-dimensional stanene (2D Sn and decorated 2D Sn (SnH and SnF honeycomb lattices by density functional theory calculations. To increase the permeability of noble gases through pristine 2D Sn at room temperature (298 K, two practical strategies (i.e., the application of strain and functionalization are proposed. With their high concentration of large pores, 2D Sn-based membrane materials demonstrate excellent helium purification and can serve as a superior membrane over traditionally used, porous materials. In addition, the separation performance of these 2D Sn-based membrane materials can be significantly tuned by application of strain to optimize the He purification properties by taking both diffusion and selectivity into account. Our results are the first calculations of He separation in a defect-free honeycomb lattice, highlighting new interesting materials for helium separation for future experimental validation.
Numerical Calculations of WR-40 Boiler Based on its Zero-Dimensional Model
Directory of Open Access Journals (Sweden)
Hernik Bartłomiej
2014-06-01
Full Text Available Generally, the temperature of flue gases at the furnace outlet is not measured. Therefore, a special computation procedure is needed to determine it. This paper presents a method for coordination of the numerical model of a pulverised fuel boiler furnace chamber with the measuring data in a situation when CFD calculations are made in regard to the furnace only. This paper recommends the use of the classical 0-dimensional balance model of a boiler, based on the use of measuring data. The average temperature of flue gases at the furnace outlet tk" obtained using the model may be considered as highly reliable. The numerical model has to show the same value of tk" . This paper presents calculations for WR-40 boiler. The CFD model was matched to the 0-dimensional tk" value by means of a selection of the furnace wall emissivity. As a result of CFD modelling, the flue gas temperature and the concentration of CO, CO2, O2 and NOx were obtained at the furnace chamber outlet. The results of numerical modelling of boiler combustion based on volumetric reactions and using the Finite-Rate/Eddy-Dissipation Model are presented.
Electronic structures of halogen-doped Cu2O based on DFT calculations
Zhao, Zong-Yan; Yi, Juan; Zhou, Da-Cheng
2014-01-01
In order to construct p—n homojunction of Cu2O-based thin film solar cells that may increase its conversion efficiency, to synthesize n-type Cu2O with high conductivity is extremely crucial, and considered as a challenge in the near future. The doping effects of halogen on electronic structure of Cu2O have been investigated by density function theory calculations in the present work. Halogen dopants form donor levels below the bottom of conduction band through gaining or losing electrons, suggesting that halogen doping could make Cu2O have n-type conductivity. The lattice distortion, the impurity formation energy, the position, and the band width of donor level of Cu2O1-xHx (H = F, Cl, Br, I) increase with the halogen atomic number. Based on the calculated results, chlorine doping is an effective n-type dopant for Cu2O, owing to the lower impurity formation energy and suitable donor level.
Directory of Open Access Journals (Sweden)
Feifei Fu
2014-01-01
Full Text Available Life cycle thinking has become widely applied in the assessment for building environmental performance. Various tool are developed to support the application of life cycle assessment (LCA method. This paper focuses on the carbon emission during the building construction stage. A partial LCA framework is established to assess the carbon emission in this phase. Furthermore, five typical LCA tools programs have been compared and analyzed for demonstrating the current application of LCA tools and their limitations in the building construction stage. Based on the analysis of existing tools and sustainability demands in building, a new computer calculation system has been developed to calculate the carbon emission for optimizing the sustainability during the construction stage. The system structure and detail functions are described in this paper. Finally, a case study is analyzed to demonstrate the designed LCA framework and system functions. This case is based on a typical building in UK with different plans of masonry wall and timber frame to make a comparison. The final results disclose that a timber frame wall has less embodied carbon emission than a similar masonry structure. 16% reduction was found in this study.
Directory of Open Access Journals (Sweden)
Hiroaki Miyagawa
2013-07-01
Full Text Available This paper proposes a method for three dimensional gait analysis using wearable sensors and quaternion calculations. Seven sensor units consisting of a tri-axial acceleration and gyro sensors, were fixed to the lower limbs. The acceleration and angular velocity data of each sensor unit were measured during level walking. The initial orientations of the sensor units were estimated using acceleration data during upright standing position and the angular displacements were estimated afterwards using angular velocity data during gait. Here, an algorithm based on quaternion calculation was implemented for orientation estimation of the sensor units. The orientations of the sensor units were converted to the orientations of the body segments by a rotation matrix obtained from a calibration trial. Body segment orientations were then used for constructing a three dimensional wire frame animation of the volunteers during the gait. Gait analysis was conducted on five volunteers, and results were compared with those from a camera-based motion analysis system. Comparisons were made for the joint trajectory in the horizontal and sagittal plane. The average RMSE and correlation coefficient (CC were 10.14 deg and 0.98, 7.88 deg and 0.97, 9.75 deg and 0.78 for the hip, knee and ankle flexion angles, respectively.
A GPU-based Monte Carlo dose calculation code for photon transport in a voxel phantom
International Nuclear Information System (INIS)
As the most accurate method to estimate absorbed dose in radiotherapy, Monte Carlo method has been widely used in radiotherapy treatment planning. Nevertheless, its efficiency can be improved for clinical routine applications. In this paper, we present the CUBMC code, a GPU-based Mc photon transport algorithm for dose calculation under the Compute Unified Device Architecture platform. The simulation of physical events is based on the algorithm used in Penelope, and the cross section table used is the one generated by the Material routine, als present in Penelope code. Photons are transported in voxel-based geometries with different compositions. To demonstrate the capabilities of the algorithm developed in the present work four 128 x 128 x 128 voxel phantoms have been considered. One of them is composed by a homogeneous water-based media, the second is composed by bone, the third is composed by lung and the fourth is composed by a heterogeneous bone and vacuum geometry. Simulations were done considering a 6 MeV monoenergetic photon point source. There are two distinct approaches that were used for transport simulation. The first of them forces the photon to stop at every voxel frontier, the second one is the Woodcock method, where the photon stop in the frontier will be considered depending on the material changing across the photon travel line. Dose calculations using these methods are compared for validation with Penelope and MCNP5 codes. Speed-up factors are compared using a NVidia GTX 560-Ti GPU card against a 2.27 GHz Intel Xeon CPU processor. (Author)
A GPU-based Monte Carlo dose calculation code for photon transport in a voxel phantom
Energy Technology Data Exchange (ETDEWEB)
Bellezzo, M.; Do Nascimento, E.; Yoriyaz, H., E-mail: mbellezzo@gmail.br [Instituto de Pesquisas Energeticas e Nucleares / CNEN, Av. Lineu Prestes 2242, Cidade Universitaria, 05508-000 Sao Paulo (Brazil)
2014-08-15
As the most accurate method to estimate absorbed dose in radiotherapy, Monte Carlo method has been widely used in radiotherapy treatment planning. Nevertheless, its efficiency can be improved for clinical routine applications. In this paper, we present the CUBMC code, a GPU-based Mc photon transport algorithm for dose calculation under the Compute Unified Device Architecture platform. The simulation of physical events is based on the algorithm used in Penelope, and the cross section table used is the one generated by the Material routine, als present in Penelope code. Photons are transported in voxel-based geometries with different compositions. To demonstrate the capabilities of the algorithm developed in the present work four 128 x 128 x 128 voxel phantoms have been considered. One of them is composed by a homogeneous water-based media, the second is composed by bone, the third is composed by lung and the fourth is composed by a heterogeneous bone and vacuum geometry. Simulations were done considering a 6 MeV monoenergetic photon point source. There are two distinct approaches that were used for transport simulation. The first of them forces the photon to stop at every voxel frontier, the second one is the Woodcock method, where the photon stop in the frontier will be considered depending on the material changing across the photon travel line. Dose calculations using these methods are compared for validation with Penelope and MCNP5 codes. Speed-up factors are compared using a NVidia GTX 560-Ti GPU card against a 2.27 GHz Intel Xeon CPU processor. (Author)
From Ontology to Semantic Similarity: Calculation of Ontology-Based Semantic Similarity
Directory of Open Access Journals (Sweden)
Mingxin Gan
2013-01-01
Full Text Available Advances in high-throughput experimental techniques in the past decade have enabled the explosive increase of omics data, while effective organization, interpretation, and exchange of these data require standard and controlled vocabularies in the domain of biological and biomedical studies. Ontologies, as abstract description systems for domain-specific knowledge composition, hence receive more and more attention in computational biology and bioinformatics. Particularly, many applications relying on domain ontologies require quantitative measures of relationships between terms in the ontologies, making it indispensable to develop computational methods for the derivation of ontology-based semantic similarity between terms. Nevertheless, with a variety of methods available, how to choose a suitable method for a specific application becomes a problem. With this understanding, we review a majority of existing methods that rely on ontologies to calculate semantic similarity between terms. We classify existing methods into five categories: methods based on semantic distance, methods based on information content, methods based on properties of terms, methods based on ontology hierarchy, and hybrid methods. We summarize characteristics of each category, with emphasis on basic notions, advantages and disadvantages of these methods. Further, we extend our review to software tools implementing these methods and applications using these methods.
An analytic linear accelerator source model for GPU-based Monte Carlo dose calculations
Tian, Zhen; Li, Yongbao; Folkerts, Michael; Shi, Feng; Jiang, Steve B.; Jia, Xun
2015-10-01
Recently, there has been a lot of research interest in developing fast Monte Carlo (MC) dose calculation methods on graphics processing unit (GPU) platforms. A good linear accelerator (linac) source model is critical for both accuracy and efficiency considerations. In principle, an analytical source model should be more preferred for GPU-based MC dose engines than a phase-space file-based model, in that data loading and CPU-GPU data transfer can be avoided. In this paper, we presented an analytical field-independent source model specifically developed for GPU-based MC dose calculations, associated with a GPU-friendly sampling scheme. A key concept called phase-space-ring (PSR) was proposed. Each PSR contained a group of particles that were of the same type, close in energy and reside in a narrow ring on the phase-space plane located just above the upper jaws. The model parameterized the probability densities of particle location, direction and energy for each primary photon PSR, scattered photon PSR and electron PSR. Models of one 2D Gaussian distribution or multiple Gaussian components were employed to represent the particle direction distributions of these PSRs. A method was developed to analyze a reference phase-space file and derive corresponding model parameters. To efficiently use our model in MC dose calculations on GPU, we proposed a GPU-friendly sampling strategy, which ensured that the particles sampled and transported simultaneously are of the same type and close in energy to alleviate GPU thread divergences. To test the accuracy of our model, dose distributions of a set of open fields in a water phantom were calculated using our source model and compared to those calculated using the reference phase-space files. For the high dose gradient regions, the average distance-to-agreement (DTA) was within 1 mm and the maximum DTA within 2 mm. For relatively low dose gradient regions, the root-mean-square (RMS) dose difference was within 1.1% and the maximum
Affine group formulation of the Standard Model coupled to gravity
Energy Technology Data Exchange (ETDEWEB)
Chou, Ching-Yi, E-mail: l2897107@mail.ncku.edu.tw [Department of Physics, National Cheng Kung University, Taiwan (China); Ita, Eyo, E-mail: ita@usna.edu [Department of Physics, US Naval Academy, Annapolis, MD (United States); Soo, Chopin, E-mail: cpsoo@mail.ncku.edu.tw [Department of Physics, National Cheng Kung University, Taiwan (China)
2014-04-15
In this work we apply the affine group formalism for four dimensional gravity of Lorentzian signature, which is based on Klauder’s affine algebraic program, to the formulation of the Hamiltonian constraint of the interaction of matter and all forces, including gravity with non-vanishing cosmological constant Λ, as an affine Lie algebra. We use the hermitian action of fermions coupled to gravitation and Yang–Mills theory to find the density weight one fermionic super-Hamiltonian constraint. This term, combined with the Yang–Mills and Higgs energy densities, are composed with York’s integrated time functional. The result, when combined with the imaginary part of the Chern–Simons functional Q, forms the affine commutation relation with the volume element V(x). Affine algebraic quantization of gravitation and matter on equal footing implies a fundamental uncertainty relation which is predicated upon a non-vanishing cosmological constant. -- Highlights: •Wheeler–DeWitt equation (WDW) quantized as affine algebra, realizing Klauder’s program. •WDW formulated for interaction of matter and all forces, including gravity, as affine algebra. •WDW features Hermitian generators in spite of fermionic content: Standard Model addressed. •Constructed a family of physical states for the full, coupled theory via affine coherent states. •Fundamental uncertainty relation, predicated on non-vanishing cosmological constant.
Synthesis and Image Matching On Structural Patterns Using Affine Transformation
Directory of Open Access Journals (Sweden)
S.Vandana
2012-06-01
Full Text Available This paper focuses in explaining a Fourier based affine estimator which is applied to the task of Image Synthesis. An affine transformation is an important class of linear 2-D geometric transformations which maps variables into new by applying a linear combination of translation, rotation, scaling and/or shearing operations. Conventional retrieval systems are very effective when knowledge information and query information are in a uniform orientation but fails in recognition when effects such as scaling, orientation exist. But as this technique is based on texture analysis, which is termed the affine estimator, it will even match the images with non-uniform orientation.
Image Information Hiding Algorithm Based on Improved Sub-affine Transformation%基于改进亚仿射变换的图像信息隐藏算法
Institute of Scientific and Technical Information of China (English)
卢斌; 王冰
2011-01-01
An information hiding algorithm of image fusion technology is proposed based on the improved sub-affine transformation.This algorithm preprocesses the secret information image by using the improved sub-affine transformation, increases the key of the original algorithm from six to eight, and completes hiding secret information by using image fusion technology based on Logistic chaos sequences.Experimental results show that sub-affine transformation has good scrambling effect and safety level, and Logistic chaos sequence which enhances the security of image hiding compared with traditional hiding algorithm's blend factors have larger space.%为改进仿射变换的自身安全性,提出一种基于改进亚仿射变换的图像融合信息隐藏算法.通过改进的亚仿射变换对秘密信息图像做预处理,将密钥从6个提升到8个,并结合Logistic混沌序列利用图像融合技术完成秘密信息的嵌入.实验表明,该亚仿射变换有较好的置乱效果和安全级别,而Logistic混沌序列相比于传统隐藏算法中的混合因子具有更大的密钥空间,能提高图像隐藏的安全性.
Monte Carlo-based treatment planning system calculation engine for microbeam radiation therapy
Energy Technology Data Exchange (ETDEWEB)
Martinez-Rovira, I.; Sempau, J.; Prezado, Y. [Institut de Tecniques Energetiques, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E-08028 (Spain) and ID17 Biomedical Beamline, European Synchrotron Radiation Facility (ESRF), 6 rue Jules Horowitz B.P. 220, F-38043 Grenoble Cedex (France); Institut de Tecniques Energetiques, Universitat Politecnica de Catalunya, Diagonal 647, Barcelona E-08028 (Spain); Laboratoire Imagerie et modelisation en neurobiologie et cancerologie, UMR8165, Centre National de la Recherche Scientifique (CNRS), Universites Paris 7 et Paris 11, Bat 440., 15 rue Georges Clemenceau, F-91406 Orsay Cedex (France)
2012-05-15
Purpose: Microbeam radiation therapy (MRT) is a synchrotron radiotherapy technique that explores the limits of the dose-volume effect. Preclinical studies have shown that MRT irradiations (arrays of 25-75-{mu}m-wide microbeams spaced by 200-400 {mu}m) are able to eradicate highly aggressive animal tumor models while healthy tissue is preserved. These promising results have provided the basis for the forthcoming clinical trials at the ID17 Biomedical Beamline of the European Synchrotron Radiation Facility (ESRF). The first step includes irradiation of pets (cats and dogs) as a milestone before treatment of human patients. Within this context, accurate dose calculations are required. The distinct features of both beam generation and irradiation geometry in MRT with respect to conventional techniques require the development of a specific MRT treatment planning system (TPS). In particular, a Monte Carlo (MC)-based calculation engine for the MRT TPS has been developed in this work. Experimental verification in heterogeneous phantoms and optimization of the computation time have also been performed. Methods: The penelope/penEasy MC code was used to compute dose distributions from a realistic beam source model. Experimental verification was carried out by means of radiochromic films placed within heterogeneous slab-phantoms. Once validation was completed, dose computations in a virtual model of a patient, reconstructed from computed tomography (CT) images, were performed. To this end, decoupling of the CT image voxel grid (a few cubic millimeter volume) to the dose bin grid, which has micrometer dimensions in the transversal direction of the microbeams, was performed. Optimization of the simulation parameters, the use of variance-reduction (VR) techniques, and other methods, such as the parallelization of the simulations, were applied in order to speed up the dose computation. Results: Good agreement between MC simulations and experimental results was achieved, even at
Lu, Hua; Zhang, Shushu; Liu, Hanzhuang; Wang, Yanwei; Shen, Zhen; Liu, Chungen; You, Xiaozeng
2009-12-01
A boron-dipyrromethene (BODIPY)-based fluorescence probe with a N,N'-(pyridine-2, 6-diylbis(methylene))-dianiline substituent (1) has been prepared by condensation of 2,6-pyridinedicarboxaldehyde with 8-(4-amino)-4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene and reduction by NaBH4. The sensing properties of compound 1 toward various metal ions are investigated via fluorometric titration in methanol, which show highly selective fluorescent turn-on response in the presence of Hg2+ over the other metal ions, such as Li+, Na+, K+, Ca2+, Mg2+, Pb2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Ag+, and Mn2+. Computational approach has been carried out to investigate the mechanism why compound 1 provides different fluorescent signal for Hg2+ and other ions. Theoretic calculations of the energy levels show that the quenching of the bright green fluorescence of boradiazaindacene fluorophore is due to the reductive photoinduced electron transfer (PET) from the aniline subunit to the excited state of BODIPY fluorophore. In metal complexes, the frontier molecular orbital energy levels changes greatly. Binding Zn2+ or Cd2+ ion leads to significant decreasing of both the HOMO and LUMO energy levels of the receptor, thus inhibit the reductive PET process, whereas an oxidative PET from the excited state fluorophore to the receptor occurs, vice versa, which also quenches the fluorescence. However, for 1-Hg2+ complex, both the reductive and oxidative PETs are prohibited; therefore, strong fluorescence emission from the fluorophore can be observed experimentally. The agreement of the experimental results and theoretic calculations suggests that our calculation method can be applicable as guidance for the design of new chemosensors for other metal ions.
Dementyeva, Svetlana; Ilin, Nikolay; Shatalina, Maria; Mareev, Evgeny
2016-04-01
Now-casting and long-term forecasting of lightning flashes occurrence are urgent problems from different points of view. There are several approaches to predicting lightning activity using indirect non-electrical parameters based on the relationship of lightning flashes with vertical fluxes of solid-phased hydrometeors but for more explicit forecasting of the lightning flashes occurrence electric processes should be considered. In addition, a factor playing a key role for now-casting of lightning activity is the earliness. We have proposed an algorithm, which makes the process of thunderstorms prediction automatic (due to automatic start of the electric parameters calculation) and quick (due to the use of simplified methods). Our forecasting was based on the use of Weather Research and Forecasting (WRF) model, which does not include the electrification processes, but it was supplemented with two modules. The first is an algorithm, which allows us to select thunderstorm events indirectly. It is based on such characteristics of thunderclouds and thunderstorms as radar reflectivity, duration and area and provides us with information about an approximate beginning and duration of the thunderstorm. The second module is a method for electric parameters calculations, which we have proposed before. It was suggested that the non-inductive mechanism of charge generation and separation plays a key role in the thundercloud electrification processes. Also charge densities of solid-phased hydrometeors are assumed to be proportional to their mass in elementary air volume. According to the models by Saunders and Takahashi, particles change the sign of charge while getting into the lower part of thundercloud from the upper and vice versa. Electric neutrality in the vertical air column was supposed in the course of vertical charge separation due to collisions between falling graupels and carried upward ice crystals. Electric potential (and consequently electric field) can be found
Energy Technology Data Exchange (ETDEWEB)
Kim, Sung Woo; Kim, Dong Jin [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)
2013-10-15
In this work, to develop novel structural materials for the IHX of a VHTR, a more systematic methodology using the design of experiments (DOE) and thermodynamic calculations was proposed. For 32 sets of designs of Ni-Cr-Co-Mo alloys with minor elements of W and Ta, the mass fraction of TCP phases and mechanical properties were calculated, and finally the chemical composition was optimized for further experimental studies by applying the proposed . The highly efficient generation of electricity and the production of massive hydrogen are possible using a very high temperature gas-cooled reactor (VHTR) among generation IV nuclear power plants. The structural material for an intermediate heat exchanger (IHX) among numerous components should be endurable at high temperature of up to 950 .deg. C during long-term operation. Impurities inevitably introduced in helium as a coolant facilitate the material degradation by corrosion at high temperature. This work is concerning a methodology of Ni-Cr-Co-Mo based superalloy developed for VHTR using the design of experiments (DOE) and thermodynamic calculationsmethodology.
Characterization of tsunamigenic earthquake in Java region based on seismic wave calculation
International Nuclear Information System (INIS)
This study is to characterize the source mechanism of tsunamigenic earthquake based on seismic wave calculation. The source parameter used are the ratio (Θ) between the radiated seismic energy (E) and seismic moment (Mo), moment magnitude (MW), rupture duration (To) and focal mechanism. These determine the types of tsunamigenic earthquake and tsunami earthquake. We calculate the formula using the teleseismic wave signal processing with the initial phase of P wave with bandpass filter 0.001 Hz to 5 Hz. The amount of station is 84 broadband seismometer with far distance of 30° to 90°. The 2 June 1994 Banyuwangi earthquake with MW=7.8 and the 17 July 2006 Pangandaran earthquake with MW=7.7 include the criteria as a tsunami earthquake which distributed about ratio Θ=−6.1, long rupture duration To>100 s and high tsunami H>7 m. The 2 September 2009 Tasikmalaya earthquake with MW=7.2, Θ=−5.1 and To=27 s which characterized as a small tsunamigenic earthquake
A 3D pencil-beam-based superposition algorithm for photon dose calculation in heterogeneous media
Tillikainen, L.; Helminen, H.; Torsti, T.; Siljamäki, S.; Alakuijala, J.; Pyyry, J.; Ulmer, W.
2008-07-01
In this work, a novel three-dimensional superposition algorithm for photon dose calculation is presented. The dose calculation is performed as a superposition of pencil beams, which are modified based on tissue electron densities. The pencil beams have been derived from Monte Carlo simulations, and are separated into lateral and depth-directed components. The lateral component is modeled using exponential functions, which allows accurate modeling of lateral scatter in heterogeneous tissues. The depth-directed component represents the total energy deposited on each plane, which is spread out using the lateral scatter functions. Finally, convolution in the depth direction is applied to account for tissue interface effects. The method can be used with the previously introduced multiple-source model for clinical settings. The method was compared against Monte Carlo simulations in several phantoms including lung- and bone-type heterogeneities. Comparisons were made for several field sizes for 6 and 18 MV energies. The deviations were generally within (2%, 2 mm) of the field central axis dmax. Significantly larger deviations (up to 8%) were found only for the smallest field in the lung slab phantom for 18 MV. The presented method was found to be accurate in a wide range of conditions making it suitable for clinical planning purposes.
Seismic ray-tracing calculation based on parabolic travel-time interpolation
Institute of Scientific and Technical Information of China (English)
周竹生; 张赛民; 陈灵君
2004-01-01
A new seismic ray-tracing method is put forward based on parabolic travel-time interpolation(PTI) method, which is more accurate than the linear travel-time interpolation (LTI) method. Both PTI method and LTI method are used to compute seismic travel-time and ray-path in a 2-D grid cell model. Firstly, some basic concepts are introduced. The calculations of travel-time and ray-path are carried out only at cell boundaries. So, the ray-path is always straight in the same cells with uniform velocity. Two steps are applied in PTI and LTI method, step 1 computes travel-time and step 2 traces ray-path. Then, the derivation of LTI formulas is described. Because of the presence of refraction wave in shot cell, the formula aiming at shot cell is also derived. Finally, PTI method is presented. The calculation of PTI method is more complex than that of LTI method, but the error is limited. The results of numerical model show that PTI method can trace ray-path more accurately and efficiently than LTI method does.
Characterization of tsunamigenic earthquake in Java region based on seismic wave calculation
Energy Technology Data Exchange (ETDEWEB)
Pribadi, Sugeng, E-mail: sugengpribadimsc@gmail.com [Badan Meteorologi Klimatologi Geofisika, Jl Angkasa I No. 2 Jakarta (Indonesia); Afnimar,; Puspito, Nanang T.; Ibrahim, Gunawan [Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132 (Indonesia)
2014-03-24
This study is to characterize the source mechanism of tsunamigenic earthquake based on seismic wave calculation. The source parameter used are the ratio (Θ) between the radiated seismic energy (E) and seismic moment (M{sub o}), moment magnitude (M{sub W}), rupture duration (T{sub o}) and focal mechanism. These determine the types of tsunamigenic earthquake and tsunami earthquake. We calculate the formula using the teleseismic wave signal processing with the initial phase of P wave with bandpass filter 0.001 Hz to 5 Hz. The amount of station is 84 broadband seismometer with far distance of 30° to 90°. The 2 June 1994 Banyuwangi earthquake with M{sub W}=7.8 and the 17 July 2006 Pangandaran earthquake with M{sub W}=7.7 include the criteria as a tsunami earthquake which distributed about ratio Θ=−6.1, long rupture duration To>100 s and high tsunami H>7 m. The 2 September 2009 Tasikmalaya earthquake with M{sub W}=7.2, Θ=−5.1 and To=27 s which characterized as a small tsunamigenic earthquake.
Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics
Hošek, Petr; Spiwok, Vojtěch
2016-01-01
Metadynamics is a highly successful enhanced sampling technique for simulation of molecular processes and prediction of their free energy surfaces. An in-depth analysis of data obtained by this method is as important as the simulation itself. Although there are several tools to compute free energy surfaces from metadynamics data, they usually lack user friendliness and a build-in visualization part. Here we introduce Metadyn View as a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. It is based on modern web technologies including HTML5, JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies and free energy differences and data/image export.
Visible calculation of mining index based on stope 3D surveying and block modeling
Institute of Scientific and Technical Information of China (English)
Liu Xiaoming; Luo Zhouquan; Yang Biao; Lu Guang; Cao Shengxiang; Jiang Xinjian
2012-01-01
Aimed at the CMS laser scanning theory and characteristic,a combined actual situation of stope N4-5 of Fankou Lead-Zinc Mine and complementary monitoring of the stope were carried out by carefully choosing two measuring points.The cavity 3D visible model was created by large-scale mining industry software Surpac after changing the measured data.The stope mine design model,bottom structural model and backfill model of the south and north sides of the stope N4-5 were established according to the stope design data.On this basis,the stope block model was established,and then block attribute was estimated.The amount the ore remains,mullock,backfill and total mined ore were calculated through the solid model restrains.Finally,the stope mining dilution rate and loss rate reached 8.2％and 1.47％,respectively.The practice indicates that the mining index visible calculation method based on cavity 3D monitoring and stope block modeling can make up the deficiency of adopting the solid model to directly carry out the Boolean operation.The stope mining indexes obtained by this method are accurate and reliable,and can be used to guide the actual production management and estimate the mining quality.
International Nuclear Information System (INIS)
In this work, to develop novel structural materials for the IHX of a VHTR, a more systematic methodology using the design of experiments (DOE) and thermodynamic calculations was proposed. For 32 sets of designs of Ni-Cr-Co-Mo alloys with minor elements of W and Ta, the mass fraction of TCP phases and mechanical properties were calculated, and finally the chemical composition was optimized for further experimental studies by applying the proposed . The highly efficient generation of electricity and the production of massive hydrogen are possible using a very high temperature gas-cooled reactor (VHTR) among generation IV nuclear power plants. The structural material for an intermediate heat exchanger (IHX) among numerous components should be endurable at high temperature of up to 950 .deg. C during long-term operation. Impurities inevitably introduced in helium as a coolant facilitate the material degradation by corrosion at high temperature. This work is concerning a methodology of Ni-Cr-Co-Mo based superalloy developed for VHTR using the design of experiments (DOE) and thermodynamic calculationsmethodology
Jacob, D.; Palacios, J. J.
2011-01-01
We study the performance of two different electrode models in quantum transport calculations based on density functional theory: parametrized Bethe lattices and quasi-one-dimensional wires or nanowires. A detailed account of implementation details in both the cases is given. From the systematic study of nanocontacts made of representative metallic elements, we can conclude that the parametrized electrode models represent an excellent compromise between computational cost and electronic structure definition as long as the aim is to compare with experiments where the precise atomic structure of the electrodes is not relevant or defined with precision. The results obtained using parametrized Bethe lattices are essentially similar to the ones obtained with quasi-one-dimensional electrodes for large enough cross-sections of these, adding a natural smearing to the transmission curves that mimics the true nature of polycrystalline electrodes. The latter are more demanding from the computational point of view, but present the advantage of expanding the range of applicability of transport calculations to situations where the electrodes have a well-defined atomic structure, as is the case for carbon nanotubes, graphene nanoribbons, or semiconducting nanowires. All the analysis is done with the help of codes developed by the authors which can be found in the quantum transport toolbox ALACANT and are publicly available.
Extension of the COSYMA-ECONOMICS module - cost calculations based on different economic sectors
International Nuclear Information System (INIS)
The COSYMA program system for evaluating the off-site consequences of accidental releases of radioactive material to the atmosphere includes an ECONOMICS module for assessing economic consequences. The aim of this module is to convert various consequences (radiation-induced health effects and impacts resulting from countermeasures) caused by an accident into the common framework of economic costs; this allows different effects to be expressed in the same terms and thus to make these effects comparable. With respect to the countermeasure 'movement of people', the dominant cost categories are 'loss-of-income costs' and 'costs of lost capital services'. In the original version of the ECONOMICS module these costs are calculated on the basis of the total number of people moved. In order to take into account also regional or local economic peculiarities of a nuclear site, the ECONOMICS module has been extended: Calculation of the above mentioned cost categories is now based on the number of employees in different economic sectors in the affected area. This extension of the COSYMA ECONOMICS module is described in more detail. (orig.)
Microcontroller-based network for meteorological sensing and weather forecast calculations
Directory of Open Access Journals (Sweden)
A. Vas
2012-06-01
Full Text Available Weather forecasting needs a lot of computing power. It is generally accomplished by using supercomputers which are expensive to rent and to maintain. In addition, weather services also have to maintain radars, balloons and pay for worldwide weather data measured by stations and satellites. Weather forecasting computations usually consist of solving differential equations based on the measured parameters. To do that, the computer uses the data of close and distant neighbor points. Accordingly, if small-sized weather stations, which are capable of making measurements, calculations and communication, are connected through the Internet, then they can be used to run weather forecasting calculations like a supercomputer does. It doesn’t need any central server to achieve this, because this network operates as a distributed system. We chose Microchip’s PIC18 microcontroller (μC platform in the implementation of the hardware, and the embedded software uses the TCP/IP Stack v5.41 provided by Microchip.
Directory of Open Access Journals (Sweden)
Chang Wook Jeong
Full Text Available OBJECTIVES: We developed a mobile application-based Seoul National University Prostate Cancer Risk Calculator (SNUPC-RC that predicts the probability of prostate cancer (PC at the initial prostate biopsy in a Korean cohort. Additionally, the application was validated and subjected to head-to-head comparisons with internet-based Western risk calculators in a validation cohort. Here, we describe its development and validation. PATIENTS AND METHODS: As a retrospective study, consecutive men who underwent initial prostate biopsy with more than 12 cores at a tertiary center were included. In the development stage, 3,482 cases from May 2003 through November 2010 were analyzed. Clinical variables were evaluated, and the final prediction model was developed using the logistic regression model. In the validation stage, 1,112 cases from December 2010 through June 2012 were used. SNUPC-RC was compared with the European Randomized Study of Screening for PC Risk Calculator (ERSPC-RC and the Prostate Cancer Prevention Trial Risk Calculator (PCPT-RC. The predictive accuracy was assessed using the area under the receiver operating characteristic curve (AUC. The clinical value was evaluated using decision curve analysis. RESULTS: PC was diagnosed in 1,240 (35.6% and 417 (37.5% men in the development and validation cohorts, respectively. Age, prostate-specific antigen level, prostate size, and abnormality on digital rectal examination or transrectal ultrasonography were significant factors of PC and were included in the final model. The predictive accuracy in the development cohort was 0.786. In the validation cohort, AUC was significantly higher for the SNUPC-RC (0.811 than for ERSPC-RC (0.768, p<0.001 and PCPT-RC (0.704, p<0.001. Decision curve analysis also showed higher net benefits with SNUPC-RC than with the other calculators. CONCLUSIONS: SNUPC-RC has a higher predictive accuracy and clinical benefit than Western risk calculators. Furthermore, it is easy
Luef, Birgit; Luef, Franz; Peduzzi, Peter
2009-01-01
Assessing viral production (VP) requires robust methodological settings combined with precise mathematical calculations. This contribution improves and standardizes mathematical calculations of VP and the assessment of the proportion of lysogenic cells in a sample. We present an online tool ‘Viral Production Calculator’ (vipcal, http://www.univie.ac.at/nuhag-php/vipcal) that calculates lytic production and the percentage of lysogenic cells based on data obtained from a viral reduction approac...
Calculation of RBE for normal tissue complications based on charged particle track structure
International Nuclear Information System (INIS)
A new approach for the calculation of RBE for normal tissue complications after charged particle and neutron irradiation is discussed. It is based on the extension of a model originally developed for the application to cell survival. It can be shown, that according to the model RBE values are determined largely by the α/β-ratio of the photon dose response curve, but are expected to be nearly independent of the absolute values of α and β. Thus, the model can be applied to normal tissue complications as well, where α/β-ratios can be determined by means of fractionation experiments. Agreement of model predictions and experimental results obtained in animal experiments confirm the appliability of the model even in the case of complex biological endpoints. (orig.)
Angenendt, Knut; Johansson, Patrik
2011-06-23
The solvation of lithium salts in ionic liquids (ILs) leads to the creation of a lithium ion carrying species quite different from those found in traditional nonaqueous lithium battery electrolytes. The most striking differences are that these species are composed only of ions and in general negatively charged. In many IL-based electrolytes, the dominant species are triplets, and the charge, stability, and size of the triplets have a large impact on the total ion conductivity, the lithium ion mobility, and also the lithium ion delivery at the electrode. As an inherent advantage, the triplets can be altered by selecting lithium salts and ionic liquids with different anions. Thus, within certain limits, the lithium ion carrying species can even be tailored toward distinct important properties for battery application. Here, we show by DFT calculations that the resulting charge carrying species from combinations of ionic liquids and lithium salts and also some resulting electrolyte properties can be predicted. PMID:21591707
Calculation of watershed flow concentration based on the grid drop concept
Institute of Scientific and Technical Information of China (English)
Rui Xiaofang; Yu Mei; Liu Fanggui; Gong Xinglong
2008-01-01
The grid drop concept is introduced and used to develop a micromechanism-based methodology for calculating watershed flow concentration. The flow path and distance traveled by a grid drop to the outlet of the watershed are obtained using a digital elevation model (DEM). Regarding the slope as an uneven carpet through which the grid drop passes, a formula for overland flow velocity differing from Manning's formula for stream flow as well as Darcy's formula for pore flow is proposed. Compared with the commonly used unit hydrograph and isochronal methods, this new methodology has outstanding advantages in that it considers the influences of the slope velocity field and the heterogeneity of spatial distribution of rainfall on the flow concentration process, and includes only one parameter that needs to be calibrated. This method can also be effectively applied to the prediction of hydrologic processes in un-gauged basins.
The solar silicon abundance based on 3D non-LTE calculations
Amarsi, A M
2016-01-01
We present three-dimensional (3D) non-local thermodynamic equilibrium (non-LTE) radiative transfer calculations for silicon in the solar photosphere, using an extensive model atom that includes recent, realistic neutral hydrogen collisional cross-sections. We find that photon losses in the SiI lines give rise to slightly negative non-LTE abundance corrections of the order -0.01 dex. We infer a 3D non-LTE based solar silicon abundance of 7.51 dex. With silicon commonly chosen to be the anchor between the photospheric and meteoritic abundances, we find that the meteoritic abundance scale remains unchanged compared with the Asplund et al. (2009) and Lodders et al. (2009) results.
International Nuclear Information System (INIS)
The decay products of 232U produced in the thorium-uranium fuel cycle emit high energy γ-rays. This affects the fuel cycle greatly. In this paper, the 232U productions in thermal reactor using thorium fuel are analyzed by ORIGEN2, SCALE5 and the code based on the Bateman method. Under normal situation, 232U is mainly produced by 232Th (n, 2n) reaction chain, and more quantity of 230Th can be transformed into 232U while the neutron spectrum is softer. The burnup calculation of CANDU reactor and PWR assembly indicates that the 232U in uranium increase with the burnup, and 230Th in fresh thorium has linear correlation with 232U/Utotal or 232U/233U at discharge burnup. (authors)
A MEMS Dielectric Affinity Glucose Biosensor.
Huang, Xian; Li, Siqi; Davis, Erin; Li, Dachao; Wang, Qian; Lin, Qiao
2013-06-20
Continuous glucose monitoring (CGM) sensors based on affinity detection are desirable for long-term and stable glucose management. However, most affinity sensors contain mechanical moving structures and complex design in sensor actuation and signal readout, limiting their reliability in subcutaneously implantable glucose detection. We have previously demonstrated a proof-of-concept dielectric glucose sensor that measured pre-mixed glucose-sensitive polymer solutions at various glucose concentrations. This sensor features simplicity in sensor design, and possesses high specificity and accuracy in glucose detection. However, lack of glucose diffusion passage, this device is unable to fulfill real-time in-vivo monitoring. As a major improvement to this device, we present in this paper a fully implantable MEMS dielectric affinity glucose biosensor that contains a perforated electrode embedded in a suspended diaphragm. This capacitive-based sensor contains no moving parts, and enables glucose diffusion and real-time monitoring. The experimental results indicate that this sensor can detect glucose solutions at physiological concentrations and possesses good reversibility and reliability. This sensor has a time constant to glucose concentration change at approximately 3 min, which is comparable to commercial systems. The sensor has potential applications in fully implantable CGM that require excellent long-term stability and reliability. PMID:24511215
Chasing polys: Interdisciplinary affinity and its connection to physics identity
Scott, Tyler D.
This research is based on two motivations that merge by means of the frameworks of interdisciplinary affinity and physics identity. First, a goal of education is to develop interdisciplinary abilities in students' thinking and work. But an often ignored factor is students interests and beliefs about being interdisciplinary. Thus, this work develops and uses a framework called interdisciplinary affinity. It encompasses students interests in making connections across disciplines and their beliefs about their abilities to make those connections. The second motivation of this research is to better understand how to engage more students with physics. Physics identity describes how a student sees themselves in relation to physics. By understanding how physics identity is developed, researchers and educators can identify factors that increase interest and engagement in physics classrooms. Therefore, physics identity was used in conjunction with interdisciplinary affinity. Using a mixed methods approach, this research used quantitative data to identify the relationships interdisciplinary affinity has with physics identity and the physics classroom. These connections were explored in more detail using a case study of three students in a high school physics class. Results showed significant and positive relationships between interdisciplinary affinity and physics identity, including the individual interest and recognition components of identity. It also identified characteristics of physics classrooms that had a significant, positive relationship with interdisciplinary affinity. The qualitative case study highlighted the importance of student interest to the relationship between interdisciplinary affinity and physics identity. It also identified interest and mastery orientation as key to understanding the link between interdisciplinary affinity and the physics classroom. These results are a positive sign that by understanding interdisciplinary affinity and physics identity
A cultural study of a science classroom and graphing calculator-based technology
Casey, Dennis Alan
Social, political, and technological events of the past two decades have had considerable bearing on science education. While sociological studies of scientists at work have seriously questioned traditional histories of science, national and state educational systemic reform initiatives have been enacted, stressing standards and accountability. Recently, powerful instructional technologies have become part of the landscape of the classroom. One example, graphing calculator-based technology, has found its way from commercial and domestic applications into the pedagogy of science and math education. The purpose of this study was to investigate the culture of an "alternative" science classroom and how it functions with graphing calculator-based technology. Using ethnographic methods, a case study of one secondary, team-taught, Environmental/Physical Science (EPS) classroom was conducted. Nearly half of the 23 students were identified as students with special education needs. Over a four-month period, field data was gathered from written observations, videotaped interactions, audio taped interviews, and document analyses to determine how technology was used and what meaning it had for the participants. Analysis indicated that the technology helped to keep students from getting frustrated with handling data and graphs. In a relatively short period of time, students were able to gather data, produce graphs, and to use inscriptions in meaningful classroom discussions. In addition, teachers used the technology as a means to involve and motivate students to want to learn science. By employing pedagogical skills and by utilizing a technology that might not otherwise be readily available to these students, an environment of appreciation, trust, and respect was fostered. Further, the use of technology by these teachers served to expand students' social capital---the benefits that come from an individual's social contacts, social skills, and social resources.
Institute of Scientific and Technical Information of China (English)
Ye Xiao-Qiu; Luo De-Li; Sang Ge; Ao Bing-Yun
2011-01-01
The alanates (complex aluminohydrides) have relatively high gravimetric hydrogen densities and are among the most promising solid-state hydrogen-storage materials. In this work, the electronic structures and the formation enthalpies of seven typical aluminum-based deuterides have been calculated by the plane-wave pseudopotential method,these being AID3, LiAID4, Li3AID6, BaAID5, Ba2AID7, LiMg(AID4)3 and LiMgAID6. The results show that all these compounds are large band gap insulators at 0 K with estimated band gaps from 2.31 eV in AID3 to 4.96 eV in LiMg(AID4)3. The band gaps are reduced when the coordination of Al varies from 4 to 6. Two peaks present in the valence bands are the common characteristics of aluminum-based deuterides containing AID4 subunits while three peaks are the common characteristics of those containing AID6 subunits. The electronic structures of these compounds are determined mainly by aluminum deuteride complexes (AID4 or AID6) and their mutual interactions. The predicted formation enthalpies are presented for the studied aluminum-based deuterides.
An ANN-based load model for fast transient stability calculations
Energy Technology Data Exchange (ETDEWEB)
Qian, Ai; Shrestha, G.B. [School of EEE, Nanyang Technological University (Singapore)
2006-01-15
Load models play an important role in the simulation and calculation of power system performance. This paper presents a new load model which is based on a particular form of artificial neural networks we call adaptive back-propagation (ABP) network. ABP has can overcome some of short-comings of common back-propagation (BP) and ABP load models offer many advantages over traditional load models as they are non-structural and can be derived quickly. The application of the method in modeling loads is illustrated using actual field test data. The load models so obtained are shown to replicate the test measurements more closely than that based on traditional load models. Further extension of the method for the identification of the parameters of the traditional load models is proposed. It is based on linear back-propagation (LBP) network. The proposed LBP load model is incorporated in a transient stability program to show that the computational time is significantly reduced. (author)
A Quadrilateral Element-based Method for Calculation of Multi-scale Temperature Field
Institute of Scientific and Technical Information of China (English)
Sun Zhigang; Zhou Chaoxian; Gao Xiguang; Song Yingdong
2010-01-01
In the analysis of functionally graded materials (FGMs),the uncoupled approach is used broadly,which is based on homogenized material property and ignores the effect of local micro-structural interaction.The higher-order theory for FGMs (HOTFGM) is a coupled approach that explicitly takes the effect of micro-structural gradation and the local interaction of the spatially variable inclusion phase into account.Based on the HOTFGM,this article presents a quadrilateral element-based method for the calculation of multi-scale temperature field (QTF).In this method,the discrete cells are quadrilateral including rectangular while the surface-averaged quantities are the primary variables which replace the coefficients employed in the tem-perature function.In contrast with the HOTFGM,this method improves the efficiency,eliminates the restriction of being rectangular cells and expands the solution scale.The presented results illustrate the efficiency of the QTF and its advantages in analyzing FGMs.
Preliminary study on CAD-based method of characteristics for neutron transport calculation
Chen, Zhen-Ping; Sun, Guang-Yao; Song, Jing; Hao, Li-Juan; Hu, Li-Qin; Wu, Yi-Can
2013-01-01
The method of characteristics (MOC) is widely used for neutron transport calculation in recent decades. However, the key problem determining whether MOC can be applied in highly heterogeneous geometry is how to combine an effective geometry modeling method with it. Most of the existing MOC codes conventionally describe the geometry model just by lines and arcs with extensive input data. Thus they have difficulty in geometry modeling and ray tracing for complicated geometries. In this study, a new method making use of a CAD-based automatic modeling tool MCAM which is a CAD/Image-based Automatic Modeling Program for Neutronics and Radiation Transport developed by FDS Team in China was introduced for geometry modeling and ray tracing of particle transport to remove those limitations. The diamond -difference scheme was applied to MOC to reduce the spatial discretization errors of the flat flux approximation. Based on MCAM and MOC, a new MOC code was developed and integrated into SuperMC system, whic h is a Super ...
Energy Technology Data Exchange (ETDEWEB)
Zhao, Ying; Hammoudeh, Dalia; Yun, Mi-Kyung; Qi, Jianjun; White, Stephen W.; Lee, Richard E. (Tennessee-HSC); (SJCH)
2012-05-29
Dihydropteroate synthase (DHPS) is the validated drug target for sulfonamide antimicrobial therapy. However, due to widespread drug resistance and poor tolerance, the use of sulfonamide antibiotics is now limited. The pterin binding pocket in DHPS is highly conserved and is distinct from the sulfonamide binding site. It therefore represents an attractive alternative target for the design of novel antibacterial agents. We previously carried out the structural characterization of a known pyridazine inhibitor in the Bacillus anthracis DHPS pterin site and identified a number of unfavorable interactions that appear to compromise binding. With this structural information, a series of 4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazines were designed to improve binding affinity. Most importantly, the N-methyl ring substitution was removed to improve binding within the pterin pocket, and the length of the side chain carboxylic acid was optimized to fully engage the pyrophosphate binding site. These inhibitors were synthesized and evaluated by an enzyme activity assay, X-ray crystallography, isothermal calorimetry, and surface plasmon resonance to obtain a comprehensive understanding of the binding interactions from structural, kinetic, and thermodynamic perspectives. This study clearly demonstrates that compounds lacking the N-methyl substitution exhibit increased inhibition of DHPS, but the beneficial effects of optimizing the side chain length are less apparent.
Directory of Open Access Journals (Sweden)
R. Frandoloso
2013-01-01
Full Text Available The expression of chemokines (CCL-2 and CXCL-8 and cytokines (IL-1α, IL-1β, IL-6, TNF-α, and IL-10 was evaluated by RT-qPCR in colostrum-deprived pigs vaccinated and challenged with Haemophilus parasuis serovar 5. Two vaccines containing native proteins with affinity to porcine transferrin (NPAPTim and NPAPTit were tested, along with two control groups: one inoculated with PBS instead of antigen (challenge group (CHG, and another one nonimmunized and noninfected (blank group. The use of NPAPTim and NPAPTit resulted in complete protection against H. parasuis (no clinical signs and/or lesions, and both vaccines were capable of avoiding the expression of the proinflammatory molecules to levels similar to physiological values in blank group. However, overexpression of all proinflammatory molecules was observed in CHG group, mainly in the target infection tissues (brain, lungs, and spleen. High expression of CCL-2, CXCL-8, IL-1α, IL-1β, and IL-6 can be considered one of the characteristics of H. parasuis infection by serovar 5.
Dolgounitcheva, O; Díaz-Tinoco, Manuel; Zakrzewski, V G; Richard, Ryan M; Marom, Noa; Sherrill, C David; Ortiz, J V
2016-02-01
Comparison of ab initio electron-propagator predictions of vertical ionization potentials and electron affinities of organic, acceptor molecules with benchmark calculations based on the basis set-extrapolated, coupled cluster single, double, and perturbative triple substitution method has enabled identification of self-energy approximations with mean, unsigned errors between 0.1 and 0.2 eV. Among the self-energy approximations that neglect off-diagonal elements in the canonical, Hartree-Fock orbital basis, the P3 method for electron affinities, and the P3+ method for ionization potentials provide the best combination of accuracy and computational efficiency. For approximations that consider the full self-energy matrix, the NR2 methods offer the best performance. The P3+ and NR2 methods successfully identify the correct symmetry label of the lowest cationic state in two cases, naphthalenedione and benzoquinone, where some other methods fail. PMID:26730459
Affinity- and topology-dependent bound on current fluctuations
Pietzonka, Patrick; Seifert, Udo
2016-01-01
We provide a proof of a recently conjectured universal bound on current fluctuations in Markovian processes. This bound establishes a link between the fluctuations of an individual observable current, the cycle affinities driving the system into a non-equilibrium steady state, and the topology of the network. The proof is based on a decomposition of the network into independent cycles with both positive affinity and positive stationary cycle current. This formalism allows for a refinement of the bound for systems in equilibrium or with locally vanishing affinities.
Design of Pd-Based Bimetallic Catalysts for ORR: A DFT Calculation Study
Directory of Open Access Journals (Sweden)
Lihui Ou
2015-01-01
Full Text Available Developing Pd-lean catalysts for oxygen reduction reaction (ORR is the key for large-scale application of proton exchange membrane fuel cells (PEMFCs. In the present paper, we have proposed a multiple-descriptor strategy for designing efficient and durable ORR Pd-based alloy catalysts. We demonstrated that an ideal Pd-based bimetallic alloy catalyst for ORR should possess simultaneously negative alloy formation energy, negative surface segregation energy of Pd, and a lower oxygen binding ability than pure Pt. By performing detailed DFT calculations on the thermodynamics, surface chemistry and electronic properties of Pd-M alloys, Pd-V, Pd-Fe, Pd-Zn, Pd-Nb, and Pd-Ta, are identified theoretically to have stable Pd segregated surface and improved ORR activity. Factors affecting these properties are analyzed. The alloy formation energy of Pd with transition metals M can be mainly determined by their electron interaction. This may be the origin of the negative alloy formation energy for Pd-M alloys. The surface segregation energy of Pd is primarily determined by the surface energy and the atomic radius of M. The metals M which have smaller atomic radius and higher surface energy would tend to favor the surface segregation of Pd in corresponding Pd-M alloys.
Egami, Yoshiyuki; Iwase, Shigeru; Tsukamoto, Shigeru; Ono, Tomoya; Hirose, Kikuji
2015-09-01
We develop a first-principles electron-transport simulator based on the Lippmann-Schwinger (LS) equation within the framework of the real-space finite-difference scheme. In our fully real-space-based LS (grid LS) method, the ratio expression technique for the scattering wave functions and the Green's function elements of the reference system is employed to avoid numerical collapse. Furthermore, we present analytical expressions and/or prominent calculation procedures for the retarded Green's function, which are utilized in the grid LS approach. In order to demonstrate the performance of the grid LS method, we simulate the electron-transport properties of the semiconductor-oxide interfaces sandwiched between semi-infinite jellium electrodes. The results confirm that the leakage current through the (001)Si-SiO_{2} model becomes much larger when the dangling-bond state is induced by a defect in the oxygen layer, while that through the (001)Ge-GeO_{2} model is insensitive to the dangling bond state. PMID:26465580
Monte Carlo calculation based on hydrogen composition of the tissue for MV photon radiotherapy.
Demol, Benjamin; Viard, Romain; Reynaert, Nick
2015-01-01
The purpose of this study was to demonstrate that Monte Carlo treatment planning systems require tissue characterization (density and composition) as a function of CT number. A discrete set of tissue classes with a specific composition is introduced. In the current work we demonstrate that, for megavoltage photon radiotherapy, only the hydrogen content of the different tissues is of interest. This conclusion might have an impact on MRI-based dose calculations and on MVCT calibration using tissue substitutes. A stoichiometric calibration was performed, grouping tissues with similar atomic composition into 15 dosimetrically equivalent subsets. To demonstrate the importance of hydrogen, a new scheme was derived, with correct hydrogen content, complemented by oxygen (all elements differing from hydrogen are replaced by oxygen). Mass attenuation coefficients and mass stopping powers for this scheme were calculated and compared to the original scheme. Twenty-five CyberKnife treatment plans were recalculated by an in-house developed Monte Carlo system using tissue density and hydrogen content derived from the CT images. The results were compared to Monte Carlo simulations using the original stoichiometric calibration. Between 300 keV and 3 MeV, the relative difference of mass attenuation coefficients is under 1% within all subsets. Between 10 keV and 20 MeV, the relative difference of mass stopping powers goes up to 5% in hard bone and remains below 2% for all other tissue subsets. Dose-volume histograms (DVHs) of the treatment plans present no visual difference between the two schemes. Relative differences of dose indexes D98, D95, D50, D05, D02, and Dmean were analyzed and a distribution centered around zero and of standard deviation below 2% (3 σ) was established. On the other hand, once the hydrogen content is slightly modified, important dose differences are obtained. Monte Carlo dose planning in the field of megavoltage photon radiotherapy is fully achievable using
He, Ling; Jia, Qi-jian; Li, Chao; Xu, Hao
2016-01-01
The rapid development of coastal economy in Hebei Province caused rapid transition of coastal land use structure, which has threatened land ecological security. Therefore, calculating ecosystem service value of land use and exploring ecological security baseline can provide the basis for regional ecological protection and rehabilitation. Taking Huanghua, a city in the southeast of Hebei Province, as an example, this study explored the joint point, joint path and joint method between ecological security and food security, and then calculated the ecological security baseline of Huanghua City based on the ecosystem service value and the food safety standard. The results showed that ecosystem service value of per unit area from maximum to minimum were in this order: wetland, water, garden, cultivated land, meadow, other land, salt pans, saline and alkaline land, constructive land. The order of contribution rates of each ecological function value from high to low was nutrient recycling, water conservation, entertainment and culture, material production, biodiversity maintenance, gas regulation, climate regulation and environmental purification. The security baseline of grain production was 0.21 kg · m⁻², the security baseline of grain output value was 0.41 yuan · m⁻², the baseline of ecosystem service value was 21.58 yuan · m⁻², and the total of ecosystem service value in the research area was 4.244 billion yuan. In 2081 the ecological security will reach the bottom line and the ecological system, in which human is the subject, will be on the verge of collapse. According to the ecological security status, Huanghua can be divided into 4 zones, i.e., ecological core protection zone, ecological buffer zone, ecological restoration zone and human activity core zone. PMID:27228612
He, Ling; Jia, Qi-jian; Li, Chao; Xu, Hao
2016-01-01
The rapid development of coastal economy in Hebei Province caused rapid transition of coastal land use structure, which has threatened land ecological security. Therefore, calculating ecosystem service value of land use and exploring ecological security baseline can provide the basis for regional ecological protection and rehabilitation. Taking Huanghua, a city in the southeast of Hebei Province, as an example, this study explored the joint point, joint path and joint method between ecological security and food security, and then calculated the ecological security baseline of Huanghua City based on the ecosystem service value and the food safety standard. The results showed that ecosystem service value of per unit area from maximum to minimum were in this order: wetland, water, garden, cultivated land, meadow, other land, salt pans, saline and alkaline land, constructive land. The order of contribution rates of each ecological function value from high to low was nutrient recycling, water conservation, entertainment and culture, material production, biodiversity maintenance, gas regulation, climate regulation and environmental purification. The security baseline of grain production was 0.21 kg · m⁻², the security baseline of grain output value was 0.41 yuan · m⁻², the baseline of ecosystem service value was 21.58 yuan · m⁻², and the total of ecosystem service value in the research area was 4.244 billion yuan. In 2081 the ecological security will reach the bottom line and the ecological system, in which human is the subject, will be on the verge of collapse. According to the ecological security status, Huanghua can be divided into 4 zones, i.e., ecological core protection zone, ecological buffer zone, ecological restoration zone and human activity core zone.
GIS supported calculations of (137)Cs deposition in Sweden based on precipitation data.
Almgren, Sara; Nilsson, Elisabeth; Erlandsson, Bengt; Isaksson, Mats
2006-09-15
It is of interest to know the spatial variation and the amount of (137)Cs e.g. in case of an accident with a radioactive discharge. In this study, the spatial distribution of the quarterly (137)Cs deposition over Sweden due to nuclear weapons fallout (NWF) during the period 1962-1966 was determined by relating the measured deposition density at a reference site to the amount of precipitation. Measured quarterly values of (137)Cs deposition density per unit precipitation at three reference sites and quarterly precipitation at 62 weather stations distributed over Sweden were used in the calculations. The reference sites were assumed to represent areas with different quarterly mean precipitation. The extent of these areas was determined from the distribution of the mean measured precipitation between 1961 and 1990 and varied according to seasonal variations in the mean precipitation pattern. Deposition maps were created by interpolation within a geographical information system (GIS). Both integrated (total) and cumulative (decay corrected) deposition densities were calculated. The lowest levels of NWF (137)Cs deposition density were noted in north-eastern and eastern parts of Sweden and the highest levels in the western parts of Sweden. Furthermore the deposition density of (137)Cs, resulting from the Chernobyl accident was determined for an area in western Sweden based on precipitation data. The highest levels of Chernobyl (137)Cs in western Sweden were found in the western parts of the area along the coast and the lowest in the east. The sum of the deposition densities from NWF and Chernobyl in western Sweden was then compared to the total activity measured in soil samples at 27 locations. Comparisons between the predicted values of this study show a good agreement with measured values and other studies. PMID:16647743
Institute of Scientific and Technical Information of China (English)
TANG Yi; FANG Yong-li; YANG Luo; SUN Yu-xin; YU Zheng-hua
2012-01-01
A new accurate calculation method of electric power harmonic parameters was presented.Based on the delay time theorem of Fourier transform,the frequency of the electric power was calculated,and then,suing interpolation in the frequency domain of the windows,the parameters (amplitude and phase) of each harmonic frequency signals were calculated accurately.In the paper,the effect of the delay time and the windows on the electric power harmonic calculation accuracy was analysed.The digital simulation and the physical measurement tests show that the proposed method is effective and has more advantages than other methods which are based on multipoint interpolation especially in calculation time cost; therefore,it is very suitable to be used in the single chip DSP micro-processor.
Design calculations of a D(d,n) reaction based PGNAA set up
International Nuclear Information System (INIS)
An accelerator-based Prompt Gamma Ray Neutron Activation Analysis (PGNAA) setup has been developed at 350 keV Accelerator Laboratory of Center of King Fahd University of Petroleum and Minerals (KFUPM) for the analysis of cement samples. The setup mainly consists of a cylindrical cement sample holder enclosed in a cylindrical high density polyethylene moderator and placed between a γ--ray detector and a 2.8 MeV neutrons source. The 2.8 MeV neutrons are moderated in the moderator to thermal energies and are captured by the cement sample atoms. The prompt γ--ray emitted by cement sample nuclei are detected by a NaI detector to determine the concentration of each elements of interest. The design of the setup was obtained through Monte Carlo simulations of a 2.8 MeV neutron based PGNAA setup for elemental analysis of the cement samples. The simulations were conducted to optimize the size of the moderator, sample and detector shielding to obtain maximum yield of prompt γ--ray at the detector. In order to verify the results of design calculations, thermal neutron intensity and prompt γ--ray yield was measured using the PGNAA facility. In both the studies a pulsed 200 keV deuteron beam with 5 ns width and 30 kHz repetition rate was used to produce 2.8 MeV neutrons via D(d,n) reaction. The thermal neutron intensity was measured as a function of thickness of the moderator. The thermal neutrons measurements were carried out using Nuclear Track Detectors (NTD). A good agreement has been found between the results of thermal neutron intensity measurements and Monte Carlo calculations. Finally, a prompt γ-ray spectrum was acquired from a Portland cement sample using a 25.4 cm x 25.4 cm (diameter x thickness) NaI detector. Well resolved peaks of prompt γ-ray from thermal capture of neutrons in calcium, silicon, and iron were detected indicating satisfactory performance of the PGNAA facility. (Author)
Comparison of CT number calibration techniques for CBCT-based dose calculation
Energy Technology Data Exchange (ETDEWEB)
Dunlop, Alex [The Royal Marsden NHS Foundation Trust, Joint Department of Physics, Institute of Cancer Research, London (United Kingdom); The Royal Marsden Hospital, Sutton, Surrey, Downs Road (United Kingdom); McQuaid, Dualta; Nill, Simeon; Hansen, Vibeke N.; Oelfke, Uwe [The Royal Marsden NHS Foundation Trust, Joint Department of Physics, Institute of Cancer Research, London (United Kingdom); Murray, Julia; Bhide, Shreerang; Harrington, Kevin [The Royal Marsden Hospital, Sutton, Surrey, Downs Road (United Kingdom); The Institute of Cancer Research, London (United Kingdom); Poludniowski, Gavin [Karolinska University Hospital, Department of Medical Physics, Stockholm (Sweden); Nutting, Christopher [The Institute of Cancer Research, London (United Kingdom); Newbold, Kate [The Royal Marsden Hospital, Sutton, Surrey, Downs Road (United Kingdom)
2015-12-15
The aim of this work was to compare and validate various computed tomography (CT) number calibration techniques with respect to cone beam CT (CBCT) dose calculation accuracy. CBCT dose calculation accuracy was assessed for pelvic, lung, and head and neck (H and N) treatment sites for two approaches: (1) physics-based scatter correction methods (CBCT{sub r}); (2) density override approaches including assigning water density to the entire CBCT (W), assignment of either water or bone density (WB), and assignment of either water or lung density (WL). Methods for CBCT density assignment within a commercially available treatment planning system (RS{sub auto}), where CBCT voxels are binned into six density levels, were assessed and validated. Dose-difference maps and dose-volume statistics were used to compare the CBCT dose distributions with the ground truth of a planning CT acquired the same day as the CBCT. For pelvic cases, all CTN calibration methods resulted in average dose-volume deviations below 1.5 %. RS{sub auto} provided larger than average errors for pelvic treatments for patients with large amounts of adipose tissue. For H and N cases, all CTN calibration methods resulted in average dose-volume differences below 1.0 % with CBCT{sub r} (0.5 %) and RS{sub auto} (0.6 %) performing best. For lung cases, WL and RS{sub auto} methods generated dose distributions most similar to the ground truth. The RS{sub auto} density override approach is an attractive option for CTN adjustments for a variety of anatomical sites. RS{sub auto} methods were validated, resulting in dose calculations that were consistent with those calculated on diagnostic-quality CT images, for CBCT images acquired of the lung, for patients receiving pelvic RT in cases without excess adipose tissue, and for H and N cases. (orig.) [German] Ziel dieser Arbeit ist der Vergleich und die Validierung mehrerer CT-Kalibrierungsmethoden zur Dosisberechnung auf der Grundlage von Kegelstrahlcomputertomographie
Energy Technology Data Exchange (ETDEWEB)
Mikell, Justin K. [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas (United States); Klopp, Ann H. [Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Gonzalez, Graciela M.N. [Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Kisling, Kelly D. [Department of Radiation Physics-Patient Care, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas (United States); Price, Michael J. [Department of Physics and Astronomy, Louisiana State University and Agricultural and Mechanical College, Baton Rouge, Louisiana, and Mary Bird Perkins Cancer Center, Baton Rouge, Louisiana (United States); Berner, Paula A. [Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Eifel, Patricia J. [Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Mourtada, Firas, E-mail: fmourtad@christianacare.org [Department of Radiation Physics-Patient Care, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Department of Experimental Diagnostic Imaging, University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Department of Radiation Oncology, Helen F. Graham Cancer Center, Newark, Delaware (United States)
2012-07-01
Purpose: To investigate the dosimetric impact of the heterogeneity dose calculation Acuros (Transpire Inc., Gig Harbor, WA), a grid-based Boltzmann equation solver (GBBS), for brachytherapy in a cohort of cervical cancer patients. Methods and Materials: The impact of heterogeneities was retrospectively assessed in treatment plans for 26 patients who had previously received {sup 192}Ir intracavitary brachytherapy for cervical cancer with computed tomography (CT)/magnetic resonance-compatible tandems and unshielded colpostats. The GBBS models sources, patient boundaries, applicators, and tissue heterogeneities. Multiple GBBS calculations were performed with and without solid model applicator, with and without overriding the patient contour to 1 g/cm{sup 3} muscle, and with and without overriding contrast materials to muscle or 2.25 g/cm{sup 3} bone. Impact of source and boundary modeling, applicator, tissue heterogeneities, and sensitivity of CT-to-material mapping of contrast were derived from the multiple calculations. American Association of Physicists in Medicine Task Group 43 (TG-43) guidelines and the GBBS were compared for the following clinical dosimetric parameters: Manchester points A and B, International Commission on Radiation Units and Measurements (ICRU) report 38 rectal and bladder points, three and nine o'clock, and {sub D2cm3} to the bladder, rectum, and sigmoid. Results: Points A and B, D{sub 2} cm{sup 3} bladder, ICRU bladder, and three and nine o'clock were within 5% of TG-43 for all GBBS calculations. The source and boundary and applicator account for most of the differences between the GBBS and TG-43 guidelines. The D{sub 2cm3} rectum (n = 3), D{sub 2cm3} sigmoid (n = 1), and ICRU rectum (n = 6) had differences of >5% from TG-43 for the worst case incorrect mapping of contrast to bone. Clinical dosimetric parameters were within 5% of TG-43 when rectal and balloon contrast were mapped to bone and radiopaque packing was not overridden
International Nuclear Information System (INIS)
Purpose: To investigate the dosimetric impact of the heterogeneity dose calculation Acuros (Transpire Inc., Gig Harbor, WA), a grid-based Boltzmann equation solver (GBBS), for brachytherapy in a cohort of cervical cancer patients. Methods and Materials: The impact of heterogeneities was retrospectively assessed in treatment plans for 26 patients who had previously received 192Ir intracavitary brachytherapy for cervical cancer with computed tomography (CT)/magnetic resonance-compatible tandems and unshielded colpostats. The GBBS models sources, patient boundaries, applicators, and tissue heterogeneities. Multiple GBBS calculations were performed with and without solid model applicator, with and without overriding the patient contour to 1 g/cm3 muscle, and with and without overriding contrast materials to muscle or 2.25 g/cm3 bone. Impact of source and boundary modeling, applicator, tissue heterogeneities, and sensitivity of CT-to-material mapping of contrast were derived from the multiple calculations. American Association of Physicists in Medicine Task Group 43 (TG-43) guidelines and the GBBS were compared for the following clinical dosimetric parameters: Manchester points A and B, International Commission on Radiation Units and Measurements (ICRU) report 38 rectal and bladder points, three and nine o’clock, and D2cm3 to the bladder, rectum, and sigmoid. Results: Points A and B, D2 cm3 bladder, ICRU bladder, and three and nine o’clock were within 5% of TG-43 for all GBBS calculations. The source and boundary and applicator account for most of the differences between the GBBS and TG-43 guidelines. The D2cm3 rectum (n = 3), D2cm3 sigmoid (n = 1), and ICRU rectum (n = 6) had differences of >5% from TG-43 for the worst case incorrect mapping of contrast to bone. Clinical dosimetric parameters were within 5% of TG-43 when rectal and balloon contrast were mapped to bone and radiopaque packing was not overridden. Conclusions: The GBBS has minimal impact on clinical
Energy Technology Data Exchange (ETDEWEB)
Lesperance, Marielle; Inglis-Whalen, M.; Thomson, R. M., E-mail: rthomson@physics.carleton.ca [Carleton Laboratory for Radiotherapy Physics, Department of Physics, Carleton University, Ottawa K1S 5B6 (Canada)
2014-02-15
Purpose : To investigate the effects of the composition and geometry of ocular media and tissues surrounding the eye on dose distributions for COMS eye plaque brachytherapy with{sup 125}I, {sup 103}Pd, or {sup 131}Cs seeds, and to investigate doses to ocular structures. Methods : An anatomically and compositionally realistic voxelized eye model with a medial tumor is developed based on a literature review. Mass energy absorption and attenuation coefficients for ocular media are calculated. Radiation transport and dose deposition are simulated using the EGSnrc Monte Carlo user-code BrachyDose for a fully loaded COMS eye plaque within a water phantom and our full eye model for the three radionuclides. A TG-43 simulation with the same seed configuration in a water phantom neglecting the plaque and interseed effects is also performed. The impact on dose distributions of varying tumor position, as well as tumor and surrounding tissue media is investigated. Each simulation and radionuclide is compared using isodose contours, dose volume histograms for the lens and tumor, maximum, minimum, and average doses to structures of interest, and doses to voxels of interest within the eye. Results : Mass energy absorption and attenuation coefficients of the ocular media differ from those of water by as much as 12% within the 20–30 keV photon energy range. For all radionuclides studied, average doses to the tumor and lens regions in the full eye model differ from those for the plaque in water by 8%–10% and 13%–14%, respectively; the average doses to the tumor and lens regions differ between the full eye model and the TG-43 simulation by 2%–17% and 29%–34%, respectively. Replacing the surrounding tissues in the eye model with water increases the maximum and average doses to the lens by 2% and 3%, respectively. Substituting the tumor medium in the eye model for water, soft tissue, or an alternate melanoma composition affects tumor dose compared to the default eye model
International Nuclear Information System (INIS)
Purpose : To investigate the effects of the composition and geometry of ocular media and tissues surrounding the eye on dose distributions for COMS eye plaque brachytherapy with125I, 103Pd, or 131Cs seeds, and to investigate doses to ocular structures. Methods : An anatomically and compositionally realistic voxelized eye model with a medial tumor is developed based on a literature review. Mass energy absorption and attenuation coefficients for ocular media are calculated. Radiation transport and dose deposition are simulated using the EGSnrc Monte Carlo user-code BrachyDose for a fully loaded COMS eye plaque within a water phantom and our full eye model for the three radionuclides. A TG-43 simulation with the same seed configuration in a water phantom neglecting the plaque and interseed effects is also performed. The impact on dose distributions of varying tumor position, as well as tumor and surrounding tissue media is investigated. Each simulation and radionuclide is compared using isodose contours, dose volume histograms for the lens and tumor, maximum, minimum, and average doses to structures of interest, and doses to voxels of interest within the eye. Results : Mass energy absorption and attenuation coefficients of the ocular media differ from those of water by as much as 12% within the 20–30 keV photon energy range. For all radionuclides studied, average doses to the tumor and lens regions in the full eye model differ from those for the plaque in water by 8%–10% and 13%–14%, respectively; the average doses to the tumor and lens regions differ between the full eye model and the TG-43 simulation by 2%–17% and 29%–34%, respectively. Replacing the surrounding tissues in the eye model with water increases the maximum and average doses to the lens by 2% and 3%, respectively. Substituting the tumor medium in the eye model for water, soft tissue, or an alternate melanoma composition affects tumor dose compared to the default eye model simulation by up to 16
DEFF Research Database (Denmark)
Petersen, Kurt Erling
1986-01-01
approaches have been introduced in some cases for the calculation of the reliability of structures or components. A new computer program has been developed based upon numerical integration in several variables. In systems reliability Monte Carlo simulation programs are used especially in analysis of very...... complex systems. In order to increase the applicability of the programs variance reduction techniques can be applied to speed up the calculation process. Variance reduction techniques have been studied and procedures for implementation of importance sampling are suggested....
Ruthenia-based electrochemical supercapacitors: insights from first-principles calculations.
Ozoliņš, Vidvuds; Zhou, Fei; Asta, Mark
2013-05-21
Electrochemical supercapacitors (ECs) have important applications in areas wherethe need for fast charging rates and high energy density intersect, including in hybrid and electric vehicles, consumer electronics, solar cell based devices, and other technologies. In contrast to carbon-based supercapacitors, where energy is stored in the electrochemical double-layer at the electrode/electrolyte interface, ECs involve reversible faradaic ion intercalation into the electrode material. However, this intercalation does not lead to phase change. As a result, ECs can be charged and discharged for thousands of cycles without loss of capacity. ECs based on hydrous ruthenia, RuO2·xH2O, exhibit some of the highest specific capacitances attained in real devices. Although RuO2 is too expensive for widespread practical use, chemists have long used it as a model material for investigating the fundamental mechanisms of electrochemical supercapacitance and heterogeneous catalysis. In this Account, we discuss progress in first-principles density-functional theory (DFT) based studies of the electronic structure, thermodynamics, and kinetics of hydrous and anhydrous RuO2. We find that DFT correctly reproduces the metallic character of the RuO2 band structure. In addition, electron-proton double-insertion into bulk RuO2 leads to the formation of a polar covalent O-H bond with a fractional increase of the Ru charge in delocalized d-band states by only 0.3 electrons. This is in slight conflict with the common assumption of a Ru valence change from Ru(4+) to Ru(3+). Using the prototype electrostatic ground state (PEGS) search method, we predict a crystalline RuOOH compound with a formation energy of only 0.15 eV per proton. The calculated voltage for the onset of bulk proton insertion in the dilute limit is only 0.1 V with respect to the reversible hydrogen electrode (RHE), in reasonable agreement with the 0.4 V threshold for a large diffusion-limited contribution measured experimentally
Calculation of Steady-State Core Thermal-Fluid Parameters Based on CORONA
Energy Technology Data Exchange (ETDEWEB)
Song, Jun Kyu; Cho, Bong Hyun; Tak, Nam-il; Jeong, Chang Joon; Jo, Chang Keun [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)
2015-10-15
CFD analysis has been successfully implemented to obtain the parameter of thermal-fluid in prismatic fuel block reactor. However it requires considerable computational power to analyze whole prismatic block core. Therefore steady-state thermal-fluid analysis code, named CORONA, has been under development in KAERI. This study aims for obtaining the thermal-fluid parameters of prismatic fuel block reactor using CORONA code and analyzing the data based on the reactor operating condition(BOC, EOC) using the core pin power obtained from DeCART code. In this paper, thermal-fluid parameters were analyzed in reactor operating condition (BOC, EOC) with CORONA code. The three representative thermal-fluid data of fuel maximum temperature, pressure drop and bypass flow rate, were calculated depending on core inlet temperature and mass flow rate. The pressure drop and bypass flow rate were increased due to rising of inlet temperature and mass flow rate. However, the maximum fuel temperature was decreased between case-1 to 5 and only the maximum fuel temperature was reacted sensitively to changing of reactor operating condition (BOC, EOC)
International Nuclear Information System (INIS)
Molecular dynamics method is used for the properties prediction of new lanthanum-strontium cuprates La2-xSrxCuO4-δ based functional materials. The most interesting phases have been synthesized, and electrophysical and thermomechanical properties have been investigated for the verification of acquired calculated data. High values of oxygen diffusion constants is demonstrated to be occurred in solid solutions La2-xSrxCuO4-δ with fine degree of substitution Sr→La (to x=1). Values of lattice parameters, thermal expansion coefficients and oxygen diffusion constants are agree with experimental data. Observed anisotropy of anion transport for all studied compositions is responsible for peculiarities of crystal structure of complex oxides. Applied molecular dynamics method permits to reveal the contribution of separate kinds of oxygen ions (equatorial and apical) in ionic transport at microscopic level, as well as really prove that the oxygen diffusion happens in the ordinary jump mechanism, mainly in (CuO2)-layers
Joint kinematic calculation based on clinical direct kinematic versus inverse kinematic gait models.
Kainz, H; Modenese, L; Lloyd, D G; Maine, S; Walsh, H P J; Carty, C P
2016-06-14
Most clinical gait laboratories use the conventional gait analysis model. This model uses a computational method called Direct Kinematics (DK) to calculate joint kinematics. In contrast, musculoskeletal modelling approaches use Inverse Kinematics (IK) to obtain joint angles. IK allows additional analysis (e.g. muscle-tendon length estimates), which may provide valuable information for clinical decision-making in people with movement disorders. The twofold aims of the current study were: (1) to compare joint kinematics obtained by a clinical DK model (Vicon Plug-in-Gait) with those produced by a widely used IK model (available with the OpenSim distribution), and (2) to evaluate the difference in joint kinematics that can be solely attributed to the different computational methods (DK versus IK), anatomical models and marker sets by using MRI based models. Eight children with cerebral palsy were recruited and presented for gait and MRI data collection sessions. Differences in joint kinematics up to 13° were found between the Plug-in-Gait and the gait 2392 OpenSim model. The majority of these differences (94.4%) were attributed to differences in the anatomical models, which included different anatomical segment frames and joint constraints. Different computational methods (DK versus IK) were responsible for only 2.7% of the differences. We recommend using the same anatomical model for kinematic and musculoskeletal analysis to ensure consistency between the obtained joint angles and musculoskeletal estimates. PMID:27139005
Fission yield calculation using toy model based on Monte Carlo simulation
Energy Technology Data Exchange (ETDEWEB)
Jubaidah, E-mail: jubaidah@student.itb.ac.id [Nuclear Physics and Biophysics Division, Department of Physics, Bandung Institute of Technology. Jl. Ganesa No. 10 Bandung – West Java, Indonesia 40132 (Indonesia); Physics Department, Faculty of Mathematics and Natural Science – State University of Medan. Jl. Willem Iskandar Pasar V Medan Estate – North Sumatera, Indonesia 20221 (Indonesia); Kurniadi, Rizal, E-mail: rijalk@fi.itb.ac.id [Nuclear Physics and Biophysics Division, Department of Physics, Bandung Institute of Technology. Jl. Ganesa No. 10 Bandung – West Java, Indonesia 40132 (Indonesia)
2015-09-30
Toy model is a new approximation in predicting fission yield distribution. Toy model assumes nucleus as an elastic toy consist of marbles. The number of marbles represents the number of nucleons, A. This toy nucleus is able to imitate the real nucleus properties. In this research, the toy nucleons are only influenced by central force. A heavy toy nucleus induced by a toy nucleon will be split into two fragments. These two fission fragments are called fission yield. In this research, energy entanglement is neglected. Fission process in toy model is illustrated by two Gaussian curves intersecting each other. There are five Gaussian parameters used in this research. They are scission point of the two curves (R{sub c}), mean of left curve (μ{sub L}) and mean of right curve (μ{sub R}), deviation of left curve (σ{sub L}) and deviation of right curve (σ{sub R}). The fission yields distribution is analyses based on Monte Carlo simulation. The result shows that variation in σ or µ can significanly move the average frequency of asymmetry fission yields. This also varies the range of fission yields distribution probability. In addition, variation in iteration coefficient only change the frequency of fission yields. Monte Carlo simulation for fission yield calculation using toy model successfully indicates the same tendency with experiment results, where average of light fission yield is in the range of 90
International Nuclear Information System (INIS)
Ship detection and classification with space-borne SAR has many potential applications within the maritime surveillance, fishery activity management, monitoring ship traffic, and military security. While ship detection techniques with SAR imagery are well established, ship classification is still an open issue. One of the main reasons may be ascribed to the difficulties on acquiring the required quantities of real data of vessels under different observation and environmental conditions with precise ground truth. Therefore, simulation of SAR images with high scenario flexibility and reasonable computation costs is compulsory for ship classification algorithms development. However, the simulation of SAR imagery of ship over sea surface is challenging. Though great efforts have been devoted to tackle this difficult problem, it is far from being conquered. This paper proposes a novel scheme for SAR imagery simulation of ship over sea surface. The simulation is implemented based on high frequency electromagnetic calculations methods of PO, MEC, PTD and GO. SAR imagery of sea clutter is modelled by the representative K-distribution clutter model. Then, the simulated SAR imagery of ship can be produced by inserting the simulated SAR imagery chips of ship into the SAR imagery of sea clutter. The proposed scheme has been validated with canonical and complex ship targets over a typical sea scene
Improvement of Power Flow Calculation with Optimization Factor Based on Current Injection Method
Directory of Open Access Journals (Sweden)
Lei Wang
2014-01-01
Full Text Available This paper presents an improvement in power flow calculation based on current injection method by introducing optimization factor. In the method proposed by this paper, the PQ buses are represented by current mismatches while the PV buses are represented by power mismatches. It is different from the representations in conventional current injection power flow equations. By using the combined power and current injection mismatches method, the number of the equations required can be decreased to only one for each PV bus. The optimization factor is used to improve the iteration process and to ensure the effectiveness of the improved method proposed when the system is ill-conditioned. To verify the effectiveness of the method, the IEEE test systems are tested by conventional current injection method and the improved method proposed separately. Then the results are compared. The comparisons show that the optimization factor improves the convergence character effectively, especially that when the system is at high loading level and R/X ratio, the iteration number is one or two times less than the conventional current injection method. When the overloading condition of the system is serious, the iteration number in this paper appears 4 times less than the conventional current injection method.
Ma, A. K.; Altaher, K.; Hussein, M. A.; Amer, M.; Farid, K. Y.; Alghamdi, A. A.
2014-02-01
In this work we will present a new set of photon fluence-to-effective dose conversion coefficients using the Saudi population-based voxel phantom developed recently by our group. The phantom corresponds to an average Saudi male of 173 cm tall weighing 77 kg. There are over 125 million voxels in the phantom each of which is 1.37×1.37×1.00 mm3. Of the 27 organs and tissues of radiological interest specified in the recommendations of ICRP Publication 103, all but the oral mucosa, extrathoracic tissue and the lymph nodes were identified in the current version of the phantom. The bone surface (endosteum) is too thin to be identifiable; it is about 10 μm thick. The dose to the endosteum was therefore approximated by the dose to the bones. Irradiation geometries included anterior-posterior (AP), left (LLAT) and rotational (ROT). The simulations were carried out with the MCNPX code version 2.5.0. The fluence in free air and the energy depositions in each organ were calculated for monoenergetic photon beams from 10 keV to 10 MeV to obtain the conversion coefficients. The radiation and tissue weighting factors were taken from ICRP Publication 60 and 103. The results from this study will also be compared with the conversion coefficients in ICRP Publication 116.
Fission yield calculation using toy model based on Monte Carlo simulation
International Nuclear Information System (INIS)
Toy model is a new approximation in predicting fission yield distribution. Toy model assumes nucleus as an elastic toy consist of marbles. The number of marbles represents the number of nucleons, A. This toy nucleus is able to imitate the real nucleus properties. In this research, the toy nucleons are only influenced by central force. A heavy toy nucleus induced by a toy nucleon will be split into two fragments. These two fission fragments are called fission yield. In this research, energy entanglement is neglected. Fission process in toy model is illustrated by two Gaussian curves intersecting each other. There are five Gaussian parameters used in this research. They are scission point of the two curves (Rc), mean of left curve (μL) and mean of right curve (μR), deviation of left curve (σL) and deviation of right curve (σR). The fission yields distribution is analyses based on Monte Carlo simulation. The result shows that variation in σ or µ can significanly move the average frequency of asymmetry fission yields. This also varies the range of fission yields distribution probability. In addition, variation in iteration coefficient only change the frequency of fission yields. Monte Carlo simulation for fission yield calculation using toy model successfully indicates the same tendency with experiment results, where average of light fission yield is in the range of 90
Calculation of saturation in carbonate reservoirs based on electrical effi ciency
Institute of Scientific and Technical Information of China (English)
Li Xiong-Yan; Qin Rui-Bao; Liu Chun-Cheng; Mao Zhi-Qiang
2014-01-01
We derived an equation for saturation in carbonate reservoirs based on the electrical effi ciency model in the case of lacking core data. Owing to the complex pore structure and strong heterogeneity in carbonate reservoirs, the relation between electrical efficiency and water porosity is either complex or linear. We proposed an electrical effi ciency equation that accounts for the relation between electrical effi ciency and water porosity. We also proposed a power-law relation between electrical effi ciency and deep-formation resistivity and analyzed the factors controlling the error in the water saturation computations. We concluded that the calculation accuracy of the electrical effi ciency is critical to the application of the saturation equation. The saturation equation was applied to the carbonate reservoirs of three wells in Iraq and Indonesia. For relative rock electrical effi ciency error below 0.1, the water saturation absolute error is also below 0.1. Therefore, we infer that the proposed saturation equation generally satisfi es the evaluation criteria for carbonate reservoirs.
Joint kinematic calculation based on clinical direct kinematic versus inverse kinematic gait models.
Kainz, H; Modenese, L; Lloyd, D G; Maine, S; Walsh, H P J; Carty, C P
2016-06-14
Most clinical gait laboratories use the conventional gait analysis model. This model uses a computational method called Direct Kinematics (DK) to calculate joint kinematics. In contrast, musculoskeletal modelling approaches use Inverse Kinematics (IK) to obtain joint angles. IK allows additional analysis (e.g. muscle-tendon length estimates), which may provide valuable information for clinical decision-making in people with movement disorders. The twofold aims of the current study were: (1) to compare joint kinematics obtained by a clinical DK model (Vicon Plug-in-Gait) with those produced by a widely used IK model (available with the OpenSim distribution), and (2) to evaluate the difference in joint kinematics that can be solely attributed to the different computational methods (DK versus IK), anatomical models and marker sets by using MRI based models. Eight children with cerebral palsy were recruited and presented for gait and MRI data collection sessions. Differences in joint kinematics up to 13° were found between the Plug-in-Gait and the gait 2392 OpenSim model. The majority of these differences (94.4%) were attributed to differences in the anatomical models, which included different anatomical segment frames and joint constraints. Different computational methods (DK versus IK) were responsible for only 2.7% of the differences. We recommend using the same anatomical model for kinematic and musculoskeletal analysis to ensure consistency between the obtained joint angles and musculoskeletal estimates.
Ma, Z.; Hou, Z.; Zang, X.
2015-09-01
As a large-scale flexible inflatable structure by a huge inner lifting gas volume of several hundred thousand cubic meters, the stratospheric airship's thermal characteristic of inner gas plays an important role in its structural performance. During the floating flight, the day-night variation of the combined thermal condition leads to the fluctuation of the flow field inside the airship, which will remarkably affect the pressure acted on the skin and the structural safety of the stratospheric airship. According to the multi-physics coupling mechanism mentioned above, a numerical procedure of structural safety analysis of stratospheric airships is developed and the thermal model, CFD model, finite element code and criterion of structural strength are integrated. Based on the computation models, the distributions of the deformations and stresses of the skin are calculated with the variation of day-night time. The effects of loads conditions and structural configurations on the structural safety of stratospheric airships in the floating condition are evaluated. The numerical results can be referenced for the structural design of stratospheric airships.
Random and bias errors in simple regression-based calculations of sea-level acceleration
Howd, P.; Doran, K. J.; Sallenger, A. H.
2012-12-01
We examine the random and bias errors associated with three simple regression-based methods used to calculate the acceleration of sea-level elevation (SL). These methods are: (1) using ordinary least-squares regression (OLSR) to fit a single second-order (in time) equation to an entire elevation time series; (2) using a sliding regression window with OLRS 2nd order fits to provide time and window length dependent estimates; and (3) using a sliding regression window with OLSR 1st order fits to provide time and window length dependent estimates of sea level rate differences (SLRD). A Monte Carlo analysis using synthetic elevation time series with 9 different noise formulations (red, AR(1), and white noise at 3 variance levels) is used to examine the error structure associated with the three analysis methods. We show that, as expected, the single-fit method (1), while providing statistically unbiased estimates of the mean acceleration over an interval, by statistical design does not provide estimates of time-varying acceleration. This technique cannot be expected to detect recent changes in SL acceleration, such as those predicted by some climate models. The two sliding window techniques show similar qualitative results for the test time series, but differ dramatically in their statistical significance. Estimates of acceleration based on the 2nd order fits (2) are numerically smaller than the rate differences (3), and in the presence of near-equal residual noise, are more difficult to detect with statistical significance. We show, using the SLRD estimates from tide gauge data, how statistically significant changes in sea level accelerations can be detected at different temporal and spatial scales.
Calculation of positron observables using a finite-element-based approach
Energy Technology Data Exchange (ETDEWEB)
Klein, B. M.; Pask, J. E.; Sterne, P.
1998-11-04
We report the development of a new method for calculating positron observables using a finite-element approach for the solution of the Schrodinger equation. This method combines the advantages of both basis-set and real-space-grid approaches. The strict locality in real space of the finite element basis functions results in a method that is well suited for calculating large systems of a thousand or more atoms, as required for calculations of extended defects such as dislocations. In addition, the method is variational in nature and its convergence can be controlled systematically. The calculation of positron observables is straightforward due to the real-space nature of this method. We illustrate the power of this method with positron lifetime calculations on defects and defect-free materials, using overlapping atomic charge densities.
International Nuclear Information System (INIS)
The programme CARE (calculation of the annual radiation exposure) calculates the annual environmental exposure of complex nuclear installations. In the diffusion calculation of pollutants, the real weather conditions of the year concerned are taken into account on an hourly basis together with the associated release rates measured for the various nuclides of individual emitters. According to their location in the plant, the contributions of the time-integrated pollutant concentrations of the individual emitters are superimposed at predefinable receiving points in the vicinity or on the boundary of an installation (plant fencing). In the conception of models for calculating the resultant 50-year dose commitments care was taken to ensure that the programme CARE is capable of treating both individual emissions limited in time and quasi-continuous emissions. The programme CARE can therefore be used also for a subsequent calculation of radiation exposure in the event of accidents. (orig.)
Bending Moment Calculations for Piles Based on the Finite Element Method
Directory of Open Access Journals (Sweden)
Yu-xin Jie
2013-01-01
Full Text Available Using the finite element analysis program ABAQUS, a series of calculations on a cantilever beam, pile, and sheet pile wall were made to investigate the bending moment computational methods. The analyses demonstrated that the shear locking is not significant for the passive pile embedded in soil. Therefore, higher-order elements are not always necessary in the computation. The number of grids across the pile section is important for bending moment calculated with stress and less significant for that calculated with displacement. Although computing bending moment with displacement requires fewer grid numbers across the pile section, it sometimes results in variation of the results. For displacement calculation, a pile row can be suitably represented by an equivalent sheet pile wall, whereas the resulting bending moments may be different. Calculated results of bending moment may differ greatly with different grid partitions and computational methods. Therefore, a comparison of results is necessary when performing the analysis.
Institute of Scientific and Technical Information of China (English)
徐晓苏; 吴剑飞; 徐胜保; 王立辉; 李佩娟
2014-01-01
ICCP匹配算法是水下组合导航系统中最为重要的匹配算法。针对传统ICCP匹配算法存在仅对水下航行器惯性导航系统指示航迹作旋转和平移的刚性变换的局限性问题，为提高水下航行器地形辅助导航系统中匹配算法的精度，分析了水下航行器惯性导航系统误差特性，建立了误差模型，提出了基于仿射修正技术的水下地形ICCP匹配算法。首先利用ICCP匹配算法对惯性导航系统指示航迹进行刚性变换，再利用最小二乘法求解仿射参数，进而对 ICCP 匹配航迹进行仿射修正。仿真研究表明，基于仿射修正技术的ICCP匹配算法能较好地解决传统ICCP匹配算法刚性变换的局限性，匹配精度优于传统ICCP算法，匹配误差小于数字地图网格间距的50%，同时仿射修正所耗费时间极少，所增加的时间仅为传统ICCP匹配算法匹配时间的千分之一。%ICCP is the most important matching algorithm used in underwater integrated navigation system. Traditional ICCP algorithm can only do rigid transformation (rotation and translation) for the indicated track of underwater vehicle’s INS. In order to overcome this problem and improve the accuracy of track matching, the error characteristics of INS are analyzed, and the error model of INS is established. Then a new ICCP algorithm based on affine correction is put forward. The track indicated by INS is transformed according to the ICCP algorithm. The affine parameters are solved with the least squares method. The ICCP matching track is modified by affine transformation. The simulations show that the defects of traditional ICCP algorithm can be avoided by affine correction, and the matching result is better than those of traditional ICCP algorithm, in which the matching error is less than 50% of digital map grid spacing. Meanwhile, the additional time consumed in affine correction is just about one thousandth of that in traditional ICCP
A thermodynamic approach to the affinity optimization of drug candidates.
Freire, Ernesto
2009-11-01
High throughput screening and other techniques commonly used to identify lead candidates for drug development usually yield compounds with binding affinities to their intended targets in the mid-micromolar range. The affinity of these molecules needs to be improved by several orders of magnitude before they become viable drug candidates. Traditionally, this task has been accomplished by establishing structure activity relationships to guide chemical modifications and improve the binding affinity of the compounds. As the binding affinity is a function of two quantities, the binding enthalpy and the binding entropy, it is evident that a more efficient optimization would be accomplished if both quantities were considered and improved simultaneously. Here, an optimization algorithm based upon enthalpic and entropic information generated by Isothermal Titration Calorimetry is presented.
Affine density in wavelet analysis
Kutyniok, Gitta
2007-01-01
In wavelet analysis, irregular wavelet frames have recently come to the forefront of current research due to questions concerning the robustness and stability of wavelet algorithms. A major difficulty in the study of these systems is the highly sensitive interplay between geometric properties of a sequence of time-scale indices and frame properties of the associated wavelet systems. This volume provides the first thorough and comprehensive treatment of irregular wavelet frames by introducing and employing a new notion of affine density as a highly effective tool for examining the geometry of sequences of time-scale indices. Many of the results are new and published for the first time. Topics include: qualitative and quantitative density conditions for existence of irregular wavelet frames, non-existence of irregular co-affine frames, the Nyquist phenomenon for wavelet systems, and approximation properties of irregular wavelet frames.
Inhomogeneous self-affine carpets
Fraser, Jonathan M.
2013-01-01
We investigate the dimension theory of inhomogeneous self-affine carpets. Through the work of Olsen, Snigireva and Fraser, the dimension theory of inhomogeneous self-similar sets is now relatively well-understood, however, almost no progress has been made concerning more general non-conformal inhomogeneous attractors. If a dimension is countably stable, then the results are immediate and so we focus on the upper and lower box dimensions and compute these explicitly for large classes of inhomo...
Protein isolation using affinity chromatography
Besselink, T.
2012-01-01
Many product or even waste streams in the food industry contain components that may have potential for e.g. functional foods. These streams are typically large in volume and the components of interest are only present at low concentrations. A robust and highly selective separation process should be developed for efficient isolation of the components. Affinity chromatography is such a selective method. Ligands immobilized to a stationary phase (e.g., a resin or membrane) are used to bind the c...
Three-dimensional thermal-hydraulic response in LBLOCA based on MARS-KS calculation
International Nuclear Information System (INIS)
Three-dimensional (3D) thermal-hydraulic analysis of an accident in Nuclear Power Plant (NPP) has been extended to use since Best-Estimate (BE) calculation was allowed for safety analysis. The present study is to discuss why and how big differences can be obtained from the 1D and 3D thermal-hydraulic calculations for large break Loss-of-Coolant Accident (LBLOCA). Calculations are performed using MARS-KS code with one-dimensional (1D) modeling and with 3D modeling for reactor vessel of Advanced Power Reactor (APR1400). For the 3D modeling, the MULTI-D component of the MARS-KS code is applied. Especially, a hot channel having a size of one fuel assembly is also simulated. From the comparison of the calculation results, four differences are found: lower blowdown Peak Cladding Temperature (PCT) in 3D calculation, instantaneous stop of cladding heat-up, extent of blowdown quenching, and milder and longer reflood process in 3D calculation. The flow distribution in the core in 3D calculation could be one of the reasons for those differences. From the sensitivity study, the initial temperature at the reactor vessel upper head is found to have strong effect on the blowdown quenching, thus the reflood PCT and needs a careful consideration. (author)
Affine Coherent States in Quantum Cosmology
Malkiewicz, Przemyslaw
2015-01-01
A brief summary of the application of coherent states in the examination of quantum dynamics of cosmological models is given. We discuss quantization maps, phase space probability distributions and semiclassical phase spaces. The implementation of coherent states based on the affine group resolves the hardest singularities, renders self-adjoint Hamiltonians without boundary conditions and provides a completely consistent semi-classical description of the involved quantum dynamics. We consider three examples: the closed Friedmann model, the anisotropic Bianchi Type I model and the deep quantum domain of the Bianchi Type IX model.
Lectin affinity chromatography of glycolipids
Energy Technology Data Exchange (ETDEWEB)
Torres, B.V.; Smith, D.F.
1987-05-01
Since glycolipids (GLs) are either insoluble or form mixed micelles in water, lectin affinity chromatography in aqueous systems has not been applied to their separation. They have overcome this problem by using tetrahydrofuran (THF) in the mobile phase during chromatography. Affinity columns prepared with the GalNAc-specific Helix pomatia agglutinin (HPA) and equilibrated in THF specifically bind the (/sup 3/H)oligosaccharide derived from Forssman GL indicating that the immobilized HPA retained its carbohydrate-binding specificity in this solvent. Intact Forssman GL was bound by the HPA-column equilibrated in THF and was specifically eluted with 0.1 mg/ml GalNAc in THF. Purification of the Forssman GL was achieved when a crude lipid extract of sheep erythrocyte membranes was applied to the HPA-column in THF. Non-specifically bound GLs were eluted from the column using a step gradient of aqueous buffer in THF, while the addition of GalNAc was required to elute the specifically bound GLs. Using this procedure the A-active GLs were purified from a crude lipid extract of type A human erythrocytes in a single chromatographic step. The use of solvents that maintain carbohydrate-binding specificity and lipid solubility will permit the application of affinity chromatography on immobilized carbohydrate-binding proteins to intact GLs.
Gu, Xuejun; Jelen, Urszula; Li, Jinsheng; Jia, Xun; Jiang, Steve B.
2011-01-01
Targeting at the development of an accurate and efficient dose calculation engine for online adaptive radiotherapy, we have implemented a finite size pencil beam (FSPB) algorithm with a 3D-density correction method on GPU. This new GPU-based dose engine is built on our previously published ultrafast FSPB computational framework. Dosimetric evaluations against Monte Carlo dose calculations are conducted on 10 IMRT treatment plans (5 head-and-neck cases and 5 lung cases). For all cases, there i...
Method for stability analysis based on the Floquet theory and Vidyn calculations
Energy Technology Data Exchange (ETDEWEB)
Ganander, Hans
2005-03-01
This report presents the activity 3.7 of the STEM-project Aerobig and deals with aeroelastic stability of the complete wind turbine structure at operation. As a consequence of the increase of sizes of wind turbines dynamic couplings are being more important for loads and dynamic properties. The steady ambition to increase the cost competitiveness of wind turbine energy by using optimisation methods lowers design margins, which in turn makes questions about stability of the turbines more important. The main objective of the project is to develop a general stability analysis tool, based on the VIDYN methodology regarding the turbine dynamic equations and the Floquet theory for the stability analysis. The reason for selecting the Floquet theory is that it is independent of number of blades, thus can be used for 2 as well as 3 bladed turbines. Although the latter ones are dominating on the market, the former has large potential when talking about offshore large turbines. The fact that cyclic and individual blade pitch controls are being developed as a mean for reduction of fatigue also speaks for general methods as Floquet. The first step of a general system for stability analysis has been developed, the code VIDSTAB. Together with other methods, as the snap shot method, the Coleman transformation and the use of Fourier series, eigenfrequences and modes can be analysed. It is general with no restrictions on the number of blades nor the symmetry of the rotor. The derivatives of the aerodynamic forces are calculated numerically in this first version. Later versions would include state space formulations of these forces. This would also be the case for the controllers of turbine rotation speed, yaw direction and pitch angle.
Current in the Protein Nanowires: Quantum Calculations of the Base States.
Suprun, Anatol D; Shmeleva, Liudmyla V
2016-12-01
It is known that synthesis of adenosine triphosphoric acid in mitochondrions may be only completed on the condition of transport of the electron pairs, which were created due to oxidation processes, to mitochondrions. As of today, many efforts were already taken in order to understand those processes that occur in the course of donor-acceptor electron transport between cellular organelles (that is, between various proteins and protein structures). However, the problem concerning the mechanisms of electron transport over these organelles still remains understudied. This paper is dedicated to the investigation of these same issues.It has been shown that regardless of the amino acid inhomogeneity of the primary structure, it is possible to apply a representation of the second quantization in respect of the protein molecule (hereinafter "numbers of filling representation"). Based on this representation, it has been established that the primary structure of the protein molecule is actually a semiconductor nanowire. In addition, at the same time, its conduction band, into which an electron is injected as the result of donor-acceptor processes, consists of five sub-bands. Three of these sub-bands have normal dispersion laws, while the rest two sub-bands have abnormal dispersion laws (reverse laws). Test calculation of the current density was made under the conditions of the complete absence of the factors, which may be interpreted as external fields. It has been shown that under such conditions, current density is exactly equal to zero. This is the evidence of correctness of the predictive model of the conductivity band of the primary structure of the protein molecule (protein nanowire). At the same time, it makes it possible to apply the obtained results in respect of the actual situation, where factors, which may be interpreted as external fields, exist. PMID:26858156
Ray tracing based path-length calculations for polarized light tomographic imaging
Manjappa, Rakesh; Kanhirodan, Rajan
2015-09-01
A ray tracing based path length calculation is investigated for polarized light transport in a pixel space. Tomographic imaging using polarized light transport is promising for applications in optical projection tomography of small animal imaging and turbid media with low scattering. Polarized light transport through a medium can have complex effects due to interactions such as optical rotation of linearly polarized light, birefringence, di-attenuation and interior refraction. Here we investigate the effects of refraction of polarized light in a non-scattering medium. This step is used to obtain the initial absorption estimate. This estimate can be used as prior in Monte Carlo (MC) program that simulates the transport of polarized light through a scattering medium to assist in faster convergence of the final estimate. The reflectance for p-polarized (parallel) and s-polarized (perpendicular) are different and hence there is a difference in the intensities that reach the detector end. The algorithm computes the length of the ray in each pixel along the refracted path and this is used to build the weight matrix. This weight matrix with corrected ray path length and the resultant intensity reaching the detector for each ray is used in the algebraic reconstruction (ART) method. The proposed method is tested with numerical phantoms for various noise levels. The refraction errors due to regions of different refractive index are discussed, the difference in intensities with polarization is considered. The improvements in reconstruction using the correction so applied is presented. This is achieved by tracking the path of the ray as well as the intensity of the ray as it traverses through the medium.
Bourguignon, Laurent; Goutelle, Sylvain; Gérard, Cécile; Guillermet, Anne; Burdin de Saint Martin, Julie; Maire, Pascal; Ducher, Michel
2009-01-01
The use of amikacin is difficult because of its toxicity and its pharmacokinetic variability. This variability is almost ignored in adult standard dosage regimens since only the weight is used in the dose calculation. Our objective is to test if the pharmacokinetic of amikacin can be regarded as homogenous, and if the method for calculating the dose according to patients' weight is appropriate. From a cohort of 580 patients, five groups of patients were created by statistical data partitioning. A population pharmacokinetic analysis was performed in each group. The adult population is not homogeneous in term of pharmacokinetics. The doses required to achieve a maximum concentration of 60 mg/L are strongly different (585 to 1507 mg) between groups. The exclusive use of the weight to calculate the dose of amikacine appears inappropriate for 80% of the patients, showing the limits of the formulae for calculating doses of aminoglycosides.
12 CFR 702.106 - Standard calculation of risk-based net worth requirement.
2010-01-01
... AFFECTING CREDIT UNIONS PROMPT CORRECTIVE ACTION Net Worth Classification § 702.106 Standard calculation of...) Allowance. Negative one hundred percent (−100%) of the balance of the Allowance for Loan and Lease...
Grid-based density functional calculation of many-electron systems
Roy, Amlan K
2010-01-01
Exploratory variational pseudopotential density functional calculations are performed for the electronic properties of many-electron systems in the 3D cartesian coordinate grid (CCG). The atom-centered localized gaussian basis set, electronic density and the two-body potentials are set up in the 3D cubic box. The classical Hartree potential is calculated accurately and efficiently through a Fourier convolution technique. As a first step, simple local density functionals of homogeneous electron gas are used for the exchange-correlation potential, while Hay-Wadt-type effective core potentials are employed to eliminate the core electrons. No auxiliary basis set is invoked. Preliminary illustrative calculations on total energies, individual energy components, eigenvalues, potential energy curves, ionization energies, atomization energies of a set of 12 molecules show excellent agreement with the corresponding reference values of atom-centered grid as well as the grid-free calculation. Results for 3 atoms are also...
Preobrazhenskii, M. P.; Rudakov, O. B.
2016-01-01
A regression model for calculating the boiling point isobars of tetrachloromethane-organic solvent binary homogeneous systems is proposed. The parameters of the model proposed were calculated for a series of solutions. The correlation between the nonadditivity parameter of the regression model and the hydrophobicity criterion of the organic solvent is established. The parameter value of the proposed model is shown to allow prediction of the potential formation of azeotropic mixtures of solvents with tetrachloromethane.
Calculation of Effective Freezing Time in Lung Cancer Cryosurgery Based on Godunov Simulation
Т.G. Kotova; V.I. Kochenov; D.Y. Madai; А.V. Gurin; S.N. Tsybusov
2016-01-01
There have been presented the results of lung cancer cryosurgery simulation using numerical solutions of enthalpy equation according to Godunov method. For the cryodestruction improvement purposes we successfully calculated the effective freezing time taking into account the evolution of an ice ball covering the tumor area. Geometrical transformation parameters of an ice ball have been measured by calculating the temperature distribution and the interface position in biological tissu...
Calculation of Effective Freezing Time in Lung Cancer Cryosurgery Based on Godunov Simulation
Т.G. Kotova; V.I. Kochenov; S.N. Tsybusov; D.Y. Madai; А.V. Gurin
2016-01-01
There have been presented the results of lung cancer cryosurgery simulation using numerical solutions of enthalpy equation according to Godunov method. For the cryodestruction improvement purposes we successfully calculated the effective freezing time taking into account the evolution of an ice ball covering the tumor area. Geometrical transformation parameters of an ice ball have been measured by calculating the temperature distribution and the interface position in biological tissue. Mathem...
Sørensen, R.; Zinko, U.; Seibert, J.
2005-01-01
The topographic wetness index (TWI, ln(a/tanβ)), which combines local upslope contributing area and slope, is commonly used to quantify topographic control on hydrological processes. Methods of computing this index differ primarily in the way the upslope contributing area is calculated. In this study we compared a number of calculation methods for TWI and evaluated them in terms of their correlation with the following measured variables: vascular plant species richness, soil pH, groundwa...
Calculation of Henry constant on the base of critical parameters of adsorbable gas
International Nuclear Information System (INIS)
Calculation of Henry constant using correlation between critical parameters Psub(c), Tsub(c) and adsorption energy, determined by the value of internal pressure in molecular field of adsorbent, has been made. The calculated Henry constants for Ar, Kr and Xe, adsorbed by MoS2 and zeolite NaX, are compared with the experimental ones. The state of the molecules adsorbed is evaluated
Directory of Open Access Journals (Sweden)
R. Sørensen
2006-01-01
Full Text Available The topographic wetness index (TWI, ln(a/tanβ, which combines local upslope contributing area and slope, is commonly used to quantify topographic control on hydrological processes. Methods of computing this index differ primarily in the way the upslope contributing area is calculated. In this study we compared a number of calculation methods for TWI and evaluated them in terms of their correlation with the following measured variables: vascular plant species richness, soil pH, groundwater level, soil moisture, and a constructed wetness degree. The TWI was calculated by varying six parameters affecting the distribution of accumulated area among downslope cells and by varying the way the slope was calculated. All possible combinations of these parameters were calculated for two separate boreal forest sites in northern Sweden. We did not find a calculation method that performed best for all measured variables; rather the best methods seemed to be variable and site specific. However, we were able to identify some general characteristics of the best methods for different groups of measured variables. The results provide guiding principles for choosing the best method for estimating species richness, soil pH, groundwater level, and soil moisture by the TWI derived from digital elevation models.
A Quick and Affine Invariance Matching Method for Oblique Images
Directory of Open Access Journals (Sweden)
XIAO Xiongwu
2015-04-01
Full Text Available This paper proposed a quick, affine invariance matching method for oblique images. It calculated the initial affine matrix by making full use of the two estimated camera axis orientation parameters of an oblique image, then recovered the oblique image to a rectified image by doing the inverse affine transform, and left over by the SIFT method. We used the nearest neighbor distance ratio(NNDR, normalized cross correlation(NCC measure constraints and consistency check to get the coarse matches, then used RANSAC method to calculate the fundamental matrix and the homography matrix. And we got the matches that they were interior points when calculating the homography matrix, then calculated the average value of the matches' principal direction differences. During the matching process, we got the initial matching features by the nearest neighbor(NN matching strategy, then used the epipolar constrains, homography constrains, NCC measure constrains and consistency check of the initial matches' principal direction differences with the calculated average value of the interior matches' principal direction differences to eliminate false matches. Experiments conducted on three pairs of typical oblique images demonstrate that our method takes about the same time as SIFT to match a pair of oblique images with a plenty of corresponding points distributed evenly and an extremely low mismatching rate.
Abrupt fault diagnosis of aero-engine based on affinity propagation clustering%基于相似性传播聚类的航空发动机突发故障诊断
Institute of Scientific and Technical Information of China (English)
李丽敏; 王仲生; 姜洪开
2014-01-01
针对航空发动机突发故障，构建了一种基于相似性传播聚类的突发故障诊断方法。首先利用突发故障历史监测数据建立突发故障数据库，通过相似性传播聚类找到数据库中所有突发故障数据的中心，当诊断新采集数据的突发故障类型时，通过相似性传播聚类找到当前新采集数据的中心，经过与突发故障数据库中的数据中心进行匹配判断该新采集数据所对应的突发故障类型。将该突发故障诊断方法应用到发动机转子实验台的突发故障诊断中，仿真和实验结果表明该方法的可行性，并通过与其他方法比较，表明该方法具有诊断时间短和误差小的优点。%Aiming at aero-engine faults,an abrupt fault diagnosis method based on affinity propagation clustering was proposed.Abrupt fault historical monitoring data were used to establish faults database.Through affinity propagation clustering,all the exemplars of abrupt faults in the database were found and the affinity propagation clustering was applied once again to find the exemplar of the new collected data.The fault type was then identified by matching the center with the centers obtained from the faults database.The method was used in the aero-engine abrupt fault diagnosis.The simulation and experiment results show that the method is feasible to diagnose abrupt fault,and compared with other methods,it needs shorter time consuming and produces lower error.
Ding, George X.; Duggan, Dennis M.; Coffey, Charles W.; Shokrani, Parvaneh; Cygler, Joanna E.
2006-06-01
The purpose of this study is to present our experience of commissioning, testing and use of the first commercial macro Monte Carlo based dose calculation algorithm for electron beam treatment planning and to investigate new issues regarding dose reporting (dose-to-water versus dose-to-medium) as well as statistical uncertainties for the calculations arising when Monte Carlo based systems are used in patient dose calculations. All phantoms studied were obtained by CT scan. The calculated dose distributions and monitor units were validated against measurements with film and ionization chambers in phantoms containing two-dimensional (2D) and three-dimensional (3D) type low- and high-density inhomogeneities at different source-to-surface distances. Beam energies ranged from 6 to 18 MeV. New required experimental input data for commissioning are presented. The result of validation shows an excellent agreement between calculated and measured dose distributions. The calculated monitor units were within 2% of measured values except in the case of a 6 MeV beam and small cutout fields at extended SSDs (>110 cm). The investigation on the new issue of dose reporting demonstrates the differences up to 4% for lung and 12% for bone when 'dose-to-medium' is calculated and reported instead of 'dose-to-water' as done in a conventional system. The accuracy of the Monte Carlo calculation is shown to be clinically acceptable even for very complex 3D-type inhomogeneities. As Monte Carlo based treatment planning systems begin to enter clinical practice, new issues, such as dose reporting and statistical variations, may be clinically significant. Therefore it is imperative that a consistent approach to dose reporting is used.
DEFF Research Database (Denmark)
Göksu, Ömer; Teodorescu, Remus; Bak-Jensen, Birgitte;
2012-01-01
As more renewable energy sources, especially more wind turbines are installed in the power system, analysis of the power system with the renewable energy sources becomes more important. Short-circuit calculation is a well known fault analysis method which is widely used for early stage analysis...... and design purposes and tuning of the network protection equipments. However, due to current controlled power converter-based grid connection of the wind turbines, short-circuit calculation cannot be performed with its current form for networks with power converter-based wind turbines. In this paper......, an iterative approach for short-circuit calculation of networks with power converter-based wind turbines is developed for both symmetrical and asymmetrical short-circuit grid faults. As a contribution to existing solutions, negative sequence current injection from the wind turbines is also taken into account...
Edimo, P; Kwato Njock, M G; Vynckier, S
2013-11-01
The purpose of the present study is to perform a clinical validation of a new commercial Monte Carlo (MC) based treatment planning system (TPS) for electron beams, i.e. the XiO 4.60 electron MC (XiO eMC). Firstly, MC models for electron beams (4, 8, 12 and 18 MeV) have been simulated using BEAMnrc user code and validated by measurements in a homogeneous water phantom. Secondly, these BEAMnrc models have been set as the reference tool to evaluate the ability of XiO eMC to reproduce dose perturbations in the heterogeneous phantom. In the homogeneous phantom calculations, differences between MC computations (BEAMnrc, XiO eMC) and measurements are less than 2% in the homogeneous dose regions and less than 1 mm shifting in the high dose gradient regions. As for the heterogeneous phantom, the accuracy of XiO eMC has been benchmarked with predicted BEAMnrc models. In the lung tissue, the overall agreement between the two schemes lies under 2.5% for the most tested dose distributions at 8, 12 and 18 MeV and is better than the 4 MeV one. In the non-lung tissue, a good agreement has been found between BEAMnrc simulation and XiO eMC computation for 8, 12 and 18 MeV. Results are worse in the case of 4 MeV calculations (discrepancies ≈ 4%). XiO eMC can predict dose perturbation induced by high-density heterogeneities for 8, 12 and 18 MeV. However, significant deviations found in the case of 4 MeV demonstrate that caution is necessary in using XiO eMC at lower electron energies. PMID:23010450
Coenzyme-like ligands for affinity isolation of cholesterol oxidase.
Xin, Yu; Lu, Liushen; Wang, Qing; Zhang, Ling; Tong, Yanjun; Wang, Wu
2016-05-15
Two coenzyme-like chemical ligands were designed and synthesized for affinity isolation of cholesterol oxidase (COD). To simulate the structure of natural coenzyme of COD (flavin adenine dinucleotide (FAD)), on Sepharose beads, 5-aminouracil, cyanuric chloride and 1, 4-butanediamine were composed and then modified. The COD gene from Brevibacterium sp. (DQ345780) was expressed in Escherichia coli BL21 (DE3), and then the sorbents were applied to adsorption analysis with the pure enzyme. Subsequently, the captured enzyme was applied to SDS-PAGE and activity analysis. As calculated, the theoretical maximum adsorption (Qmax) of the two affinity sorbents (RL-1 and RL-2) were ∼83.5 and 46.3mg/g wet gel; and the desorption constant Kd of the two sorbents were ∼6.02×10(-4) and 1.19×10(-4)μM. The proteins after cell lysis were applied to affinity isolation, and then after one step of affinity binding on the two sorbents, the protein recoveries of RL-1 and RL-2 were 9.2% and 9.7%; the bioactivity recoveries were 92.7% and 91.3%, respectively. SDS-PAGE analysis revealed that the purities of COD isolated with the two affinity sorbents were approximately 95%. PMID:26856529
Manifolds with integrable affine shape operator
Directory of Open Access Journals (Sweden)
Daniel A. Joaquín
2005-05-01
Full Text Available This work establishes the conditions for the existence of vector fields with the property that theirs covariant derivative, with respect to the affine normal connection, be the affine shape operatorS in hypersurfaces. Some results are obtained from this property and, in particular, for some kind of affine decomposable hypersurfaces we explicitely get the actual vector fields.
Li, Zhiming; Zhu, Guohui; Liu, Jiaming; Lu, Qiaomei; Yang, Minlan; Wu, Hong; Shi, Xiumei; Chen, Xinhua
2007-08-01
A new phosphorescence labeling reagent Triton-100X-4.0G-D (4.0G-D refers to 4.0-generation dendrimers) was found. Quantitative specific affinity adsorption (AA) reaction between Triton-100X-4.0G-D-WGA and glucose (G) was carried out on the surface of nitrocellulose membrane (NCM), and the Δ Ip of the product of AA reaction was linear correlation to the content of G. Based on the facts above, a new method for the determination of trace G was established by WGA labeled with Triton-100X-4.0G-D affinity adsorption solid substrate room temperature phosphorimetry (Triton-100X-4.0G-D-WGA-AA-SS-RTP). This research showed that AA-SS-RTP for either direct method or sandwich method could combine very well the characteristics of both the high sensitivity of SS-RTP and the specificity of the AA reaction. Detection limits (LD) were 0.24 fg spot -1 for direct method and 0.18 fg spot -1 for sandwich method, indicating both of them were of high sensitivity. The method has been applied to the determination of the content of G in human serum, and the results were coincided with those obtained by glucose oxidize enzyme method. It can also be applied to forecast accurately some human diseases, such as primary hepatic carcinoma, cirrhosis, acute and chronic hepatitis, transfer hepatocellular, etc. Meanwhile, the mechanism for the determination of G with AA-SS-RTP was discussed.
Mitsui, Takaaki; Watanabe-Takahashi, Miho; Shimizu, Eiko; Zhang, Baihao; Funamoto, Satoru; Yamasaki, Shinji; Nishikawa, Kiyotaka
2016-09-01
Shiga toxin (Stx), a major virulence factor of enterohemorrhagic Escherichia coli (EHEC), can be classified into two subgroups, Stx1 and Stx2, each consisting of various closely related subtypes. Stx2 subtypes Stx2a and Stx2d are highly virulent and linked with serious human disorders, such as acute encephalopathy and hemolytic-uremic syndrome. Through affinity-based screening of a tetravalent peptide library, we previously developed peptide neutralizers of Stx2a in which the structure was optimized to bind to the B-subunit pentamer. In this study, we identified Stx2d-selective neutralizers by targeting Asn16 of the B subunit, an amino acid unique to Stx2d that plays an essential role in receptor binding. We synthesized a series of tetravalent peptides on a cellulose membrane in which the core structure was exactly the same as that of peptides in the tetravalent library. A total of nine candidate motifs were selected to synthesize tetravalent forms of the peptides by screening two series of the tetravalent peptides. Five of the tetravalent peptides effectively inhibited the cytotoxicity of Stx2a and Stx2d, and notably, two of the peptides selectively inhibited Stx2d. These two tetravalent peptides bound to the Stx2d B subunit with high affinity dependent on Asn16. The mechanism of binding to the Stx2d B subunit differed from that of binding to Stx2a in that the peptides covered a relatively wide region of the receptor-binding surface. Thus, this highly optimized screening technique enables the development of subtype-selective neutralizers, which may lead to more sophisticated treatments of infections by Stx-producing EHEC. PMID:27382021
基于仿射混杂系统控制设计的机器人导航控制%Robot Navigation Based on Control Synthesis of Piecewise Affine Hybrid Systems
Institute of Scientific and Technical Information of China (English)
王慧芳; 陈阳舟
2008-01-01
Control synthesis and reachability analysis of the piecewise affine hybrid systems on simplices were applied for safely steering a robot from a given position to a final position with consideration of optimality. Based on the triangulation of the state space of a robot, a dual graph was constructed following the target attractive principle, and then a path planning algorithm was presented to find a sequence of adjacent triangles that were traversed by the shortest path. According to the characteristics of affine systems on simplices, a motion planning algorithm was proposed to determine the translational and rotational velocities for a robot. The simulation results demonstrate the effectiveness of the algorithms.%根据单纯形仿射混杂系统的可达性分析设计控制律,使机器人在平面任意两点间运行,保证其安全性并考虑其最优性.对机器人的状态空间进行三角划分,根据目标吸引原理来建立其对偶图,针对对偶图提出路径规划算法得到最短路径穿越的三角形序列.然后根据仿射系统在单纯形中的性质,提出运动规划算法,得到机器人的角速度和线速度,控制机器人穿越给定的三角形序列到达目标点.仿真结果表明了方法的有效性.
Energy Technology Data Exchange (ETDEWEB)
Abdel-Khalik, Hany S. [North Carolina State Univ., Raleigh, NC (United States); Zhang, Qiong [North Carolina State Univ., Raleigh, NC (United States)
2014-05-20
The development of hybrid Monte-Carlo-Deterministic (MC-DT) approaches, taking place over the past few decades, have primarily focused on shielding and detection applications where the analysis requires a small number of responses, i.e. at the detector locations(s). This work further develops a recently introduced global variance reduction approach, denoted by the SUBSPACE approach is designed to allow the use of MC simulation, currently limited to benchmarking calculations, for routine engineering calculations. By way of demonstration, the SUBSPACE approach is applied to assembly level calculations used to generate the few-group homogenized cross-sections. These models are typically expensive and need to be executed in the order of 10^{3} - 10^{5} times to properly characterize the few-group cross-sections for downstream core-wide calculations. Applicability to k-eigenvalue core-wide models is also demonstrated in this work. Given the favorable results obtained in this work, we believe the applicability of the MC method for reactor analysis calculations could be realized in the near future.
Python-based framework for coupled MC-TH reactor calculations
International Nuclear Information System (INIS)
We have developed a set of Python packages to provide a modern programming interface to codes used for analysis of nuclear reactors. Python classes can be classified by their functionality into three groups: low-level interfaces, general model classes and high-level interfaces. A low-level interface describes an interface between Python and a particular code. General model classes can be used to describe calculation geometry and meshes to represent system variables. High-level interface classes are used to convert geometry described with general model classes into instances of low-level interface classes and to put results of code calculations (read by low-interface classes) back to general model. The implementation of Python interfaces to the Monte Carlo neutronics code MCNP and thermo-hydraulic code SCF allow efficient description of calculation models and provide a framework for coupled calculations. In this paper we illustrate how these interfaces can be used to describe a pin model, and report results of coupled MCNP-SCF calculations performed for a PWR fuel assembly, organized by means of the interfaces
X-ray tube output based calculation of patient entrance surface dose: validation of the method
Energy Technology Data Exchange (ETDEWEB)
Harju, O.; Toivonen, M.; Tapiovaara, M.; Parviainen, T. [Radiation and Nuclear Safety Authority, Helsinki (Finland)
2003-06-01
X-ray departments need methods to monitor the doses delivered to the patients in order to be able to compare their dose level to established reference levels. For this purpose, patient dose per radiograph is described in terms of the entrance surface dose (ESD) or dose-area product (DAP). The actual measurement is often made by using a DAP-meter or thermoluminescent dosimeters (TLD). The third possibility, the calculation of ESD from the examination technique factors, is likely to be a common method for x-ray departments that do not have the other methods at their disposal or for examinations where the dose may be too low to be measured by the other means (e.g. chest radiography). We have developed a program for the determination of ESD by the calculation method and analysed the accuracy that can be achieved by this indirect method. The program calculates the ESD from the current time product, x-ray tube voltage, beam filtration and focus- to-skin distance (FSD). Additionally, for calibrating the dose calculation method and thereby improving the accuracy of the calculation, the x-ray tube output should be measured for at least one x-ray tube voltage value in each x-ray unit. The aim of the present work is to point out the restrictions of the method and details of its practical application. The first experiences from the use of the method will be summarised. (orig.)
Nonlinear Optimization Method of Ship Floating Condition Calculation in Wave Based on Vector
Institute of Scientific and Technical Information of China (English)
丁宁; 余建星
2014-01-01
Ship-floating-condition-in-regular-waves-is-calculated.-New-equations-controlling-any-ship’s-floating-condition-are-proposed-by-use-of-the-vector-operation.-This-form-is-a-nonlinear-optimization-problem-which-can-be-solved-using-the-penalty-function-method-with-constant-coefficients.-And-the-solving-process-is-accelerated-by-dichotomy.-During-the-solving-process,-the-ship’s-displacement-and-buoyant-centre-have-been-calculated-by-the-integration-of-the-ship-surface-according-to-the-waterline.-The-ship-surface-is-described-using-an-accumulative-chord-length-theory-in-order-to-determine-the-displacement,-the-buoyancy-center-and-the-waterline.-The-draught-forming-the-waterline-at-each-station-can-be-found-out-by-calculating-the-intersection-of-the-ship-surface-and-the-wave-surface.-The-results-of-an-example-indicate-that-this-method-is-exact-and-efficient.-It-can-calculate-the-ship-floating-condition-in-regular-waves-as-well-as-simplify-the-calculation-and-improve-the-computational-efficiency-and-the-precision-of-results.
Pence, Thomas J; Monroe, Ryan J; Wright, Neil T
2008-08-01
Some recent analyses modeled the response of collagenous tissues, such as epicardium, using a hypothetical network consisting of interconnected springlike fibers. The fibers in the network were organized such that internal nodes served as the connection point between three such collagen springs. The results for assumed affine and nonaffine deformations are contrasted after a homogeneous deformation at the boundary. Affine deformation provides a stiffer mechanical response than nonaffine deformation. In contrast to nonaffine deformation, affine deformation determines the displacement of internal nodes without imposing detailed force balance, thereby complicating the simplest intuitive notion of stress, one based on free body cuts, at the single node scale. The standard notion of stress may then be recovered via average field theory computations based on large micromesh realizations. An alternative and by all indications complementary viewpoint for the determination of stress in these collagen fiber networks is discussed here, one in which stress is defined using elastic energy storage, a notion which is intuitive at the single node scale. It replaces the average field theory computations by an averaging technique over randomly oriented isolated simple elements. The analytical operations do not require large micromesh realizations, but the tedious nature of the mathematical manipulation is clearly aided by symbolic algebra calculation. For the example case of linear elastic deformation, this results in material stiffnesses that relate the infinitesimal strain and stress. The result that the affine case is stiffer than the nonaffine case is recovered, as would be expected. The energy framework also lends itself to the natural inclusion of changes in mechanical response due to the chemical, electrical, or thermal environment. PMID:18601451
Energy Technology Data Exchange (ETDEWEB)
Kang, M. Y.; Kim, J. H.; Choi, H. D.; Sun, G. M. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)
2014-10-15
To calculate the full energy (FE) absorption peak efficiency for arbitrary volume sample, we developed and verified the Effective Solid Angle (ESA) Code. The procedure for semi-empirical determination of the FE efficiency for the arbitrary volume sources and the calculation principles and processes about ESA code is referred to, and the code was validated with a HPGe detector (relative efficiency 32%, n-type) in previous studies. In this study, we use different type and efficiency of HPGe detectors, in order to verify the performance of the ESA code for the various detectors. We calculated the efficiency curve of voluminous source and compared with experimental data. We will carry out additional validation by measurement of various medium, volume and shape of CRM volume sources with detector of different efficiency and type. And we will reflect the effect of the dead layer of p-type HPGe detector and coincidence summing correction technique in near future.
Douillard, J M; Henry, M
2003-07-15
A very simple route to calculation of the surface energy of solids is proposed because this value is very difficult to determine experimentally. The first step is the calculation of the attractive part of the electrostatic energy of crystals. The partial charges used in this calculation are obtained by using electronegativity equalization and scales of electronegativity and hardness deduced from physical characteristics of the atom. The lattice energies of the infinite crystal and of semi-infinite layers are then compared. The difference is related to the energy of cohesion and then to the surface energy. Very good results are obtained with ice, if one compares with the surface energy of liquid water, which is generally considered a good approximation of the surface energy of ice.
A Kernel-Based Calculation of Information on a Metric Space
Directory of Open Access Journals (Sweden)
Conor J. Houghton
2013-10-01
Full Text Available Kernel density estimation is a technique for approximating probability distributions. Here, it is applied to the calculation of mutual information on a metric space. This is motivated by the problem in neuroscience of calculating the mutual information between stimuli and spiking responses; the space of these responses is a metric space. It is shown that kernel density estimation on a metric space resembles the k-nearest-neighbor approach. This approach is applied to a toy dataset designed to mimic electrophysiological data.
Autoradiography-based, three-dimensional calculation of dose rate for murine, human-tumor xenografts
International Nuclear Information System (INIS)
A Fast Fourier Transform method for calculating the three-dimensional dose rate distribution for murine, human-tumour xenografts is outlined. The required input includes evenly-spaced activity slices which span the tumour. Numerical values in these slices are determined by quantitative 125I autoradiography. For the absorbed dose-rate calculation, we assume the activity from both 131I- and 90Y-labeled radiopharmaceuticals would be distributed as is measured with the 125I label. Two example cases are presented: an ovarian-carcinoma xenograft with an IgG 2ak monoclonal antibody and a neuroblastoma xenograft with meta-iobenzylguanidine (MIBG). (Author)
An accurate potential energy curve for helium based on ab initio calculations
Janzen, A. R.; Aziz, R. A.
1997-07-01
Korona, Williams, Bukowski, Jeziorski, and Szalewicz [J. Chem. Phys. 106, 1 (1997)] constructed a completely ab initio potential for He2 by fitting their calculations using infinite order symmetry adapted perturbation theory at intermediate range, existing Green's function Monte Carlo calculations at short range and accurate dispersion coefficients at long range to a modified Tang-Toennies potential form. The potential with retardation added to the dipole-dipole dispersion is found to predict accurately a large set of microscopic and macroscopic experimental data. The potential with a significantly larger well depth than other recent potentials is judged to be the most accurate characterization of the helium interaction yet proposed.
Spectral linelist of HD16O molecule based on VTT calculations for atmospheric application
Voronin, B. A.
2014-11-01
Three version line-list of dipole transition for isotopic modification of water molecule HD16O are presented. Line-lists have been created on the basis of VTT calculations (Voronin, Tennyson, Tolchenov et al. MNRAS, 2010) by adding air- and self-broadening coefficient, and temperature exponents for HD16O-air case. Three cut-of values for the line intensities were used: 1e-30, 1e-32 and 1e-35 cm/molecule. Calculated line-lists are available on the site ftp://ftp.iao.ru/pub/VTT/VTT-296/.
Monte Carlo calculations for design of An accelerator based PGNAA facility
International Nuclear Information System (INIS)
Monte Carlo calculations were carried out for design of a set up for Prompt Gamma Ray Neutron Activation Analysis (PGNAA) by 14 MeV neutrons to analyze cement raw material samples. The calculations were carried out using code the MCNP4B2. Various geometry parameters of the PGNAA experimental setup such as sample thickness, moderator geometry and detector shielding etc were optimized by maximizing the prompt gamma ray yield of different elements of sample material. Finally calibration curve of the PGNAA setup were generated for various concentrations of calcium in the material sample. Results of this simulation are presented. (author)
Monte Carlo calculations for design of An accelerator based PGNAA facility
Energy Technology Data Exchange (ETDEWEB)
Nagadi, M.M.; Naqvi, A.A. [King Fahd University of Petroleum and Minerals, Center for Applied Physical Sciences, Dhahran (Saudi Arabia); Rehman, Khateeb-ur; Kidwai, S. [King Fahd University of Petroleum and Minerals, Department of Physics, Dhahran (Saudi Arabia)
2002-08-01
Monte Carlo calculations were carried out for design of a set up for Prompt Gamma Ray Neutron Activation Analysis (PGNAA) by 14 MeV neutrons to analyze cement raw material samples. The calculations were carried out using code the MCNP4B2. Various geometry parameters of the PGNAA experimental setup such as sample thickness, moderator geometry and detector shielding etc were optimized by maximizing the prompt gamma ray yield of different elements of sample material. Finally calibration curve of the PGNAA setup were generated for various concentrations of calcium in the material sample. Results of this simulation are presented. (author)
Interpretation of the resonance Raman spectra of linear tetrapyrroles based on DFT calculations
Kneip, Christa; Hildebrandt, Peter; Németh, Károly; Mark, Franz; Schaffner, Kurt
1999-10-01
Raman spectra of linear methine-bridged tetrapyrroles in different conformational and protonation states were calculated on the basis of scaled force fields obtained by density functional theory. Results are reported for protonated phycocyanobilin in the extended ZZZasa configuration, as it is found in C-phycocyanin of cyanobacteria. The calculated spectra are in good agreement with experimental spectra of the protein-bound chromophore in the α-subunit of C-phycocyanin and allow a plausible and consistent assignment of most of the observed resonance Raman bands in the region between 1000 and 1700 cm -1.
Torpedo's Search Trajectory Design Based on Acquisition and Hit Probability Calculation
Institute of Scientific and Technical Information of China (English)
LI Wen-zhe; ZHANG Yu-wen; FAN Hui; WANG Yong-hu
2008-01-01
Taking aim at light torpedo search trajectory characteristic of warship, by analyzing common used torpedo search trajectory, a better torpedo search trajectory is designed, a mathematic model is built up, and the simulation calculation taking MK46 torpedo for example is carried out. The calculation results testify that this method can increase acquisition probability and hit probability by about 10%-30% at some situations and becomes feasible for the torpedo trajectory design. The research is of great reference value for the acoustic homing torpedo trajectory design and the torpedo combat efficiency research.
A Bolus Calculator Based on Continuous-Discrete Unscented Kalman Filtering for Type 1 Diabetics
DEFF Research Database (Denmark)
Boiroux, Dimitri; Aradóttir, Tinna Björk; Hagdrup, Morten;
2015-01-01
after or 30 minutes after the beginning of the meal). We implement a continuous-discrete unscented Kalman filter to estimate the states and insulin sensitivity. These estimates are used in a bolus calculator. The numerical results demonstrate that administering the meal bolus 15 minutes after mealtime...
BERGSTRA, A; VANDIJK, RB; HILLEGE, HL; LIE, KI; MOOK, GA
1995-01-01
This study was performed because of observed differences between dye dilution cardiac output and the Fick cardiac output, calculated from estimated oxygen consumption according to LaFarge and Miettinen, and to find a better formula for assumed oxygen consumption. In 250 patients who underwent left a
Baraffe, [No Value; Alibert, Y; Mera, D; Charbrier, G; Beaulieu, JP
1998-01-01
We have computed stellar evolutionary models for stars in a mass range characteristic of Cepheid variables (3
Backward Calculation Based on the Advection and Diffusion of Oil Spills on the Sea Surface
Institute of Scientific and Technical Information of China (English)
LIU Hao; YIN Baoshu; LIN Jianguo
2005-01-01
In the light of the problem of oil pollution brought about by ships, in this paper we present the concept of backward tracing oil spills. In the course of backward calculation of the two-dimensional convection & diffusion equation, on the one hand,the advection term itself has the strong unilateral property, which means information in the upper reaches is transmitted downstream via the advection term; on the other hand,because of the opposite direction of calculation, it is essential for information to be conveyed upstream by means of the advection term. In addition, unlike that in the forward calculation, the diffusion term in the backward calculation is prone to accumulate errors, and thus renders the whole scheme unstable. Therefore, we adopt the central difference to deal with both the convectional term and the diffusion term. By examining two practical examples (1) under the unlimited boundary condition, and (2) under the limited boundary condition, it is proven that this method could achieve fundamentally satisfactory results not only in the open ocean but also in the closed or semi-closed bay.
DEFF Research Database (Denmark)
Sauer, Stephan P. A.; Pitzner-Frydendahl, Henrik Frank; Buse, Mogens;
2015-01-01
methods, the original SOPPA method as well as SOPPA(CCSD) and RPA(D) in the calculation of vertical electronic excitation energies and oscillator strengths is investigated for a large benchmark set of 28 medium-size molecules with 139 singlet and 71 triplet excited states. The results are compared with...
International Nuclear Information System (INIS)
In our country, in last congresses, Gomez et al carried out reactivity calculations based on the solution of the diffusion equation for an energy group using nodal methods in one dimension and the TPL approach (Lineal Perturbation Theory). Later on, Mugica extended the application to the case of multigroup so much so much in one as in two dimensions (X Y geometry) with excellent results. Presently work is carried out similar calculations but this time based on the solution of the neutron transport equation in X Y geometry using nodal methods and again the TPL approximation. The idea is to provide a calculation method that allows to obtain in quick form the reactivity solving the direct problem as well as the enclosed problem of the not perturbed problem. A test problem for the one that results are provided for the effective multiplication factor is described and its are offered some conclusions. (Author)
Application of perturbation theory to lattice calculations based on method of cyclic characteristics
Assawaroongruengchot, Monchai
computing time when both direct and adjoint solutions are required. A problem that arises for the generalized adjoint problem is that the direct use of the negative external generalized adjoint sources in the adjoint solution algorithm results in negative generalized adjoint functions. A coupled flux biasing/decontamination scheme is applied to make the generalized adjoint functions positive using the adjoint functions in such a way that it can be used for the multigroup rebalance technique. Next we consider the application of the perturbation theory to the reactor problems. Since the coolant void reactivity (CVR) is a important factor in reactor safety analysis, we have decided to select this parameter for optimization studies. We consider the optimization and adjoint sensitivity techniques for the adjustments of CVR at beginning of burnup cycle (BOC) and k eff at end of burnup cycle (EOC) for a 2D Advanced CANDU Reactor (ACR) lattice. The sensitivity coefficients are evaluated using the perturbation theory based on the integral transport equations. Three sets of parameters for CVR-BOC and keff-EOC adjustments are studied: (1) Dysprosium density in the central pin with Uranium enrichment in the outer fuel rings, (2) Dysprosium density and Uranium enrichment both in the central pin, and (3) the same parameters as in the first case but the objective is to obtain a negative checkerboard CVR at beginning of cycle (CBCVR-BOC). To approximate the sensitivity coefficient at EOC, we perform constant-power burnup/depletion calculations for 600 full power days (FPD) using a slightly perturbed nuclear library and the unperturbed neutron fluxes to estimate the variation of nuclide densities at EOC. Sensitivity analyses of CVR and eigenvalue are included in the study. In addition the optimization and adjoint sensitivity techniques are applied to the CBCVR-BOC and keff-EOC adjustment of the ACR lattices with Gadolinium in the central pin. Finally we apply these techniques to the CVR
Senol, Ali; Dündar, Sefa; Gündüz, Nazan
2015-01-01
The aim of this study are to examine the relationship between prospective classroom teachers' estimation skills based on calculation and their number sense and to investigate whether their number sense and estimation skills change according to their class level and gender. The participants of the study are 125 prospective classroom teachers…
Gangarapu, S.; Marcelis, A.T.M.; Zuilhof, H.
2013-01-01
The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum mode
Stur, J.; Bos, M.; Linden, van der W.E.
1984-01-01
Fast and accurate calculation procedures for pH and redox potentials are required for optimum control of automatic titrations. The procedure suggested is based on a three-dimensional titration curve V = f(pH, redox potential). All possible interactions between species in the solution, e.g., changes
The edge-based face element method for 3D-stream function and flux calculations in porous media flow
Zijl, W.; Nawalany, M.
2004-01-01
We present a velocity-oriented discrete analog of the partial differential equations governing porous media flow: the edge-based face element method. Conventional finite element techniques calculate pressures in the nodes of the grid. However, such methods do not satisfy the requirement of flux cont
Bekker, H.; Brink, A.A.; Roerdink, J.B.T.M.
2009-01-01
To calculate the Minkowski-sum based similarity measure of two convex polyhedra, many relative orientations have to be considered. These relative orientations are characterized by the fact that some faces and edges of the polyhedra are parallel. For every relative orientation of the polyhedra, the v
Steiner, Wolfgang
2012-01-01
An integral self-affine tile is the solution of a set equation $\\mathbf{A} \\mathcal{T} = \\bigcup_{d \\in \\mathcal{D}} (\\mathcal{T} + d)$, where $\\mathbf{A}$ is an $n \\times n$ integer matrix and $\\mathcal{D}$ is a finite subset of $\\mathbb{Z}^n$. In the recent decades, these objects and the induced tilings have been studied systematically. We extend this theory to matrices $\\mathbf{A} \\in \\mathbb{Q}^{n \\times n}$. We define rational self-affine tiles as compact subsets of the open subring $\\mathbb{R}^n\\times \\prod_\\mathfrak{p} K_\\mathfrak{p}$ of the ad\\'ele ring $\\mathbb{A}_K$, where the factors of the (finite) product are certain $\\mathfrak{p}$-adic completions of a number field $K$ that is defined in terms of the characteristic polynomial of $\\mathbf{A}$. Employing methods from classical algebraic number theory, Fourier analysis in number fields, and results on zero sets of transfer operators, we establish a general tiling theorem for these tiles. We also associate a second kind of tiles with a rational matr...
Graded electron affinity electron source
Energy Technology Data Exchange (ETDEWEB)
Shaw, J.L.; Gray, H.F.; Jensen, K.L.; Jung, T.M. [Naval Research Laboratory, Washington, DC 20375 (United States)
1996-05-01
We describe a new electron source using electric field and low electron affinity semiconductor materials to bring charge to potential energy levels near the vacuum level while still in the solid. The basic idea involves moving some of the potential barrier from the surface to the bulk, and distributing the barrier over a thin layer below the surface. In so doing, the emission physics is changed fundamentally from a quantum mechanical tunneling process largely controlled by surface properties to a classical transport process largely controlled by the band structure of a wide bandgap semiconductor. The composition of the thin layer below the surface would be graded such that the conduction band minimum changes from an energy close to the substrate Fermi level to an energy significantly closer to the vacuum level. Electrons from the substrate would be drawn into the graded composition layer with an electric field produced by a pointed emitter structure and extraction gate similar to that used in field emitter arrays. Relative to a conventional field emitter array, the new source is expected to require lower extraction fields and exhibit improved emission uniformity, stability, and noise. The {ital I}{endash}{ital V} characteristics are not Fowler{endash}Nordheim and may include a saturation effect at high current densities that could be engineered to improve reliability and uniformity. The group III nitrides can be grown with a continuous range of composition that provides the range of electron affinity needed to produce the proposed electronic structure. {copyright} {ital 1996 American Vacuum Society}
The affine quantum gravity programme
International Nuclear Information System (INIS)
The central principle of affine quantum gravity is securing and maintaining the strict positivity of the matrix { g-hat ab(x)} composed of the spatial components of the local metric operator. On spectral grounds, canonical commutation relations are incompatible with this principle, and they must be replaced by noncanonical, affine commutation relations. Due to the partial second-class nature of the quantum gravitational constraints, it is advantageous to use the recently developed projection operator method, which treats all quantum constraints on an equal footing. Using this method, enforcement of regularized versions of the gravitational operator constraints is formulated quite naturally by means of a novel and relatively well-defined functional integral involving only the same set of variables that appears in the usual classical formulation. It is anticipated that skills and insight to study this formulation can be developed by studying special, reduced-variable models that still retain some basic characteristics of gravity, specifically a partial second-class constraint operator structure. Although perturbatively nonrenormalizable, gravity may possibly be understood nonperturbatively from a hard-core perspective that has proved valuable for specialized models. Finally, developing a procedure to pass to the genuine physical Hilbert space involves several interconnected steps that require careful coordination
Shebl, Magdy
2014-01-01
The 1:1 condensation of o-acetoacetylphenol and 1,2-diaminopropane under condition of high dilution gives the mono-condensed Schiff base, (E)-3-(1-aminopropan-2-ylimino)-1-(2-hydroxyphenyl)butan-1-one. The mono-condensed Schiff base has been used for further condensation with isatin to obtain the new asymmetrical dicompartmental Schiff base ligand, (E)-3-(2-((E)-4-(2-hydroxyphenyl)-4-oxobutan-2-ylideneamino) propylimino)indolin-2-one (H3L) with a N2O3 donor set. Reactions of the ligand with metal salts give a series of new binuclear complexes. The ligand and its metal complexes were characterized by elemental analyses, IR, 1H and 13C NMR, electronic, ESR and mass spectra, conductivity and magnetic susceptibility measurements as well as thermal analyses. The analytical and spectroscopic tools showed that the complexes can be formulated as: [(HL)(VO)2(SO4)(H2O)]·4H2O, [(HL)Fe2Cl4(H2O)3]·EtOH, [(HL)Fe2(ox)Cl2(H2O)3]·2H2O, [(L)M2(OAc)(H2O)m]·nH2O; M = Co, Ni or Cu, m = 4, 0 and n = 2, 3, [(HL)Cu2Cl]Cl·6H2O and [(L)(UO2)2(OAc)(H2O)3]·6H2O. The metal complexes exhibited octahedral geometrical arrangements except copper complexes that exhibited tetrahedral geometries and uranyl complex in which the metal ion is octa-coordinated. The Schiff base and its metal complexes were evaluated for antimicrobial activity against Gram positive bacteria (Staphylococcus aureus), Gram negative bacteria (Escherichia coli) and fungi (Candida albicans and Aspergillus flavus). The ligand and some of its complexes were found to be biologically active. The DNA-binding properties of the copper complexes (6 and 7) have been investigated by electronic absorption, fluorescence and viscosity measurements. The results obtained indicate that these complexes bind to DNA via an intercalation binding mode with an intrinsic binding constant, Kb of 1.34 × 104 and 2.5 × 104 M-1, respectively.
Directory of Open Access Journals (Sweden)
Song Hua
2015-01-01
Full Text Available The wheel/rail rolling contact can not only lead to rail fatigue damage but also bring rail corrugation. According to the wheel/rail rolling contact problem, based on the ANSYS/LS-DYNA explicit analysis software, this paper established the finite element model of wheel/rail rolling contact in non-linear steady-state curve negotiation, and proposed the explicit-explicit sequence calculation method that can be used to solve this model. The explicit-explicit sequence calculation method uses explicit solver in calculating the rail pre-stressing force and the process of wheel/rail rolling contact. Compared with the implicit-explicit sequence calculation method that has been widely applied, the explicit-explicit sequence calculation method including similar precision in calculation with faster speed and higher efficiency, make it more applicable to solve the wheel/rail rolling contact problem of non-linear steady-state curving with a large solving model or a high non-linear degree.
Tissue decomposition from dual energy CT data for MC based dose calculation in particle therapy
Energy Technology Data Exchange (ETDEWEB)
Hünemohr, Nora, E-mail: n.huenemohr@dkfz.de; Greilich, Steffen [Medical Physics in Radiation Oncology, German Cancer Research Center, 69120 Heidelberg (Germany); Paganetti, Harald; Seco, Joao [Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 (United States); Jäkel, Oliver [Medical Physics in Radiation Oncology, German Cancer Research Center, 69120 Heidelberg, Germany and Department of Radiation Oncology and Radiation Therapy, University Hospital of Heidelberg, 69120 Heidelberg (Germany)
2014-06-15
Purpose: The authors describe a novel method of predicting mass density and elemental mass fractions of tissues from dual energy CT (DECT) data for Monte Carlo (MC) based dose planning. Methods: The relative electron density ϱ{sub e} and effective atomic number Z{sub eff} are calculated for 71 tabulated tissue compositions. For MC simulations, the mass density is derived via one linear fit in the ϱ{sub e} that covers the entire range of tissue compositions (except lung tissue). Elemental mass fractions are predicted from the ϱ{sub e} and the Z{sub eff} in combination. Since particle therapy dose planning and verification is especially sensitive to accurate material assignment, differences to the ground truth are further analyzed for mass density, I-value predictions, and stopping power ratios (SPR) for ions. Dose studies with monoenergetic proton and carbon ions in 12 tissues which showed the largest differences of single energy CT (SECT) to DECT are presented with respect to range uncertainties. The standard approach (SECT) and the new DECT approach are compared to reference Bragg peak positions. Results: Mean deviations to ground truth in mass density predictions could be reduced for soft tissue from (0.5±0.6)% (SECT) to (0.2±0.2)% with the DECT method. Maximum SPR deviations could be reduced significantly for soft tissue from 3.1% (SECT) to 0.7% (DECT) and for bone tissue from 0.8% to 0.1%. MeanI-value deviations could be reduced for soft tissue from (1.1±1.4%, SECT) to (0.4±0.3%) with the presented method. Predictions of elemental composition were improved for every element. Mean and maximum deviations from ground truth of all elemental mass fractions could be reduced by at least a half with DECT compared to SECT (except soft tissue hydrogen and nitrogen where the reduction was slightly smaller). The carbon and oxygen mass fraction predictions profit especially from the DECT information. Dose studies showed that most of the 12 selected tissues would
TH-A-19A-06: Site-Specific Comparison of Analytical and Monte Carlo Based Dose Calculations
Energy Technology Data Exchange (ETDEWEB)
Schuemann, J; Grassberger, C; Paganetti, H [Massachusetts General Hospital and Harvard Medical School, Boston, MA (United States); Dowdell, S [Illawarra Shoalhaven Local Health District, Wollongong (Australia)
2014-06-15
Purpose: To investigate the impact of complex patient geometries on the capability of analytical dose calculation algorithms to accurately predict dose distributions and to verify currently used uncertainty margins in proton therapy. Methods: Dose distributions predicted by an analytical pencilbeam algorithm were compared with Monte Carlo simulations (MCS) using TOPAS. 79 complete patient treatment plans were investigated for 7 disease sites (liver, prostate, breast, medulloblastoma spine and whole brain, lung and head and neck). A total of 508 individual passively scattered treatment fields were analyzed for field specific properties. Comparisons based on target coverage indices (EUD, D95, D90 and D50) were performed. Range differences were estimated for the distal position of the 90% dose level (R90) and the 50% dose level (R50). Two-dimensional distal dose surfaces were calculated and the root mean square differences (RMSD), average range difference (ARD) and average distal dose degradation (ADD), the distance between the distal position of the 80% and 20% dose levels (R80- R20), were analyzed. Results: We found target coverage indices calculated by TOPAS to generally be around 1–2% lower than predicted by the analytical algorithm. Differences in R90 predicted by TOPAS and the planning system can be larger than currently applied range margins in proton therapy for small regions distal to the target volume. We estimate new site-specific range margins (R90) for analytical dose calculations considering total range uncertainties and uncertainties from dose calculation alone based on the RMSD. Our results demonstrate that a reduction of currently used uncertainty margins is feasible for liver, prostate and whole brain fields even without introducing MC dose calculations. Conclusion: Analytical dose calculation algorithms predict dose distributions within clinical limits for more homogeneous patients sites (liver, prostate, whole brain). However, we recommend
Azuri, Ido; Adler-Abramovich, Lihi; Gazit, Ehud; Hod, Oded; Kronik, Leeor
2014-01-22
The diphenylalanine peptide self-assembles to form nanotubular structures of remarkable mechanical, piezolelectrical, electrical, and optical properties. The tubes are unexpectedly stiff, with reported Young's moduli of 19-27 GPa that were extracted using two independent techniques. Yet the physical basis for the remarkable rigidity is not fully understood. Here, we calculate the Young's modulus for bulk diphenylalanine peptide from first principles, using density functional theory with dispersive corrections. The calculation demonstrates that at least half of the stiffness of the material is the result of dispersive interactions. We further quantify the nature of various inter- and intramolecular interactions. We reveal that despite the porous nature of the lattice, there is an array of rigid nanotube backbones with interpenetrating "zipper-like" aromatic interlocks that result in stiffness and robustness. This presents a general strategy for the analysis of bioinspired functional materials and may pave the way for rational design of bionanomaterials. PMID:24368025
Optimized load calculation in piping systems based on new experimental data
Energy Technology Data Exchange (ETDEWEB)
Popp, Margit [AREVA NP GmbH, Erlangen (Germany)
2009-07-01
The aim of dynamic fluid calculation is to efficiently design piping systems for power plants. Sudden changes of the fluid velocity, caused by e.g. pump or valve trips produce high pressure surges which exceed many times the operational system pressure. The existing piping codes consider most of the standard load cases satisfactorily. Nevertheless, due to increasing requirements on piping systems and for costreduction, the actual unused potential shall be accessed by calculating the fluid loads more realistically and less conservatively. Especially for the computer simulation of dynamic incidents there is still space for innovation and improvement. Since 2006 the AREVA NP GmbH in cooperation with the University of Erlangen-Nuernberg is investigating pressure surge effects in water-filled piping systems (Figure 1, [1]). By means of the experimental data, the existing piping codes shall be validated to improve the models and to get more realistic loads. (orig.)
Navier-Stokes calculations on multi-element airfoils using a chimera-based solver
Jasper, Donald W.; Agrawal, Shreekant; Robinson, Brian A.
1993-01-01
A study of Navier-Stokes calculations of flows about multielement airfoils using a chimera grid approach is presented. The chimera approach utilizes structured, overlapped grids which allow great flexibility of grid arrangement and simplifies grid generation. Calculations are made for two-, three-, and four-element airfoils, and modeling of the effect of gap distance between elements is demonstrated for a two element case. Solutions are obtained using the thin-layer form of the Reynolds averaged Navier-Stokes equations with turbulence closure provided by the Baldwin-Lomax algebraic model or the Baldwin-Barth one equation model. The Baldwin-Barth turbulence model is shown to provide better agreement with experimental data and to dramatically improve convergence rates for some cases. Recently developed, improved farfield boundary conditions are incorporated into the solver for greater efficiency. Computed results show good comparison with experimental data which include aerodynamic forces, surface pressures, and boundary layer velocity profiles.
Aspects of affine Toda field theory
International Nuclear Information System (INIS)
The report is devoted to properties of the affine Toda field theory, the intention being to highlight a selection of curious properties that should be explicable in terms of the underlying group theory but for which in most cases there are no explanation. The motivation for exploring the ideas contained in this report came principally from the recent work of Zamolodchikov concerning the two dimensional Ising model at critical temperature perturbed by a magnetic field. Hollowood and Mansfield pointed out that since Toda field theory is conformal the perturbation considered by Zamolodchikov might well be best regarded as a perturbation of a Toda field theory. This work made it seem plausible that the theory sought by Zamolodchikov was actually affine E8 Toda field theory. However, this connection required an imaginary value of the coupling constant. Investigations here concerning exact S-matrices use a perturbative approach based on real coupling and the results differ in various ways from those thought to correspond to perturbed conformal field theory. A further motivation is to explore the connection between conformal and perturbed conformal field theories in other contexts using similar ideas. (N.K.)
Sauer, Kenneth; Scheer, Hugo; Sauer, Peter
1987-01-01
Excitation energy transfer in C-phycocyanin is modeled using the Forster inductive resonance mechanism. Detailed calculations are carried out using coordinates and orientations of the chromophores derived from X-ray crystallographic studies of C-phycocyanin from two different species (Schirmer et al, J. Mol. Biol. 184, 257–277 (1985) and ibid., 188, 651-677 (1986)). Spectral overlap integrals are estimated from absorption and fluorescence spectra of C-phycocyanin of Mastigocladus laminosus an...
Duality-based calculations for transition probabilities in birth-death processes
Ohkubo, Jun
2015-01-01
Transition probabilities in birth-death processes are fomulated via the corresponding dual birth-death processes. In order to obtain the corresponding dual processes, the Doi-Peliti formalism is employed. Conventional numerical evaluation enables us to obtain the transition probabilities from a fixed initial state; on the other hand, the duality relation gives us a useful method to calculate the transition probabilities to a fixed final state. Furthermore, it is clarified that the transition ...
Calculated neutron KERMA factors based on the LLNL ENDL data file. Volume 27
International Nuclear Information System (INIS)
Neutron KERMA factors calculated from the LLNL ENDL data file are tabulated for 15 composite materials and for the isotopes or elements in the ENDL file from Z = 1 to Z = 29. The incident neutron energies range from 1.882 x 10-5 to 20. MeV for the composite materials and from 1.30 x 10-9 to 20. MeV for the isotopes and elements
Calculations of the hurricane eye motion based on singularity propagation theory
Directory of Open Access Journals (Sweden)
Vladimir Danilov
2002-02-01
Full Text Available We discuss the possibility of using calculating singularities to forecast the dynamics of hurricanes. Our basic model is the shallow-water system. By treating the hurricane eye as a vortex type singularity and truncating the corresponding sequence of Hugoniot type conditions, we carry out many numerical experiments. The comparison of our results with the tracks of three actual hurricanes shows that our approach is rather fruitful.
Comparison of lysimeter based and calculated ASCE reference evapotranspiration in a subhumid climate
Nolz, Reinhard; Cepuder, Peter; Eitzinger, Josef
2016-04-01
The standardized form of the well-known FAO Penman-Monteith equation, published by the Environmental and Water Resources Institute of the American Society of Civil Engineers (ASCE-EWRI), is recommended as a standard procedure for calculating reference evapotranspiration (ET ref) and subsequently plant water requirements. Applied and validated under different climatic conditions it generally achieved good results compared to other methods. However, several studies documented deviations between measured and calculated reference evapotranspiration depending on environmental and weather conditions. Therefore, it seems generally advisable to evaluate the model under local environmental conditions. In this study, reference evapotranspiration was determined at a subhumid site in northeastern Austria from 2005 to 2010 using a large weighing lysimeter (ET lys). The measured data were compared with ET ref calculations. Daily values differed slightly during a year, at which ET ref was generally overestimated at small values, whereas it was rather underestimated when ET was large, which is supported also by other studies. In our case, advection of sensible heat proved to have an impact, but it could not explain the differences exclusively. Obviously, there were also other influences, such as seasonal varying surface resistance or albedo. Generally, the ASCE-EWRI equation for daily time steps performed best at average weather conditions. The outcomes should help to correctly interpret ET ref data in the region and in similar environments and improve knowledge on the dynamics of influencing factors causing deviations.
Polynomial regression calculation of the Earth's position based on millisecond pulsar timing
International Nuclear Information System (INIS)
Prior to achieving high precision navigation of a spacecraft using X-ray observations, a pulsar rotation model must be built and analysis of the precise position of the Earth should be performed using ground pulsar timing observations. We can simulate time-of-arrival ground observation data close to actual observed values before using pulsar timing observation data. Considering the correlation between the Earth's position and its short arc section of an orbit, we use polynomial regression to build the correlation. Regression coefficients can be calculated using the least square method, and a coordinate component series can also be obtained; that is, we can calculate Earth's position in the Barycentric Celestial Reference System according to pulse arrival time data and a precise pulsar rotation model. In order to set appropriate parameters before the actual timing observations for Earth positioning, we can calculate the influence of the spatial distribution of pulsars on errors in the positioning result and the influence of error source variation on positioning by simulation. It is significant that the threshold values of the observation and systematic errors can be established before an actual observation occurs; namely, we can determine the observation mode with small errors and reject the observed data with big errors, thus improving the positioning result.
A User Differential Range Error Calculating Algorithm Based on Analytic Method
Institute of Scientific and Technical Information of China (English)
SHAO Bo; LIU Jiansheng; ZHAO Ruibin; HUANG Zhigang; LI Rui
2011-01-01
To enhance the integrity,an analytic method (AM) which has less execution time is proposed to calculate the user differential range error (UDRE) used by the user to detect the potential risk.An ephemeris and clock correction calculation method is introduced first.It shows that the most important thing of computing UDRE is to find the worst user location (WUL) in the service volume.Then,a UDRE algorithm using AM is described to solve this problem.By using the covariance matrix of the error vector,the searching of WUL is converted to an analytic geometry problem.The location of WUL can be obtained directly by mathematical derivation.Experiments are conducted to compare the performance between the proposed AM algorithm and the exhaustive grid search (EGS) method used in the master station.The results show that the correctness of the AM algorithm can be proved by the EGS method and the AM algorithm can reduce the calculation time by more than 90%.The computational complexity of this proposed algorithm is better than that of EGS.Thereby this algorithm is more suitable for computing UDRE at the master station.
Directory of Open Access Journals (Sweden)
S. Mattedi
2000-12-01
Full Text Available A modified form of the Hicks and Young algorithm was used with the Mattedi-Tavares-Castier lattice equation of state (MTC lattice EOS to calculate critical points of binary mixtures that exhibit several types of critical behavior. Several qualitative aspects of the critical curves, such as maxima and minima in critical pressure, and minima in critical temperature, could be predicted using the MTC lattice EOS. These results were in agreement with experimental information available in the literature, illustrating the flexibility of the functional form of the MTC lattice EOS. We observed however that the MTC lattice EOS failed to predict maxima in pressure for two of the studied systems: ethane + ethanol and methane + n-hexane. We also observed that the agreement between the calculated and experimental critical properties was at most semi-quantitative in some examples. Despite these limitations, in many ways similar to those of other EOS in common use when applied to critical point calculations, we can conclude that the MTC lattice EOS has the ability to predict several types of critical curves of complex shape.
Calculation of Effective Freezing Time in Lung Cancer Cryosurgery Based on Godunov Simulation
Directory of Open Access Journals (Sweden)
Т.G. Kotova
2016-03-01
Full Text Available There have been presented the results of lung cancer cryosurgery simulation using numerical solutions of enthalpy equation according to Godunov method. For the cryodestruction improvement purposes we successfully calculated the effective freezing time taking into account the evolution of an ice ball covering the tumor area. Geometrical transformation parameters of an ice ball have been measured by calculating the temperature distribution and the interface position in biological tissue. Mathematical cryosurgical procedures are described by heat transfer equations in solid and liquid phases. Numerical results for one-dimensional case were verified by comparing with exact solutions. In twodimensional modeling an effective cryotherapy time, which corresponds to freezing time of all tumor parts, was calculated as the area of forming ice balls covering all tumor region. The findings enable to set the effective time of a cryosurgical procedure in lung cancer. The knowledge of temperature distribution and interface position in biological tissue offers an opportunity to a cryosurgeon to finish the procedure within a certain time period to minimize the healthy tissue damage and destroy tumor cells to the maximum. Simulation application enables to schedule cryotherapy in lung cancer more effectively and to a good quality.
Energy Technology Data Exchange (ETDEWEB)
Song, Chan-Ho; Park, Hee-Seong; Ha, Jea-Hyun; Jin, Hyung-Gon; Park, Seung-Kook [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)
2015-05-15
The KAERI be used to calculate the decommissioning cost and manage the data of decommissioning activity experience through systems such as the decommissioning information management system (DECOMMIS), Decommissioning Facility Characterization DB System (DEFACS), decommissioning work-unit productivity calculation system (DEWOCS). Some country such as Japan and The United States have the information for decommissioning experience of the NPP and publish reports on decommissioning cost analysis. These reports as valuable data be used to compare with the decommissioning unit cost. In particular, need a method to estimate the decommissioning cost of the NPP because there is no decommissioning experience of NPP in case of Korea. makes possible to predict the more precise prediction about the decommissioning unit cost. But still, there are many differences on calculation for the decommissioning unit cost in domestic and foreign country. Typically, it is difficult to compare with data because published not detailed reports. Therefore, field of estimation for decommissioning cost have to use a unified framework in order to the decommissioning cost be provided to exact of the decommissioning cost.
Ying, Zhang; Zhengqiang, Li; Yan, Wang
2014-03-01
Anthropogenic aerosols are released into the atmosphere, which cause scattering and absorption of incoming solar radiation, thus exerting a direct radiative forcing on the climate system. Anthropogenic Aerosol Optical Depth (AOD) calculations are important in the research of climate changes. Accumulation-Mode Fractions (AMFs) as an anthropogenic aerosol parameter, which are the fractions of AODs between the particulates with diameters smaller than 1μm and total particulates, could be calculated by AOD spectral deconvolution algorithm, and then the anthropogenic AODs are obtained using AMFs. In this study, we present a parameterization method coupled with an AOD spectral deconvolution algorithm to calculate AMFs in Beijing over 2011. All of data are derived from AErosol RObotic NETwork (AERONET) website. The parameterization method is used to improve the accuracies of AMFs compared with constant truncation radius method. We find a good correlation using parameterization method with the square relation coefficient of 0.96, and mean deviation of AMFs is 0.028. The parameterization method could also effectively solve AMF underestimate in winter. It is suggested that the variations of Angstrom indexes in coarse mode have significant impacts on AMF inversions.
International Nuclear Information System (INIS)
Anthropogenic aerosols are released into the atmosphere, which cause scattering and absorption of incoming solar radiation, thus exerting a direct radiative forcing on the climate system. Anthropogenic Aerosol Optical Depth (AOD) calculations are important in the research of climate changes. Accumulation-Mode Fractions (AMFs) as an anthropogenic aerosol parameter, which are the fractions of AODs between the particulates with diameters smaller than 1μm and total particulates, could be calculated by AOD spectral deconvolution algorithm, and then the anthropogenic AODs are obtained using AMFs. In this study, we present a parameterization method coupled with an AOD spectral deconvolution algorithm to calculate AMFs in Beijing over 2011. All of data are derived from AErosol RObotic NETwork (AERONET) website. The parameterization method is used to improve the accuracies of AMFs compared with constant truncation radius method. We find a good correlation using parameterization method with the square relation coefficient of 0.96, and mean deviation of AMFs is 0.028. The parameterization method could also effectively solve AMF underestimate in winter. It is suggested that the variations of Angstrom indexes in coarse mode have significant impacts on AMF inversions
GIS supported calculations of 137Cs deposition in Sweden based on precipitation data
International Nuclear Information System (INIS)
137Cs deposition maps were made using Kriging interpolation in a Geographical Information System (GIS). Quarterly values of 137Cs deposition density per unit precipitation (Bq/m2/mm) at three reference sites and quarterly precipitation at 62 weather stations distributed over Sweden were used in the calculations of Nuclear Weapons Fallout (NWF). The deposition density of 137Cs, resulting from the Chernobyl accident, was calculated for western Sweden using precipitation data from 46 stations. The lowest levels of NWF 137Cs deposition density were noted in the northeastern and eastern Sweden and the highest levels in the western parts of Sweden. The Chernobyl 137Cs deposition density is highest along the coast in the selected area and the lowest in the southeastern part and along the middle. The sum of the calculated deposition density from NWF and Chernobyl in western Sweden was compared to accumulated activities in soil samples at 27 locations. Comparisons between the predicted values of this study show a good agreement with measured values
Uncertainties in Monte Carlo-based absorbed dose calculations for an experimental benchmark
International Nuclear Information System (INIS)
There is a need to verify the accuracy of general purpose Monte Carlo codes like EGSnrc, which are commonly employed for investigations of dosimetric problems in radiation therapy. A number of experimental benchmarks have been published to compare calculated values of absorbed dose to experimentally determined values. However, there is a lack of absolute benchmarks, i.e. benchmarks without involved normalization which may cause some quantities to be cancelled. Therefore, at the Physikalisch-Technische Bundesanstalt a benchmark experiment was performed, which aimed at the absolute verification of radiation transport calculations for dosimetry in radiation therapy. A thimble-type ionization chamber in a solid phantom was irradiated by high-energy bremsstrahlung and the mean absorbed dose in the sensitive volume was measured per incident electron of the target. The characteristics of the accelerator and experimental setup were precisely determined and the results of a corresponding Monte Carlo simulation with EGSnrc are presented within this study. For a meaningful comparison, an analysis of the uncertainty of the Monte Carlo simulation is necessary. In this study uncertainties with regard to the simulation geometry, the radiation source, transport options of the Monte Carlo code and specific interaction cross sections are investigated, applying the general methodology of the Guide to the expression of uncertainty in measurement. Besides studying the general influence of changes in transport options of the EGSnrc code, uncertainties are analyzed by estimating the sensitivity coefficients of various input quantities in a first step. Secondly, standard uncertainties are assigned to each quantity which are known from the experiment, e.g. uncertainties for geometric dimensions. Data for more fundamental quantities such as photon cross sections and the I-value of electron stopping powers are taken from literature. The significant uncertainty contributions are identified as
Uncertainties in Monte Carlo-based absorbed dose calculations for an experimental benchmark.
Renner, F; Wulff, J; Kapsch, R-P; Zink, K
2015-10-01
There is a need to verify the accuracy of general purpose Monte Carlo codes like EGSnrc, which are commonly employed for investigations of dosimetric problems in radiation therapy. A number of experimental benchmarks have been published to compare calculated values of absorbed dose to experimentally determined values. However, there is a lack of absolute benchmarks, i.e. benchmarks without involved normalization which may cause some quantities to be cancelled. Therefore, at the Physikalisch-Technische Bundesanstalt a benchmark experiment was performed, which aimed at the absolute verification of radiation transport calculations for dosimetry in radiation therapy. A thimble-type ionization chamber in a solid phantom was irradiated by high-energy bremsstrahlung and the mean absorbed dose in the sensitive volume was measured per incident electron of the target. The characteristics of the accelerator and experimental setup were precisely determined and the results of a corresponding Monte Carlo simulation with EGSnrc are presented within this study. For a meaningful comparison, an analysis of the uncertainty of the Monte Carlo simulation is necessary. In this study uncertainties with regard to the simulation geometry, the radiation source, transport options of the Monte Carlo code and specific interaction cross sections are investigated, applying the general methodology of the Guide to the expression of uncertainty in measurement. Besides studying the general influence of changes in transport options of the EGSnrc code, uncertainties are analyzed by estimating the sensitivity coefficients of various input quantities in a first step. Secondly, standard uncertainties are assigned to each quantity which are known from the experiment, e.g. uncertainties for geometric dimensions. Data for more fundamental quantities such as photon cross sections and the I-value of electron stopping powers are taken from literature. The significant uncertainty contributions are identified as
An angular momentum conserving Affine-Particle-In-Cell method
Jiang, Chenfanfu; Teran, Joseph
2016-01-01
We present a new technique for transferring momentum and velocity between particles and grid with Particle-In-Cell (PIC) calculations which we call Affine-Particle-In-Cell (APIC). APIC represents particle velocities as locally affine, rather than locally constant as in traditional PIC. We show that this representation allows APIC to conserve linear and angular momentum across transfers while also dramatically reducing numerical diffusion usually associated with PIC. Notably, conservation is achieved with lumped mass, as opposed to the more commonly used Fluid Implicit Particle (FLIP) transfers which require a 'full' mass matrix for exact conservation. Furthermore, unlike FLIP, APIC retains a filtering property of the original PIC and thus does not accumulate velocity modes on particles as FLIP does. In particular, we demonstrate that APIC does not experience velocity instabilities that are characteristic of FLIP in a number of Material Point Method (MPM) hyperelasticity calculations. Lastly, we demonstrate th...
DEFF Research Database (Denmark)
Gedeborg, R.; Warner, M.; Chen, L. H.;
2014-01-01
BACKGROUND: The International Statistical Classification of Diseases, 10th Revision (ICD-10) -based Injury Severity Score (ICISS) performs well but requires diagnosis-specific survival probabilities (DSPs), which are empirically derived, for its calculation. The objective was to examine if DSPs...... country's own DSPs for ICISS calculation, the pooled DSPs resulted in somewhat reduced discrimination in predicting mortality (difference in c statistic varied from 0.006 to 0.04). Calibration was generally good when the predicted mortality risk was less than 20%. When Danish and Swedish data were used...
Gu, Xuejun; Jelen, Urszula; Li, Jinsheng; Jia, Xun; Jiang, Steve B.
2011-01-01
Targeting at the development of an accurate and efficient dose calculation engine for online adaptive radiotherapy, we have implemented a finite size pencil beam (FSPB) algorithm with a 3D-density correction method on GPU. This new GPU-based dose engine is built on our previously published ultrafast FSPB computational framework [Gu et al. Phys. Med. Biol. 54 6287-97, 2009]. Dosimetric evaluations against Monte Carlo dose calculations are conducted on 10 IMRT treatment plans (5 head-and-neck c...
Directory of Open Access Journals (Sweden)
Jeffrey Klarenbeek
Full Text Available Epac-based FRET sensors have been widely used for the detection of cAMP concentrations in living cells. Originally developed by us as well as others, we have since then reported several important optimizations that make these sensors favourite among many cell biologists. We here report cloning and characterization of our fourth generation of cAMP sensors, which feature outstanding photostability, dynamic range and signal-to-noise ratio. The design is based on mTurquoise2, currently the brightest and most bleaching-resistant donor, and a new acceptor cassette that consists of a tandem of two cp173Venus fluorophores. We also report variants with a single point mutation, Q270E, in the Epac moiety, which decreases the dissociation constant of cAMP from 9.5 to 4 μM, and thus increases the affinity ~ 2.5-fold. Finally, we also prepared and characterized dedicated variants with non-emitting (dark acceptors for single-wavelength FLIM acquisition that display an exceptional near-doubling of fluorescence lifetime upon saturation of cAMP levels. We believe this generation of cAMP outperforms all other sensors and therefore recommend these sensors for all future studies.