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. PMID:26269224
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...
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.
Kang, Youngho; Jeon, Sang Ho; Cho, Youngmi; Han, Seungwu
2016-01-01
We investigate the vertical ionization potential (IP) and electron affinity (EA) of organic semiconductors in the solid state that govern the optoelectrical property of organic devices using a fully ab initio way. The present method combines the density functional theory and many-body perturbation theory based on G W approximations. To demonstrate the accuracy of this approach, we carry out calculations on several prototypical organic molecules. Since IP and EA depend on the molecular orientation at the surface, the molecular geometry of the surface is explicitly considered through the slab model. The computed IP and EA are in reasonable and consistent agreements with spectroscopic data on organic surfaces with various molecular arrangements. However, the transport gaps are slightly underestimated in calculations, which can be explained by different screening effects between surface and bulk regions.
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
Affine invariant texture analysis based on structural properties
Zhang, Jianguo; Tan, Tieniu
2002-01-01
This paper presents a new texture analysis method based on structural properties. The texture features extracted using this algorithm are invariant to affine transform (including rotation, translation, scaling, and skewing). Affine invariant structural properties are derived based on texel areas. An area-ratio map utilizing these properties is introduced to characterize texture images. Histogram based on this map is constructed for texture classification. Efficiency of this algorithm for affi...
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.
Czech Academy of Sciences Publication Activity Database
Ehala, Sille; Dybal, Jiří; Makrlík, E.; Kašička, Václav
2009-01-01
Roč. 32, č. 4 (2009), s. 597-604. ISSN 1615-9306 R&D Projects: GA ČR(CZ) GA203/06/1044; GA ČR(CZ) GA203/08/1428; GA AV ČR 1ET400500402 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z40500505 Keywords : capillary affinity electrophoresis * valinomycin * ab initio calculation Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.551, year: 2009
Affinity based and molecularly imprinted cryogels: Applications in biomacromolecule purification.
Andaç, Müge; Galaev, Igor Yu; Denizli, Adil
2016-05-15
The publications in macro-molecularly imprinted polymers have increased drastically in recent years with the development of water-based polymer systems. The macroporous structure of cryogels has allowed the use of these materials within different applications, particularly in affinity purification and molecular imprinting based methods. Due to their high selectivity, specificity, efficient mass transfer and good reproducibility, molecularly imprinted cryogels (MICs) have become attractive for researchers in the separation and purification of proteins. In this review, the recent developments in affinity based cryogels and molecularly imprinted cryogels in protein purification are reviewed comprehensively. PMID:26454622
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.
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.
Electron Affinity Calculations for Atoms: Sensitive Probe of Many-Body Effects
Felfli, Z.; Msezane, A. Z.
2016-05-01
Electron-electron correlations and core-polarization interactions are crucial for the existence and stability of most negative ions. Therefore, they can be used as a sensitive probe of many-body effects in the calculation of the electron affinities (EAs) of atoms. The importance of relativistic effects in the calculation of the EAs of atoms has recently been assessed to be insignificant up to Z of 85. Here we use the complex angular momentum (CAM) methodology wherein is embedded fully the electron-electron correlations, to investigate core-polarization interactions in low-energy electron elastic scattering from the atoms In, Sn, Eu, Au and At through the calculation of their EAs. For the core-polarization interaction we use the 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 CAM 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 correlations and core polarization interactions (both major many-body effects) are accounted for adequately the importance of relativity on the calculation of the EAs of atoms can be assessed. Even for the high Z (85) At atom relativistic effects are estimated to contribute a maximum of 3.6% to its EA calculation.
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.
Kool, J.; N. Jonker; Irth, H.; Niessen, W.M.A.
2011-01-01
This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein–protein and protein–immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of prote...
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.
Affinity approaches in RNAi-based therapeutics purification.
Pereira, Patrícia; Queiroz, João A; Figueiras, Ana; Sousa, Fani
2016-05-15
The recent investigation on RNA interference (RNAi) related mechanisms and applications led to an increased awareness of the importance of RNA in biology. Nowadays, RNAi-based technology has emerged as a potentially powerful tool for silencing gene expression, being exploited to develop new therapeutics for treating a vast number of human disease conditions, as it is expected that this technology can be translated onto clinical applications in a near future. This approach makes use of a large number of small (namely short interfering RNAs, microRNAs and PIWI-interacting RNAs) and long non-coding RNAs (ncRNAs), which are likely to have a crucial role as the next generation therapeutics. The commercial and biomedical interest in these RNAi-based therapy applications have fostered the need to develop innovative procedures to easily and efficiently purify RNA, aiming to obtain the final product with high purity degree, good quality and biological activity. Recently, affinity chromatography has been applied to ncRNAs purification, in view of the high specificity. Therefore, this article intends to review the biogenesis pathways of regulatory ncRNAs and also to discuss the most significant and recent developments as well as applications of affinity chromatography in the challenging task of purifying ncRNAs. In addition, the importance of affinity chromatography in ncRNAs purification is addressed and prospects for what is forthcoming are presented. PMID:26830537
Realization of parking task based on affine system modeling
International Nuclear Information System (INIS)
This paper presents a motion control system of an unmanned vehicle, where parallel parking task is realized based on a self-organizing affine system modeling and a quadratic programming based robust controller. Because of non-linearity of the vehicle system and complexity of the task to realize, control objective is not always realized with a single algorithm or control mode. This paper presents a hybrid model for parallel parking task in which seven modes for describing sub-tasks constitute an entire model
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
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
Sippl, Wolfgang
2002-12-01
We have recently reported the development of a 3-D QSAR model for estrogen receptor ligands showing a significant correlation between calculated molecular interaction fields and experimentally measured binding affinity. The ligand alignment obtained from docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection procedure, a significant and robust model was obtained (q(2)(LOO)=0.921, SDEP=0.345). To further analyze the robustness and the predictivity of the established model several recently developed estrogen receptor ligands were selected as external test set. An excellent agreement between predicted and experimental binding data was obtained indicated by an external SDEP of 0.531. Two other traditionally used prediction techniques were applied in order to check the performance of the receptor-based 3-D QSAR procedure. The interaction energies calculated on the basis of receptor-ligand complexes were correlated with experimentally observed affinities. Also ligand-based 3-D QSAR models were generated using program FlexS. The interaction energy-based model, as well as the ligand-based 3-D QSAR models yielded models with lower predictivity. The comparison with the interaction energy-based model and with the ligand-based 3-D QSAR models, respectively, indicates that the combination of receptor-based and 3-D QSAR methods is able to improve the quality of prediction. PMID:12413831
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...
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 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
Standard Bases for Affine SL(n)-Modules
Kreiman, V.; Lakshmibai, V.; Magyar, P.; Weyman, J.
2004-01-01
We give an elementary and easily computable basis for the Demazure modules in the basic representation of the affine Lie algebra sl(n)-hat (and the loop group SL(n)-hat). A novel feature is that we define our basis ``bottom-up'' by raising each extremal weight vector, rather than ``top-down'' by lowering the highest weight vector. Our basis arises naturally from the combinatorics of its indexing set, which consists of certain subsets of the integers first specified by the Kyoto school in term...
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...
Li, Peng; He, Tingting; Hu, Xiaohua; Zhao, Junmin; Shen, Xianjun; Zhang, Ming; Wang, Yan
2014-06-01
A novel algorithm based on Connected Affinity Clique Extension (CACE) for mining overlapping functional modules in protein interaction network is proposed in this paper. In this approach, the value of protein connected affinity which is inferred from protein complexes is interpreted as the reliability and possibility of interaction. The protein interaction network is constructed as a weighted graph, and the weight is dependent on the connected affinity coefficient. The experimental results of our CACE in two test data sets show that the CACE can detect the functional modules much more effectively and accurately when compared with other state-of-art algorithms CPM and IPC-MCE. PMID:24803142
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
Experimental Immunization Based on Plasmodium Antigens Isolated by Antibody Affinity
Kamali, Ali N.; Marín-García, Patricia; Azcárate, Isabel G.; Puyet, Antonio; Diez, Amalia; Bautista, José M.
2015-01-01
Vaccines blocking malaria parasites in the blood-stage diminish mortality and morbidity caused by the disease. Here, we isolated antigens from total parasite proteins by antibody affinity chromatography to test an immunization against lethal malaria infection in a murine model. We used the sera of malaria self-resistant ICR mice to lethal Plasmodium yoelii yoelii 17XL for purification of their IgGs which were subsequently employed to isolate blood-stage parasite antigens that were inoculated to immunize BALB/c mice. The presence of specific antibodies in vaccinated mice serum was studied by immunoblot analysis at different days after vaccination and showed an intensive immune response to a wide range of antigens with molecular weight ranging between 22 and 250 kDa. The humoral response allowed delay of the infection after the inoculation to high lethal doses of P. yoelii yoelii 17XL resulting in a partial protection against malaria disease, although final survival was managed in a low proportion of challenged mice. This approach shows the potential to prevent malaria disease with a set of antigens isolated from blood-stage parasites. PMID:26539558
Witos, Joanna; Samuelsson, Jörgen; Cilpa-Karhu, Geraldine; Metso, Jari; Jauhiainen, Matti; Riekkola, Marja-Liisa
2015-05-01
In this work, a method to study and analyze the interaction data in free solution by exploiting partial filling affinity capillary electrophoresis (PF-ACE) followed by adsorption energy distribution calculations (AED) prior model fit to adsorption isotherms will be demonstrated. PF-ACE-AED approach allowed the possibility to distinguish weak and strong interactions of the binding processes between the most common apolipoprotein E protein isoforms (apoE2, apoE3, apoE4) of high density lipoprotein (HDL) and apoE-containing HDL2 with major glycosaminoglycan (GAG) chain of proteoglycans (PGs), chondroitin-6-sulfate (C6S). The AED analysis clearly revealed the heterogeneity of the binding processes. The major difference was that they were heterogeneous with two different adsorption sites for apoE2 and apoE4 isoforms, whereas interestingly for apoE3 and apoE-containing HDL2, the binding was homogeneous (one site) adsorption process. Moreover, our results allowed the evaluation of differences in the binding process strengths giving the following order with C6S: apoE-containing HDL2 > apoE2 > apoE4 > apoE3. In addition, the affinity constant values determined could be compared with those obtained in our previous studies for the interactions between apoE isoforms and another important GAG chain of PGs - dermatan sulfate (DS). The success of the combination of AED calculations prior to non-linear adsorption isotherm model fit with PF-ACE when the concentration range was extended, confirmed the power of the system in the clarification of the heterogeneity of biological processes studied. PMID:25751597
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
Preparation of Affinity Column Based on Zr{sup 4+} Ion for Phosphoproteins Isolation
Energy Technology Data Exchange (ETDEWEB)
Lee, Seon Mi; Bae, In Ae; Park, Jung Hyen; Kim, Tae Dong; Choi, Seong Ho [Hannam University, Daejeon (Korea, Republic of)
2009-06-15
This paper has described about preparation of Zr{sup 4+} affinity column based on the poly(styreneco- glycidyl methacrylate) prepared by emulsion polymerization of styrene and glycidyl methacrylate in order to isolate phosphopeptide. The Zr{sup 4+} ions were introduced after the phophonation of an epoxy group on polymeric microspheres. The successful preparation of Zr{sup 4+}-immobilized polymeric microsphere stationary phase was confirmed through Fourier transform infrared spectra, optical microscopy, scanning electron microscopy, X-ray photoelectron spectra and inductively coupled plasma-atomic emission spectrometer. The separation efficiency for Zr{sup 4+} affinity column prepared by slurry packing was tested to phosphonated casein and dephosphonated casein. The resolution time (min) of the phosphonated casein was higher than that of dephosphated casein for Zr{sup 4+} affinity polymeric microsphere by liquid chromatography. This Zr{sup 4+} affinity column can be used for isolation of phosphonated casein from casein using liquid chromatography.
Preparation of Affinity Column Based on Zr4+ Ion for Phosphoproteins Isolation
International Nuclear Information System (INIS)
This paper has described about preparation of Zr4+ affinity column based on the poly(styreneco- glycidyl methacrylate) prepared by emulsion polymerization of styrene and glycidyl methacrylate in order to isolate phosphopeptide. The Zr4+ ions were introduced after the phophonation of an epoxy group on polymeric microspheres. The successful preparation of Zr4+-immobilized polymeric microsphere stationary phase was confirmed through Fourier transform infrared spectra, optical microscopy, scanning electron microscopy, X-ray photoelectron spectra and inductively coupled plasma-atomic emission spectrometer. The separation efficiency for Zr4+ affinity column prepared by slurry packing was tested to phosphonated casein and dephosphonated casein. The resolution time (min) of the phosphonated casein was higher than that of dephosphated casein for Zr4+ affinity polymeric microsphere by liquid chromatography. This Zr4+ affinity column can be used for isolation of phosphonated casein from casein using liquid chromatography
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.
Quantum image encryption based on generalized affine transform and logistic map
Liang, Hao-Ran; Tao, Xiang-Yang; Zhou, Nan-Run
2016-03-01
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.
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.
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 ...
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 constraint optimization for nearly-automatic vessel segmentation
Cooper, O.; Freiman, M.; Joskowicz, L.; Lischinski, D.
2010-03-01
We present an affinity-based optimization method for nearly-automatic vessels segmentation in CTA scans. The desired segmentation is modeled as a function that minimizes a quadratic affinity-based functional. The functional incorporates intensity and geometrical vessel shape information and a smoothing constraint. Given a few user-defined seeds, the minimum of the functional is obtained by solving a single set of linear equations. The binary segmentation is then obtained by applying a user-selected threshold. The advantages of our method are that it requires fewer initialization seeds, is robust, and yields better results than existing graph-based interactive segmentation methods. Experimental results on 20 vessel segments including the carotid arteries bifurcation and noisy parts of the carotid yield a mean symmetric surface error of 0.54mm (std=0.28).
Data base to compare calculations and observations
International Nuclear Information System (INIS)
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
Continuous Equilibrium in Affine and Information-Based Capital Asset Pricing Models
Horst, U.; Kupper, M.; Macrina, A; Mainberger, C.
2012-01-01
We consider a class of generalized capital asset pricing models in continuous time with a finite number of agents and tradable securities. The securities may not be sufficient to span all sources of uncertainty. If the agents have exponential utility functions and the individual endowments are spanned by the securities, an equilibrium exists and the agents' optimal trading strategies are constant. Affine processes, and the theory of information-based asset pricing are used to model the endoge...
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.
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...
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.
Lipid A-based affinity biosensor for screening anti-sepsis components from herbs
Directory of Open Access Journals (Sweden)
Jie Yao
2014-05-01
Full Text Available LPS (lipopolysaccharide, an outer membrane component of Gram-negative bacteria, plays an important role in the pathogenesis of sepsis and lipid A is known to be essential for its toxicity. Therefore it could be an effective measure to prevent sepsis by neutralizing or destroying LPS. Numerous studies have indicated that many traditional Chinese medicines are natural antagonists of LPS in vitro and in vivo. The goal of this study is to develop a rapid method to screen anti-sepsis components from Chinese herbs by use of a direct lipid A-based affinity biosensor technology based on a resonant mirror. The detergent OG (n-octyl β-D-glucopyranoside was immobilized on a planar non-derivatized cuvette which provided an alternative surface to bind the terminal hydrophilic group of lipid A. A total of 78 herbs were screened based on the affinity biosensor with a target of lipid A. The aqueous extract of PSA (Paeonia suffruticosa Andr was found to possess the highest capability of binding lipid A. Therefore an aqueous extraction from this plant was investigated further by our affinity biosensor, polyamide chromatography and IEC–HPLC. Finally, we obtained a component (PSA-I-3 from Paeonia suffruticosa Andr that was evaluated with the affinity biosensor. We also studied the biological activities of PSA-I-3 against sepsis in vitro and in vivo to further confirm the component we screened with the biosensor. In vitro, we found that PSA-I-3 could decrease TNFα (tumour necrosis factor α release from RAW264.7 cells induced by LPS in a dose-dependent manner. In vivo, it increased remarkably the survival of KM (KunMing mice by challenging both lethal-dose LPS and heat-killed Escherichia coli compared with control groups. Our results suggest that the constructed affinity biosensor can successfully screen the anti-sepsis component from Chinese herbs.
Simulation of fires based on flow calculation
International Nuclear Information System (INIS)
The fire simulation based on flow calculation is described in the publication, and the calculated result is compared with the results obtained from fire tests. The tests have been made in Germany in a nuclear power plant removed from service. The simulation describes the flow field of the entire building, the main features of the construction effecting on it and the edge conditions. The fire is described as a given source, the value of which varies as a function of time. Heat transfer into the constructions is described using a separate heat transfer program. The result obtained from calculation describes the flow and temperature fields formed in a fire generally correctly. Due to the used sparse calculation network the results contain locally large deviations. The discrete-transfer radiation calculation method used for calculation of burning and heat transfer, and testing of it are described in the appendix. The method describes the heat radiation propagating diagonally to the calculation network better than the six-flux method used before
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...
Fractal-based exponential distribution of urban density and self-affine fractal forms of cities
International Nuclear Information System (INIS)
Highlights: ► The model of urban population density differs from the common exponential function. ► Fractal landscape influences the exponential distribution of urban density. ► The exponential distribution of urban population suggests a self-affine fractal. ► Urban space can be divided into three layers with scaling and non-scaling regions. ► The dimension of urban form with characteristic scale can be treated as 2. - Abstract: 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 verify the theoretical inference. Based on the empirical analysis, a three-ring model of cities is presented and a city is conceptually divided into three layers from core to periphery. The scaling region and non-scaling region appear alternately in the city. This model may be helpful for future urban studies and city planning.
DEFF Research Database (Denmark)
Guglielmi, Michel; Johannesen, Hl
, Essex, Hertfordshire, Norfolk and Suffolk. Research found that there was a lack of identity or sense of belonging and nothing anchoring people to the region as a whole. Common affinity is somehow forced to the people of East England and thereby we came to the conclusion that a single landmark or a...... a sense 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...
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.
Gaussian Affine Feature Detector
Xu, Xiaopeng
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 achieves or outperforms existing approaches in term of accuracy, speed and stability. The method can detect small, long or thin objects precisely, and works well under general conditions, such as for low contrast, blurred or noisy images.
Improving Network Performance with Affinity based Mobility Model in Opportunistic Network
Batabyal, Suvadip; 10.5121/ijwmn.2012.4213
2012-01-01
Opportunistic network is a type of Delay Tolerant Network which is characterized by intermittent connectivity amongst the nodes and communication largely depends upon the mobility of the participating nodes. The network being highly dynamic, traditional MANET protocols cannot be applied and the nodes must adhere to store-carry-forward mechanism. Nodes do not have the information about the network topology, number of participating nodes and the location of the destination node. Hence, message transfer reliability largely depends upon the mobility pattern of the nodes. In this paper we have tried to find the impact of RWP (Random Waypoint) mobility on packet delivery ratio. We estimate mobility factors like number of node encounters, contact duration(link time) and inter-contact time which in turn depends upon parameters like playfield area (total network area), number of nodes, node velocity, bit-rate and RF range of the nodes. We also propose a restricted form of RWP mobility model, called the affinity based ...
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.
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.
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 k...
Dimension theory and fractal constructions based on self-affine carpets
Fraser, Jonathan M.
2013-01-01
The aim of this thesis is to develop the dimension theory of self-affine carpets in several directions. Self-affine carpets are an important class of planar self-affine sets which have received a great deal of attention in the literature on fractal geometry over the last 30 years. These constructions are important for several reasons. In particular, they provide a bridge between the relatively well-understood world of self-similar sets and the far from understood world of general self-affi...
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.
GPU-based calculations in digital holography
Madrigal, R.; Acebal, P.; Blaya, S.; Carretero, L.; Fimia, A.; Serrano, F.
2013-05-01
In this work we are going to apply GPU (Graphical Processing Units) with CUDA environment for scientific calculations, concretely high cost computations on the field of digital holography. For this, we have studied three typical problems in digital holography such as Fourier transforms, Fresnel reconstruction of the hologram and the calculation of vectorial diffraction integral. In all cases the runtime at different image size and the corresponding accuracy were compared to the obtained by traditional calculation systems. The programs have been carried out on a computer with a graphic card of last generation, Nvidia GTX 680, which is optimized for integer calculations. As a result a large reduction of runtime has been obtained which allows a significant improvement. Concretely, 15 fold shorter times for Fresnel approximation calculations and 600 times for the vectorial diffraction integral. These initial results, open the possibility for applying such kind of calculations in real time digital holography.
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.
The Lectin Frontier Database (LfDB, and Data Generation Based on Frontal Affinity Chromatography
Directory of Open Access Journals (Sweden)
Jun Hirabayashi
2015-01-01
Full Text Available Lectins are a large group of carbohydrate-binding proteins, having been shown to comprise at least 48 protein scaffolds or protein family entries. They occur ubiquitously in living organisms—from humans to microorganisms, including viruses—and while their functions are yet to be fully elucidated, their main underlying actions are thought to mediate cell-cell and cell-glycoconjugate interactions, which play important roles in an extensive range of biological processes. The basic feature of each lectin’s function resides in its specific sugar-binding properties. In this regard, it is beneficial for researchers to have access to fundamental information about the detailed oligosaccharide specificities of diverse lectins. In this review, the authors describe a publicly available lectin database named “Lectin frontier DataBase (LfDB”, which undertakes the continuous publication and updating of comprehensive data for lectin-standard oligosaccharide interactions in terms of dissociation constants (Kd’s. For Kd determination, an advanced system of frontal affinity chromatography (FAC is used, with which quantitative datasets of interactions between immobilized lectins and >100 fluorescently labeled standard glycans have been generated. The FAC system is unique in its clear principle, simple procedure and high sensitivity, with an increasing number (>67 of associated publications that attest to its reliability. Thus, LfDB, is expected to play an essential role in lectin research, not only in basic but also in applied fields of glycoscience.
Clustering Protein Sequences Using Affinity Propagation Based on an Improved Similarity Measure
Directory of Open Access Journals (Sweden)
Fan Yang
2010-01-01
Full Text Available The sizes of the protein databases are growing rapidly nowadays, thus it becomes increasingly important to cluster protein sequences only based on sequence information. In this paper we improve the similarity measure proposed by Kelil et al, then cluster sequences using the Affinity propagation (AP algorithm and provide a method to decide the input preference of AP algorithm. We tested our method extensively and compared its performance with other four methods on several datasets of COG, G protein, CAZy, SCOP database. We consistently observed that, the number of clusters that we obtained for a given set of proteins approximate to the correct number of clusters in that set. Moreover, in our experiments, the quality of the clusters when quantified by F-measure was better than that of other algorithms (on average, it is 15% better than that of BlastClust, 56% better than that of TribeMCL, 23% better than that of CLUSS, and 42% better than that of Spectral clustering.
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.
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.
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...
Directory of Open Access Journals (Sweden)
Luigi Capoferri
Full Text Available Prediction of human Cytochrome P450 (CYP binding affinities of small ligands, i.e., substrates and inhibitors, represents an important task for predicting drug-drug interactions. A quantitative assessment of the ligand binding affinity towards different CYPs can provide an estimate of inhibitory activity or an indication of isoforms prone to interact with the substrate of inhibitors. However, the accuracy of global quantitative models for CYP substrate binding or inhibition based on traditional molecular descriptors can be limited, because of the lack of information on the structure and flexibility of the catalytic site of CYPs. Here we describe the application of a method that combines protein-ligand docking, Molecular Dynamics (MD simulations and Linear Interaction Energy (LIE theory, to allow for quantitative CYP affinity prediction. Using this combined approach, a LIE model for human CYP 1A2 was developed and evaluated, based on a structurally diverse dataset for which the estimated experimental uncertainty was 3.3 kJ mol-1. For the computed CYP 1A2 binding affinities, the model showed a root mean square error (RMSE of 4.1 kJ mol-1 and a standard error in prediction (SDEP in cross-validation of 4.3 kJ mol-1. A novel approach that includes information on both structural ligand description and protein-ligand interaction was developed for estimating the reliability of predictions, and was able to identify compounds from an external test set with a SDEP for the predicted affinities of 4.6 kJ mol-1 (corresponding to 0.8 pKi units.
International Nuclear Information System (INIS)
Highlights: • Applying chemical affinity for investigating the effects of additives. • Effects of thermodynamic additives on methane hydrate formation kinetics. • Determining kinetic parameters for methane hydrate formation with additives. • A unique path for the methane hydrate formation with aqueous solution of addetives. - Abstract: In this work, methane hydrate formation process (as a process for energy conversion and cool-energy storage) with or without additives was investigated. First, the effects of initial pressure and three surfactants (sodium dodecyl sulfate (SDS), dodecyltrimethyl ammonium bromide (DTAB) and Triton X-100 (TX-100)) and two thermodynamic additives (tetrahydrofuran (THF) and tetra butyl ammonium bromide (TBAB)) on methane hydrate formation kinetics were experimentally studied. Then the macroscopic modeling of methane hydrate formation kinetics with and without additives based on chemical affinity was done. The kinetic parameters of the chemical affinity model were determined for methane hydrate formation with and without additives. The effects of initial pressure and additives on the chemical affinity model parameters were also investigated. In addition, the results of the model were in a good agreement with experimental data
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…
Hung, KP; Cheung, PYS; Yung, NHC
1996-01-01
In page-based distributed shared memory systems, a large page size makes efficient use of interconnection network, but increases the chance of false sharing, while a small page size reduces the level of false sharing but results in an inefficient use of the network. This paper proposes a technique that uses process affinity to achieve data pages clustering so as to optimize the temporal data locality on DSM systems, and therefore reduces the chance of false sharing and improves the data local...
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 ...
Modification of silica-based monolithic capillary columns for boronate affinity chromatography
Czech Academy of Sciences Publication Activity Database
Moravcová, Dana; Planeta, Josef; Kahle, Vladislav; Roth, Michal
2011. P2-G-471-WE. ISBN 978-963-89335-0-8. [International Symposium on High - Performance Liquid Phase Separations and Related Techniques /36./. 19.06.2011-23.06.2011, Budapest] R&D Projects: GA AV ČR IAAX00310701; GA MŠk LC06023 Institutional research plan: CEZ:AV0Z40310501 Keywords : silicagel monolithic column * boronate affinity chromatography Subject RIV: CB - Analytical Chemistry, Separation
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
Passive Fault Tolerant Control of Piecewise Affine Systems Based on H Infinity Synthesis
DEFF Research Database (Denmark)
Gholami, Mehdi; Cocquempot, vincent; Schiøler, Henrik; Bak, Thomas
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...... 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....
Directory of Open Access Journals (Sweden)
Haiquan Zhao
2014-01-01
Full Text Available A new improved memorised improved proportionate affine projection algorithm (IMIPAPA is proposed to improve the convergence performance of sparse system identification, which incorporates l(0-norm as a measure of sparseness into a recently proposed MIPAPA algorithm. In addition, a simplified implementation of the IMIPAPA (SIMIPAPA with low-computational burden is presented while maintaining the consistent convergence performance. The simulation results demonstrate that the IMIPAPA and SIMIPAPA algorithms outperform the MIPAPA algorithm for sparse system identification.
Automated evaluation of protein binding affinity of anti-inflammatory choline based ionic liquids.
Ribeiro, Rosa; Pinto, Paula C A G; Azevedo, Ana M O; Bica, Katharina; Ressmann, Anna K; Reis, Salette; Saraiva, M Lúcia M F S
2016-04-01
In this work, an automated system for the study of the interaction of drugs with human serum albumin (HSA) was developed. The methodology was based on the quenching of the intrinsic fluorescence of HSA by binding of the drug to one of its binding sites. The fluorescence quenching assay was implemented in a sequential injection analysis (SIA) system and the optimized assay was applied to ionic liquids based on the association of non-steroidal anti-inflammatory drugs with choline (IL-API). In each cycle, 100µL of HSA and 100µL of IL-API (variable concentration) were aspirated at a flow rate of 1mLmin(-1) and then sent through the reaction coil to the detector where the fluorescence intensity was measured. In the optimized conditions the effect of increasing concentrations of choline ketoprofenate and choline naproxenate (and respective starting materials: ketoprofen and naproxen) on the intrinsic fluorescence of HSA was studied and the dissociation constants (Kd) were calculated by means of models of drug-protein binding in the equilibrium. The calculated Kd showed that all the compounds bind strongly to HSA (Kd<100µmolL(-1)) and that the use of the drugs in the IL format does not affect or can even improve their HSA binding. The obtained results were compared with those provided by a conventional batch assay and the relative errors were lower than 4.5%. The developed SIA methodology showed to be robust and exhibited good repeatability in all the assay conditions (rsd<6.5%). PMID:26838377
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.
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.)
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.
Rivera-Delgado, Edgardo; Sadeghi, Zhina; Wang, Nick X; Kenyon, Jonathan; Satyanarayan, Sapna; Kavran, Michael; Flask, Chris; Hijaz, Adonis Z; von Recum, Horst A
2016-01-01
The protein chemokine (C-C motif) ligand 7 (CCL7) is significantly over-expressed in urethral and vaginal tissues immediately following vaginal distention in a rat model of stress urinary incontinence. Further evidence, in this scenario and other clinical scenarios, indicates CCL7 stimulates stem cell homing for regenerative repair. This CCL7 gradient is likely absent or compromised in the natural repair process of women who continue to suffer from SUI into advanced age. We evaluated the feasibility of locally providing this missing CCL7 gradient by means of an affinity-based implantable polymer. To engineer these polymers we screened the affinity of different proteoglycans, to use them as CCL7-binding hosts. We found heparin to be the strongest binding host for CCL7 with a 0.323 nM dissociation constant. Our experimental approach indicates conjugation of heparin to a polymer backbone (using either bovine serum albumin or poly (ethylene glycol) as the base polymer) can be used as a delivery system capable of providing sustained concentrations of CCL7 in a therapeutically useful range up to a month in vitro. With this approach we are able to detect, after polymer implantation, significant increase in CCL7 in the urethral tissue directly surrounding the polymer implants with only trace amounts of human CCL7 present in the blood of the animals. Whole animal serial sectioning shows evidence of retention of locally injected human mesenchymal stem cells (hMSCs) only in animals with sustained CCL7 delivery, 2 weeks after affinity-polymers were implanted. PMID:27097800
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.
Samanta, Pabitra Narayan; Das, Kalyan Kumar
2016-01-01
Inhibition activities of a series of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamides against the human carbonic anhydrase II (HCAII) enzyme have been explored by employing molecular docking and hybrid QM/MM methods. The docking protocol has been employed to assess the best pose of each ligand in the active site cavity of the enzyme, and probe the interactions with the amino acid residues. The docking calculations reveal that the inhibitor binds to the catalytic Zn(2+) site through the deprotonated sulfonamide nitrogen atom by making several hydrophobic and hydrogen bond interactions with the side chain residues depending on the substituted moiety. A cross-docking approach has been adopted prior to the hybrid QM/MM calculation to validate the docked poses. A correlation between the experimental dissociation constants and the docked free energies for the enzyme-inhibitor complexes has been established. Two-layered ONIOM calculations based on QM/MM approach have been performed to evaluate the binding efficacy of the inhibitors. The inhibitor potency has been predicted from the computed binding energies after taking into account of the electronic phenomena associated with enzyme-inhibitor interactions. Both the hybrid (B3LYP) and meta-hybrid (M06-2X) functionals are used for the description of the QM region. To improve the correlation between the experimental biological activity and the theoretical results, a three-layered ONIOM calculation has been carried out and verified for some of the selected inhibitors. The charge transfer stabilization energies are calculated via natural bond orbital analysis to recognize the donor-acceptor interaction in the binding pocket of the enzyme. The nature of binding between the inhibitors and HCAII active site is further analyzed from the electron density distribution maps. PMID:26619075
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
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
Gan, Haitao; Sang, Nong; Huang, Rui
2014-01-01
Face recognition is one of the most important applications of machine learning and computer vision. The traditional supervised learning methods require a large amount of labeled face images to achieve good performance. In practice, however, labeled images are usually scarce while unlabeled ones may be abundant. In this paper, we introduce a semi-supervised face recognition method, in which semi-supervised linear discriminant analysis (SDA) and affinity propagation (AP) are integrated into a self-training framework. In particular, SDA is employed to compute the face subspace using both labeled and unlabeled images, and AP is used to identify the exemplars of different face classes in the subspace. The unlabeled data can then be classified according to the exemplars and the newly labeled data with the highest confidence are added to the labeled data, and the whole procedure iterates until convergence. A series of experiments on four face datasets are carried out to evaluate the performance of our algorithm. Experimental results illustrate that our algorithm outperforms the other unsupervised, semi-supervised, and supervised methods. PMID:24561932
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.
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
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.
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
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.
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
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.
Programmable calculator: alternative to minicomputer-based analyzer
International Nuclear Information System (INIS)
Described are a number of typical field and laboratory counting systems that use standard stand-alone multichannel analyzers (MCA) interfaced to a Hewlett-Packard Company (HP 9830) programmable calculator. Such systems can offer significant advantages in cost and flexibility over a minicomputyr-based system. Because most laboratories tend to accumulate MCA's over the years, the programmable calculator also offers an easy way to upgrade the laboratory while making optimum use of existing systems. Software programs are easily tailored to fit a variety of general or specific applications. The only disadvantage of the calculator vs a computer-based system is in speed of analyses; however, for most applications this handicap is minimal. Applications discussed give a brief overview of the power and flexibility of the MCA-calculator approach to automated counting and data reduction
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) ...
On the calculation of percentile-based bibliometric indicators
Waltman, Ludo
2012-01-01
A percentile-based bibliometric indicator is an indicator that values publications based on their position within the citation distribution of their field. The most straightforward percentile-based indicator is the proportion of frequently cited publications, for instance the proportion of publications that belong to the top 10% most frequently cited of their field. Recently, more complex percentile-based indicators were proposed. A difficulty in the calculation of percentile-based indicators is caused by the discrete nature of citation distributions combined with the presence of many publications with the same number of citations. We introduce an approach to calculating percentile-based indicators that deals with this difficulty in a more satisfactory way than earlier approaches suggested in the literature. We show in a formal mathematical framework that our approach leads to indicators that do not suffer from biases in favor of or against particular fields of science.
Affine General Equilibrium Models
Bjørn Eraker
2008-01-01
No-arbitrage models are extremely flexible modelling tools but often lack economic motivation. This paper describes an equilibrium consumption-based CAPM framework based on Epstein-Zin preferences, which produces analytic pricing formulas for stocks and bonds under the assumption that macro growth rates follow affine processes. This allows the construction of equilibrium pricing formulas while maintaining the same flexibility of state dynamics as in no-arbitrage models. In demonstrating the a...
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
Enhancement of affinity-based biosensors: effect of sensing chamber geometry on sensitivity
Czech Academy of Sciences Publication Activity Database
Lynn, Nicholas Scott; Šípová, Hana; Adam, Pavel; Homola, Jiří
2013-01-01
Roč. 13, č. 7 (2013), s. 1413-1421. ISSN 1473-0197 R&D Projects: GA ČR GBP205/12/G118 Institutional support: RVO:67985882 Keywords : SURFACE-BASED BIOSENSORS * DIFFUSION * PLASMON RESONANCE BIOSENSOR Subject RIV: BH - Optics, Masers, Lasers Impact factor: 5.748, year: 2013
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.
Investigations on Monte Carlo based coupled core calculations
International Nuclear Information System (INIS)
The present trend in advanced and next generation nuclear reactor core designs is towards increased material heterogeneity and geometry complexity. The continuous energy Monte Carlo method has the capability of modeling such core environments with high accuracy. This paper presents results from feasibility studies being performed at the Pennsylvania State University (PSU) on both accelerating Monte Carlo criticality calculations by using hybrid nodal diffusion Monte Carlo schemes and thermal-hydraulic feedback modeling in Monte Carlo core calculations. The computation process is greatly accelerated by calculating the three-dimensional (3D) distributions of fission source and thermal-hydraulics parameters with the coupled NEM/COBRA-TF code and then using coupled MCNP5/COBRA-TF code to fine tune the results to obtain an increased accuracy. The PSU NEM code employs cross-sections generated by MCNP5 for pin-cell based nodal compositions. The implementation of different code modifications facilitating coupled calculations are presented first. Then the coupled hybrid Monte Carlo based code system is applied to a 3D 2*2 pin array extracted from a Boiling Water Reactor (BWR) assembly with reflective radial boundary conditions. The obtained results are discussed and it is showed that performing Monte-Carlo based coupled core steady state calculations are feasible. (authors)
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
DFT study on the effect of exocyclic substituents on the proton affinity of 1-methylimidazole
Energy Technology Data Exchange (ETDEWEB)
Liu, Haining; Bara, Jason E.; Turner, C. Heath, E-mail: hturner@eng.ua.edu
2013-04-18
Highlights: • DFT calculations are used to predict the proton affinity of 1-methylimidazoles. • The electron-withdrawing groups dominate the predicted proton affinity. • The effects of multiple substituents on the proton affinity can be accurately predicted. • Large compound libraries can be screened for imidazoles with tailored reactivity. - Abstract: A deeper understanding of the acid/base properties of imidazole derivatives will aid the development of solvents, polymer membranes and other materials that can be used for CO{sub 2} capture and acid gas removal. In this study, we employ density functional theory calculations to investigate the effect of various electron-donating and electron-withdrawing groups on the proton affinity of 1-methylimidazole. We find that electron-donating groups are able to increase the proton affinity relative to 1-methylimidazole, i.e., making the molecule more basic. In contrast, electron-withdrawing groups cause a decrease of the proton affinity. When multiple substituents are present, their effects on the proton affinity were found to be additive. This finding offers a quick approach for predicting and targeting the proton affinities of this series of molecules, and we show the strong correlation between the calculated proton affinities and experimental pK{sub a} values.
Algorithm for calculating torque base in vehicle traction control system
Li, Hongzhi; Li, Liang; Song, Jian; Wu, Kaihui; Qiao, Yanjuan; Liu, Xingchun; Xia, Yongguang
2012-11-01
Existing research on the traction control system(TCS) mainly focuses on control methods, such as the PID control, fuzzy logic control, etc, aiming at achieving an ideal slip rate of the drive wheel over long control periods. The initial output of the TCS (referred to as the torque base in this paper), which has a great impact on the driving performance of the vehicle in early cycles, remains to be investigated. In order to improve the control performance of the TCS in the first several cycles, an algorithm is proposed to determine the torque base. First, torque bases are calculated by two different methods, one based on states judgment and the other based on the vehicle dynamics. The confidence level of the torque base calculated based on the vehicle dynamics is also obtained. The final torque base is then determined based on the two torque bases and the confidence level. Hardware-in-the-loop(HIL) simulation and vehicle tests emulating sudden start on low friction roads have been conducted to verify the proposed algorithm. The control performance of a PID-controlled TCS with and without the proposed torque base algorithm is compared, showing that the proposed algorithm improves the performance of the TCS over the first several cycles and enhances about 5% vehicle speed by contrast. The proposed research provides a more proper initial value for TCS control, and improves the performance of the first several control cycles of the TCS.
Data base for terrestrial food pathways dose commitment calculations
International Nuclear Information System (INIS)
A computer program is under development to allow calculation of the dose-to-man in Georgia and South Carolina from ingestion of radionuclides in terrestrial foods resulting from deposition of airborne radionuclides. This program is based on models described in Regulatory Guide 1.109 (USNRC, 1977). The data base describes the movement of radionuclides through the terrestrial food chain, growth and consumption factors for a variety of radionuclides
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
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
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
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
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.
Cross section library based discrepancies in MCNP criticality calculations
International Nuclear Information System (INIS)
In nuclear engineering several reactor physics problems can be approached using Monte Carlo neutron transport techniques, which usually give reliable results when properly used. The quality of the results is largely determined by the accuracy of the geometry model and the statistical uncertainty of the Monte Carlo calculation. There is, however, another potential source of error, namely the cross section data used with the Monte Carlo codes. It has been shown in several studies that there may be significant discrepancies between results calculated using cross section libraries based on different evaluated nuclear data files. These discrepancies are well known to the evaluators of nuclear data but less acknowledged by reactor physicists, who often rely on a single cross section library in their calculations. In this study, discrepancies originating from base nuclear data were investigated in a systematic manner using the MCNP4C code. Calculations on simplified UOX and MOX fuelled LWR lattices were carried out using cross section libraries based on ENDF/B-VI.8, JEFF-3.0, JENDL-3.3, JEF-2.2 and JENDL-3.2 evaluated data files. The neutron spectrum of the system was varied over a wide range by changing the ratio of hydrogen to heavy metal atoms. The essential isotopes underlying the discrepancies were identified and the roles of fission and absorption cross sections of the most important nuclides assessed. The results confirm that there are large systematic differences up to a few per cent in the multiplication factors of LWR lattices. The discrepancies are strongly dependent on material compositions and neutron spectra, and largely originate from U-238 and the primary fissile isotopes. It is concluded that these discrepancies should be taken into account in all reactor physics calculations, and that reactor physicists should not rely on results based on a single cross section library. (author)
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...
Borisevich, Alex; Schullerus, Gernot
2012-01-01
In the article the problem of output setpoint tracking for affine non-linear system is considered. Presented approach combines state feedback linearization and homotopy numerical continuation in subspaces of phase space where feedback linearization fails. The method of numerical parameter continuation for solving systems of nonlinear equations is generalized to control affine non-linear dynamical systems. The illustrative example of control of MIMO system which is not static feedback lineariz...
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
Binding energies and electron affinities of small silicon clusters (n=2--5)
International Nuclear Information System (INIS)
The Gaussian-2 (G2) theoretical procedure, based on ab initio molecular orbital theory, is used to calculate the energies of Sin and Si-n (n=1--5) clusters. The G2 energies are used to derive accurate binding energies and electron affinities of these clusters. The calculated electron affinities of Si2--Si4 are in agreement to within 0.1 eV with results from recent photoelectron spectroscopic measurements
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...
International Nuclear Information System (INIS)
Current cardiac interventions are performed under 2D fluoroscopy, which comes along with well-known burdens to patients and physicians, such as x-ray exposure and the use of contrast agent. Furthermore, the navigation on complex structures such as the coronaries is complicated by the use of 2D images in which the catheter position is only visible while the contrast agent is introduced. In this work, a new method is presented, which circumvents these drawbacks and enables the cardiac interventional navigation on motion-compensated 3D static roadmaps. For this, the catheter position is continuously reconstructed within a previously acquired 3D roadmap of the coronaries. The motion compensation makes use of an affine motion model for compensating the respiratory motion and compensates the motion due to cardiac contraction by gating the catheter position. In this process, only those positions which have been acquired during the rest phase of the heart are used for the reconstruction. The method necessitates the measurement of the catheter position, which is done by using a magnetic tracking system. Nevertheless, other techniques, such as image-based catheter tracking, can be applied. This motion compensation has been tested on a dynamic heart phantom. The evaluation shows that the algorithm can reconstruct the catheter position on the 3D static roadmap precisely with a residual motion of 1.0 mm and less
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
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.
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...
J. Navarro; Sancho, C.; Sancho, P.
2009-01-01
A functor of sets $\\mathbb X$ over the category of $K$-commutative algebras is said to be an affine functor if its functor of functions, $\\mathbb A_{\\mathbb X}$, is reflexive and $\\mathbb X=\\Spec \\mathbb A_{\\mathbb X}$. We prove that affine functors are equal to a direct limit of affine schemes and that affine schemes, formal schemes, the completion of affine schemes along a closed subscheme, etc., are affine functors. Endowing an affine functor $\\mathbb X$ with a functor of monoids structure...
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
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
Shen, Xianjun; Yi, Li; Jiang, Xingpeng; He, Tingting; Hu, Xiaohua; Yang, Jincai
2016-01-01
The identification of temporal protein complexes would make great contribution to our knowledge of the dynamic organization characteristics in protein interaction networks (PINs). Recent studies have focused on integrating gene expression data into static PIN to construct dynamic PIN which reveals the dynamic evolutionary procedure of protein interactions, but they fail in practice for recognizing the active time points of proteins with low or high expression levels. We construct a Time-Evolving PIN (TEPIN) with a novel method called Deviation Degree, which is designed to identify the active time points of proteins based on the deviation degree of their own expression values. Owing to the differences between protein interactions, moreover, we weight TEPIN with connected affinity and gene co-expression to quantify the degree of these interactions. To validate the efficiencies of our methods, ClusterONE, CAMSE and MCL algorithms are applied on the TEPIN, DPIN (a dynamic PIN constructed with state-of-the-art three-sigma method) and SPIN (the original static PIN) to detect temporal protein complexes. Each algorithm on our TEPIN outperforms that on other networks in terms of match degree, sensitivity, specificity, F-measure and function enrichment etc. In conclusion, our Deviation Degree method successfully eliminates the disadvantages which exist in the previous state-of-the-art dynamic PIN construction methods. Moreover, the biological nature of protein interactions can be well described in our weighted network. Weighted TEPIN is a useful approach for detecting temporal protein complexes and revealing the dynamic protein assembly process for cellular organization. PMID:27100396
Directory of Open Access Journals (Sweden)
Bogdanović Ozren
2011-08-01
Full Text Available Abstract Background DNA methylation is a widespread epigenetic modification in vertebrate genomes. Genomic sites of DNA methylation can be bound by methyl-CpG-binding domain proteins (MBDs and specific zinc finger proteins, which can recruit co-repressor complexes to silence transcription on targeted loci. The binding to methylated DNA may be regulated by post-translational MBD modifications. Findings A methylated DNA affinity precipitation method was implemented to assay binding of proteins to methylated DNA. Endogenous MeCP2 and MBD3 were precipitated from Xenopus oocyte extracts and conditions for methylation-specific binding were optimized. For a reverse experiment, DNA methylation in early Xenopus embryos was assessed by MBD affinity capture. Conclusions A methylated DNA affinity resin can be applied to probe for MBD activity in extracts. This assay has a broad application potential as it can be coupled to downstream procedures such as western blotting, fluorimetric HDAC assays and quantitative mass spectrometry. Methylated DNA affinity capture by methyl-CpG binding proteins produces fractions highly enriched for methylated DNA, suitable for coupling to next generation sequencing technologies. The two enrichment strategies allow probing of methyl-CpG protein interactions in early vertebrate oocytes and embryos.
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 differ...
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
Jet identification based on probability calculations using Bayes' theorem
International Nuclear Information System (INIS)
The problem of identifying jets at LEP and HERA has been studied. Identification using jet energies and fragmentation properties was treated separately in order to investigate the degree of quark-gluon separation that can be achieved by either of these approaches. In the case of the fragmentation-based identification, a neural network was used, and a test of the dependence on the jet production process and the fragmentation model was done. Instead of working with the separation variables directly, these have been used to calculate probabilities of having a specific type of jet, according to Bayes' theorem. This offers a direct interpretation of the performance of the jet identification and provides a simple means of combining the results of the energy- and fragmentation-based identifications. (orig.)
Directory of Open Access Journals (Sweden)
Patricio Iturriaga-Vásquez
2013-04-01
Full Text Available A series of novel 2-pyridylbenzimidazole derivatives was rationally designed and synthesized based on our previous studies on benzimidazole 14, a CB1 agonist used as a template for optimization. In the present series, 21 compounds displayed high affinities with Ki values in the nanomolar range. JM-39 (compound 39 was the most active of the series (KiCB1 = 0.53 nM, while compounds 31 and 44 exhibited similar affinities to WIN 55212-2. CoMFA analysis was performed based on the biological data obtained and resulted in a statistically significant CoMFA model with high predictive value (q2 = 0.710, r2 = 0.998, r2pred = 0.823.
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 ...
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...
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)
The PHREEQE Geochemical equilibrium code data base and calculations
International Nuclear Information System (INIS)
Compilation of a thermodynamic data base for actinides and fission products for use with PHREEQE has begun and a preliminary set of actinide data has been tested for the PHREEQE code in a version run on an IBM XT computer. The work until now has shown that the PHREEQE code mostly gives satisfying results for specification of actinides in natural water environment. For U and Np under oxidizing conditions, however, the code has difficulties to converge with pH and Eh conserved when a solubility limit is applied. For further calculations of actinide and fission product specification and solubility in a waste repository and in the surrounding geosphere, more data are needed. It is necessary to evaluate the influence of the large uncertainties of some data. A quality assurance and a check on the consistency of the data base is also needed. Further work with data bases should include: an extension to fission products, an extension to engineering materials, an extension to other ligands than hydroxide and carbonate, inclusion of more mineral phases, inclusion of enthalpy data, a control of primary references in order to decide if values from different compilations are taken from the same primary reference and contacts and discussions with other groups, working with actinide data bases, e.g. at the OECD/NEA and at the IAEA. (author)
Jose Isagani Janairo; Gerardo Janairo; Frumencio Co; Derrick Ethelbhert Yu
2011-01-01
The activity of a selected class of DPP4 inhibitors was preliminarily assessed using chemical descriptors derived AM1 optimized geometries. Using multiple linear regression model, it was found that ?E0, LUMO energy, area, molecular weight and ?H0 are the significant descriptors that can adequately assess the binding affinity of the compounds. The derived multiple linear regression (MLR) model was validated using rigorous statistical analysis. The preliminary model suggests t...
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.
[Calculating method for crop water requirement based on air temperature].
Tao, Guo-Tong; Wang, Jing-Lei; Nan, Ji-Qin; Gao, Yang; Chen, Zhi-Fang; Song, Ni
2014-07-01
The importance of accurately estimating crop water requirement for irrigation forecast and agricultural water management has been widely recognized. Although it has been broadly adopted to determine crop evapotranspiration (ETc) via meteorological data and crop coefficient, most of the data in whether forecast are qualitative rather than quantitative except air temperature. Therefore, in this study, how to estimate ETc precisely only using air temperature data in forecast was explored, the accuracy of estimation based on different time scales was also investigated, which was believed to be beneficial to local irrigation forecast as well as optimal management of water and soil resources. Three parameters of Hargreaves equation and two parameters of McClound equation were corrected by using meteorological data of Xinxiang from 1970 to 2010, and Hargreaves equation was selected to calculate reference evapotranspiration (ET0) during the growth period of winter wheat. A model of calculating crop water requirement was developed to predict ETc at time scales of 1, 3, and 7 d intervals through combining Hargreaves equation and crop coefficient model based on air temperature. Results showed that the correlation coefficients between measured and predicted values of ETc reached 0.883 (1 d), 0.933 (3 d), and 0.959 (7 d), respectively. The consistency indexes were 0.94, 0.95 and 0.97, respectively, which showed that forecast error decreased with the increasing time scales. Forecasted accuracy with an error less than 1 mm x d(-1) was more than 80%, and that less than 2 mm x d(-1) was greater than 90%. This study provided sound basis for irrigation forecast and agricultural management in irrigated areas since the forecasted accuracy at each time scale was relatively high. PMID:25345053
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
Meyer, Mathieu; Schuett, Carsten; Werner, Elisabeth M.
2013-01-01
An affine invariant point on the class of convex bodies in R^n, endowed with the Hausdorff metric, is a continuous map p which is invariant under one-to-one affine transformations A on R^n, that is, p(A(K))=A(p(K)). We define here the new notion of dual affine point q of an affine invariant point p by the formula q(K^{p(K)})=p(K) for every convex body K, where K^{p(K)} denotes the polar of K with respect to p(K). We investigate which affine invariant points do have a dual point, whether this ...
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)
A brachytherapy model-based dose calculation algorithm -AMIGOBrachy
International Nuclear Information System (INIS)
Brachytherapy treatments have been performed based on TG-43U1 water dose formalism which neglects human tissues density and composition, body interfaces and applicator effects. As these effects could be relevant for brachytherapy energy range, modern treatment planning systems (TPS) are now available that are based on model-based dose calculation algorithms (MBDCA) enabling heterogeneity corrections, which are needed to replace the TG-43U1 water dose formalism for a more accurate approach. The recently published AAPM TG-186 report is the first step towards to a TPS taking into account heterogeneities, applicators and human body complexities. This report presents the current status, recommendations for clinical implementation and specifies research areas where considerable efforts are necessary to move forward with MBDCA. Monte Carlo (MC) codes are an important part of the current algorithms due their flexibility and accuracy, although, almost all MC codes present no interface to process the large amount of data necessary to perform clinical cases simulations, which may include hundreds of dwell positions, inter-seed attenuation, image processing and others time consuming issues that can make MC simulation unfeasible without a pre-processing interface. This work presents the AMIGOBrachy interface tool (Algorithm for Medical Image-based Generating Object - Brachytherapy module) which provides all the pre-processing task needed for the simulation. This software can import and edit treatments plans from BrachyVision™ (Varian Medical Systems, Inc., Palo Alto, CA) and ONCENTRA™ (Elekta AB, Stockholm, Sweden), and also create a new plan through contouring resources, needle recognition, HU segmentation, combining voxels phantoms with analytical geometries to define applicators and other resources used to create MCNP5 input and analyze the results. This work presents some results used to validate the software and to evaluate the heterogeneities impact in a clinical case
A CNS calculation line based on a Monte Carlo method
International Nuclear Information System (INIS)
Full text: The design of the moderator cell of a Cold Neutron Source (CNS) involves many different considerations regarding geometry, location, and materials. Decisions taken in this sense affect not only the neutron flux in the source neighborhood, which can be evaluated by a standard empirical method, but also the neutron flux values in experimental positions far away of the neutron source. At long distances from the neutron source, very time consuming 3D deterministic methods or Monte Carlo transport methods are necessary in order to get accurate figures. Standard and typical terminology such as average neutron flux, neutron current, angular flux, luminosity, are magnitudes very difficult to evaluate in positions located several meters away from the neutron source. The Monte Carlo method is a unique and powerful tool to transport neutrons. Its use in a bootstrap scheme appears to be an appropriate solution for this type of systems. The proper use of MCNP as the main tool leads to a fast and reliable method to perform calculations in a relatively short time with low statistical errors. The design goal is to evaluate the performance of the neutron sources, their beam tubes and neutron guides at specific experimental locations in the reactor hall as well as in the neutron or experimental hall. In this work, the calculation methodology used to design Cold, Thermal and Hot Neutron Sources and their associated Neutron Beam Transport Systems, based on the use of the MCNP code, is presented. This work also presents some changes made to the cross section libraries in order to cope with cryogenic moderators such as liquid hydrogen and liquid deuterium. (author)
Structural determinants of sigma receptor affinity
International Nuclear Information System (INIS)
The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-[3H]3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent
Structural determinants of sigma receptor affinity
Energy Technology Data Exchange (ETDEWEB)
Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.
1987-12-01
The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.
Fast calculation of object infrared spectral scattering based on CUDA
Li, Liang-chao; Niu, Wu-bin; Wu, Zhen-sen
2010-11-01
Computational unified device architecture (CUDA) is used for paralleling the spectral scattering calculation from non-Lambertian object of sky and earth background irradiation. The bidirectional reflectance distribution function (BRDF) of five parameter model is utilized in object surface element scattering calculation. The calculation process is partitioned into many threads running in GPU kernel and each thread computes a visible surface element infrared spectral scattering intensity in a specific incident direction, all visible surface elements' intensity are weighted and averaged to obtain the object surface scattering intensity. The comparison of results of the CPU calculation and CUDA parallel calculation of a cylinder shows that the CUDA parallel calculation speed improves more than two hundred times in meeting the accuracy, with a high engineering value.
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
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...... 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...
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.
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...
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....
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
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.
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.
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...
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.
Affine Constellations Without Mutually Unbiased Counterparts
Weigert, Stefan
2010-01-01
It has been conjectured that a complete set of mutually unbiased bases in a space of dimension d exists if and only if there is an affine plane of order d. We introduce affine constellations and compare their existence properties with those of mutually unbiased constellations, mostly in dimension six. The observed discrepancies make a deeper relation between the two existence problems unlikely.
Affine constellations without mutually unbiased counterparts
Energy Technology Data Exchange (ETDEWEB)
Weigert, Stefan [Department of Mathematics, University of York, York YO10 5DD (United Kingdom); Durt, Thomas, E-mail: slow500@york.ac.u, E-mail: thomdurt@vub.ac.b [IR-TONA, VUB, BE-1050 Brussels (Belgium)
2010-10-08
It has been conjectured that a complete set of mutually unbiased bases in a space of dimension d exists if and only if there is an affine plane of order d. We introduce affine constellations and compare their existence properties with those of mutually unbiased constellations. The observed discrepancies make a deeper relation between the two existence problems unlikely. (fast track communication)
Affine constellations without mutually unbiased counterparts
International Nuclear Information System (INIS)
It has been conjectured that a complete set of mutually unbiased bases in a space of dimension d exists if and only if there is an affine plane of order d. We introduce affine constellations and compare their existence properties with those of mutually unbiased constellations. The observed discrepancies make a deeper relation between the two existence problems unlikely. (fast track communication)
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...
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.
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
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 ...
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
Affine and Projective Geometry
Bennett, M K
1995-01-01
An important new perspective on AFFINE AND PROJECTIVE GEOMETRY. This innovative book treats math majors and math education students to a fresh look at affine and projective geometry from algebraic, synthetic, and lattice theoretic points of view. Affine and Projective Geometry comes complete with ninety illustrations, and numerous examples and exercises, covering material for two semesters of upper-level undergraduate mathematics. The first part of the book deals with the correlation between synthetic geometry and linear algebra. In the second part, geometry is used to introduce lattice theory
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.
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.
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...
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.
Paul, Tanima; Chatterjee, Saptarshi; Bandyopadhyay, Arghya; Chattopadhyay, Dwiptirtha; Basu, Semanti; Sarkar, Keka
2015-08-18
Surface-functionalized adsorbant particles in combination with magnetic separation techniques have received considerable attention in recent years. Selective manipulation on such magnetic nanoparticles permits separation with high affinity in the presence of other suspended solids. Amylase is used extensively in food and allied industries. Purification of amylase from bacterial sources is a matter of concern because most of the industrial need for amylase is met by microbial sources. Here we report a simple, cost-effective, one-pot purification technique for bacterial amylase directly from fermented broth of Bacillus megaterium utilizing starch-coated superparamagnetic iron oxide nanoparticles (SPION). SPION was prepared by co-precipitation method and then functionalized by starch coating. The synthesized nanoparticles were characterized by transmission electron microscopy (TEM), a superconducting quantum interference device (SQUID, zeta potential, and ultraviolet-visible (UV-vis) and Fourier-transform infrared (FTIR) spectroscopy. The starch-coated nanoparticles efficiently purified amylase from bacterial fermented broth with 93.22% recovery and 12.57-fold purification. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) revealed that the molecular mass of the purified amylase was 67 kD, and native gel showed the retention of amylase activity even after purification. Optimum pH and temperature of the purified amylase were 7 and 50°C, respectively, and it was stable over a range of 20°C to 50°C. Hence, an improved one-pot bacterial amylase purification method was developed using starch-coated SPION. PMID:24840788
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
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
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.
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...
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
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...
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
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...
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
Virtual-real spatial information visualization registration using affine representations
Wu, Xueling; Ren, Fu; Du, Qingyun
2009-10-01
Virtual-real registration in Outdoor Augmented Reality is committed to enhance user's spatial cognition by overlaying virtual geographical objects on real scene. According to analyze fiducial detection registration method in indoor AR, for the purpose of avoiding complex and tedious process of position tracking and camera calibration in traditional registration methods, it puts forward and practices a virtual-real spatial information visualization registration method using affine representations. Based on the observation from Koenderink and van Doorn, Ullman and Basri in 1991 which is given a set of four or more non-coplanar 3D points, the projection of all points in the set can be computed as a linear combination of the projection of just four of the points, it sets up global affine coordinate system in light of world coordinates, camera coordinates and virtual coordinates and extracts four feature points from scene image and calculates the global affine coordinates of key points of virtual objects. Then according to a linear homogeneous coordinates of the four feature point's projection, it calculates projection pixel coordinates of key points of virtual objects. In addition, it proposes an approach to obtain pixel relative depth for hidden surface removal. Finally, by a case study, it verifies the feasibility and efficiency of the registration methods. The method would not only explore a new research direction for Geographical Information Science, but also would provide location-based information and services for outdoor AR.
DEFF Research Database (Denmark)
Poongavanam, Vasanthanathan; Svendsen, Casper Steinmann; Kongsted, Jacob
2014-01-01
of the methods based on the use of a training set of molecules, QM based chelation calculations were used as filter in virtual screening of compounds in the ZINC database. By this, we find, compared to regular docking, QM based chelation calculations to significantly reduce the large number of false...
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...
Mukherjee, Somnath; Ura, Marcin; Hoey, Robert J; Kossiakoff, Anthony A
2015-08-14
Reversible, high-affinity immobilization tags are critical tools for myriad biological applications. However, inherent issues are associated with a number of the current methods of immobilization. Particularly, a critical element in phage display sorting is functional immobilization of target proteins. To circumvent these problems, we have used a mutant (N5A) of calmodulin binding peptide (CBP) as an immobilization tag in phage display sorting. The immobilization relies on the ultra high affinity of calmodulin to N5A mutant CBP (RWKKNFIAVSAANRFKKIS) in presence of calcium (KD~2 pM), which can be reversed by EDTA allowing controlled "capture and release" of the specific binders. To evaluate the capabilities of this system, we chose eight targets, some of which were difficult to overexpress and purify with other tags and some had failed in sorting experiments. In all cases, specific binders were generated using a Fab phage display library with CBP-fused constructs. KD values of the Fabs were in subnanomolar to low nanomolar (nM) ranges and were successfully used to selectively recognize antigens in cell-based experiments. Some of these targets were problematic even without any tag; thus, the fact that all led to successful selection endpoints means that borderline cases can be worked on with a high probability of a positive outcome. Taken together with examples of successful case specific, high-level applications like generation of conformation-, epitope- and domain-specific Fabs, we feel that the CBP tag embodies all the attributes of covalent immobilization tags but does not suffer from some of their well-documented drawbacks. PMID:26159704
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...
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
Glass viscosity calculation based on a global statistical modeling approach
International Nuclear Information System (INIS)
A global statistical glass viscosity model was developed for predicting the complete viscosity curve, based on more than 2200 composition-property data of silicate glasses from the scientific literature, including soda-lime-silica container and float glasses, TV panel glasses, borosilicate fiber wool and E type glasses, low expansion borosilicate glasses, glasses for nuclear waste vitrification, lead crystal glasses, binary alkali silicates, and various further compositions from over half a century. It is shown that within a measurement series from a specific laboratory the reported viscosity values are often over-estimated at higher temperatures due to alkali and boron oxide evaporation during the measurement and glass preparation, including data by Lakatos et al. (1972) and the recently published High temperature glass melt property database for process modeling by Seward et al. (2005). Similarly, in the glass transition range many experimental data of borosilicate glasses are reported too high due to phase separation effects. The developed global model corrects those errors. The model standard error was 9-17 C, with R2 = 0.985-0.989. The prediction 95% confidence interval for glass in mass production largely depends on the glass composition of interest, the composition uncertainty, and the viscosity level. New insights in the mixed-alkali effect are provided
Glass viscosity calculation based on a global statistical modelling approach
Energy Technology Data Exchange (ETDEWEB)
Fluegel, Alex
2007-02-01
A global statistical glass viscosity model was developed for predicting the complete viscosity curve, based on more than 2200 composition-property data of silicate glasses from the scientific literature, including soda-lime-silica container and float glasses, TV panel glasses, borosilicate fiber wool and E type glasses, low expansion borosilicate glasses, glasses for nuclear waste vitrification, lead crystal glasses, binary alkali silicates, and various further compositions from over half a century. It is shown that within a measurement series from a specific laboratory the reported viscosity values are often over-estimated at higher temperatures due to alkali and boron oxide evaporation during the measurement and glass preparation, including data by Lakatos et al. (1972) and the recently published High temperature glass melt property database for process modeling by Seward et al. (2005). Similarly, in the glass transition range many experimental data of borosilicate glasses are reported too high due to phase separation effects. The developed global model corrects those errors. The model standard error was 9-17°C, with R^2 = 0.985-0.989. The prediction 95% confidence interval for glass in mass production largely depends on the glass composition of interest, the composition uncertainty, and the viscosity level. New insights in the mixed-alkali effect are provided.
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.
Validation of KENO-based criticality calculations at Rocky Flats
International Nuclear Information System (INIS)
In the absence of experimental data, it is necessary to rely on computer-based computational methods in evaluating the criticality condition of a nuclear system. The validity of the computer codes is established in a two-part procedure as outlined in ANSI/ANS 8.1. The first step, usually the responsibility of the code developer, involves verification that the algorithmic structure of the code is performing the intended mathematical operations correctly. The second step involves an assessment of the code's ability to realistically portray the governing physical processes in question. This is accomplished by determining the code's bias, or systematic error, through a comparison of computational results to accepted values obtained experimentally. In this paper, the authors discuss the validation process for KENO and the Hansen-Roach cross sections in use at EG and G Rocky Flats. The validation process at Rocky Flats consists of both global and local techniques. The global validation resulted in a maximum keff limit of 0.95 for the limiting-accident scanarios of a criticality evaluation
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...
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...... of HLA molecules, giving a selective force in the binding. The peptide libraries can be designed so that the sequence length, the alignment of binding registers, the numbers and composition of random positions are controlled, and also modified amino acids can be included. Selected library peptides...... bound 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...
Lipovsek, Dasa; Lippow, Shaun M; Hackel, Benjamin J; Gregson, Melissa W; Cheng, Paul; Kapila, Atul; Wittrup, K Dane
2007-05-11
The 10th human fibronectin type III domain ((10)Fn3) is one of several protein scaffolds used to design and select families of proteins that bind with high affinity and specificity to macromolecular targets. To date, the highest affinity (10)Fn3 variants have been selected by mRNA display of libraries generated by randomizing all three complementarity-determining region -like loops of the (10)Fn3 scaffold. The sub-nanomolar affinities of such antibody mimics have been attributed to the extremely large size of the library accessible by mRNA display (10(12) unique sequences). Here we describe the selection and affinity maturation of (10)Fn3-based antibody mimics with dissociation constants as low as 350 pM selected from significantly smaller libraries (10(7)-10(9) different sequences), which were constructed by randomizing only 14 (10)Fn3 residues. The finding that two adjacent loops in human (10)Fn3 provide a large enough variable surface area to select high-affinity antibody mimics is significant because a smaller deviation from wild-type (10)Fn3 sequence is associated with a higher stability of selected antibody mimics. Our results also demonstrate the utility of an affinity-maturation strategy that led to a 340-fold improvement in affinity by maximizing sampling of sequence space close to the original selected antibody mimic. A striking feature of the highest affinity antibody mimics selected against lysozyme is a pair of cysteines on adjacent loops, in positions 28 and 77, which are critical for the affinity of the (10)Fn3 variant for its target and are close enough to form a disulfide bond. The selection of this cysteine pair is structurally analogous to the natural evolution of disulfide bonds found in new antigen receptors of cartilaginous fish and in camelid heavy-chain variable domains. We propose that future library designs incorporating such an interloop disulfide will further facilitate the selection of high-affinity, highly stable antibody mimics from
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
DEFF Research Database (Denmark)
Skjødt, Mette Louise
Yeast surface display is an effective tool for antibody affinity maturation because yeast can be used as an all-in-one workhorse to assemble, display and screen diversified antibody libraries. By employing the natural ability of yeast Saccharomyces cerevisiae to efficiently recombine multiple DNA...
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...
Energy Technology Data Exchange (ETDEWEB)
Zdenek Klika; Lenka Ambruzova; Ivana Sykorova; Jana Seidlerova; Ivan Kolomaznik [VSB-Technical University Ostrava, Ostrava (Czech Republic)
2009-10-15
The affinities of Ga and Ge in lignite were determined using sequential extraction (SE) and element affinity calculation (EAC) based on sink-float data. For this study a bulk lignite sample was fractioned into two sets. The first set of samples (A) consisted of the different grain sizes fractions; the second one set (B) was prepared by density fractionation. Sequential extractions (1) were performed on both sets of fractions with very good agreement between determined organic elements affinities (OEA of Ga evaluated from A data is 32%, from B data 35%; OEA of Ge evaluated from A data is 31% and from B data 26%). The data of B lignite fractions were evaluated using two element affinity calculations: (a) EAC (I) of Klika and Kolomaznk (2) and (b) newly prepared subroutine EAC (II) based on quantitative contents of lignite macerals and minerals. There was also good agreement between both methods obtained (OEA of Ga calculated by EAC (I) is 83% and by EAC (II) 77%; OEA of Ge calculated by EAC (I) is 89% and by EAC (II) 97%). The significant differences of organic elements affinities of Ga and Ge evaluated by sequential extraction and by element affinity calculation based on sink-float data are discussed. 34 refs., 7 figs., 6 tabs.
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
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)
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.
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).
Energy Technology Data Exchange (ETDEWEB)
Borbulevych, Oleg Y.; Do, Priscilla; Baker, Brian M. (Notre)
2010-09-07
Presentation of peptides by class I or class II major histocompatibility complex (MHC) molecules is required for the initiation and propagation of a T cell-mediated immune response. Peptides from the Wilms Tumor 1 transcription factor (WT1), upregulated in many hematopoetic and solid tumors, can be recognized by T cells and numerous efforts are underway to engineer WT1-based cancer vaccines. Here we determined the structures of the class I MHC molecule HLA-A*0201 bound to the native 126-134 epitope of the WT1 peptide and a recently described variant (R1Y) with improved MHC binding. The R1Y variant, a potential vaccine candidate, alters the positions of MHC charged side chains near the peptide N-terminus and significantly reduces the peptide/MHC electrostatic surface potential. These alterations indicate that the R1Y variant is an imperfect mimic of the native WT1 peptide, and suggest caution in its use as a therapeutic vaccine. Stability measurements revealed how the R1Y substitution enhances MHC binding affinity, and together with the structures suggest a strategy for engineering WT1 variants with improved MHC binding that retain the structural features of the native peptide/MHC complex.
Borbulevych, Oleg Y; Do, Priscilla; Baker, Brian M
2010-09-01
Presentation of peptides by class I or class II major histocompatibility complex (MHC) molecules is required for the initiation and propagation of a T cell-mediated immune response. Peptides from the Wilms Tumor 1 transcription factor (WT1), upregulated in many hematopoetic and solid tumors, can be recognized by T cells and numerous efforts are underway to engineer WT1-based cancer vaccines. Here we determined the structures of the class I MHC molecule HLA-A*0201 bound to the native 126-134 epitope of the WT1 peptide and a recently described variant (R1Y) with improved MHC binding. The R1Y variant, a potential vaccine candidate, alters the positions of MHC charged side chains near the peptide N-terminus and significantly reduces the peptide/MHC electrostatic surface potential. These alterations indicate that the R1Y variant is an imperfect mimic of the native WT1 peptide, and suggest caution in its use as a therapeutic vaccine. Stability measurements revealed how the R1Y substitution enhances MHC binding affinity, and together with the structures suggest a strategy for engineering WT1 variants with improved MHC binding that retain the structural features of the native peptide/MHC complex. PMID:20619457
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.
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.
Organ dose calculation in CT based on scout image data and automatic image registration
International Nuclear Information System (INIS)
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
International Nuclear Information System (INIS)
This system (THEXSYST) will be used for control, analysis and presentation of thermal hydraulic simulation calculations of light water reactors. THEXSYST is a modular system consisting of an expert shell with user interface, a data base, and a simulation program and uses techniques available in RSYST. A knowledge base, which was created to control the simulational calculation of pressurized water reactors, includes both the steady state calculation and the transient calculation in the domain of the depressurization, as a result of a small break loss of coolant accident. The methods developed are tested using a simulational calculation with RELAP5/Mod2. It will be seen that the application of knowledge base techniques may be a helpful tool to support existing solutions especially in graphical analysis. (orig./HP)
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.
International Nuclear Information System (INIS)
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
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.
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 $_{-p}K$.
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
International Nuclear Information System (INIS)
Windows based application has been developed for the calculation of atomic hyperfine spectrum of odd isotopes keeping in view of the needs of the atomic spectroscopists. The application can also calculate the hyperfine spectrum of another odd isotope if hyperfine structure constants of one isotope are known. Various features of the developed application are discussed. (author)
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.
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...
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
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
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. PMID:27214273
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.
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
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
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
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…
An affine framework for analytical mechanics
Urbanski, Pawel
2003-01-01
An affine Cartan calculus is developed. The concepts of special affine bundles and special affine duality are introduced. The canonical isomorphisms, fundamental for Lagrangian and Hamiltonian formulations of the dynamics in the affine setting are proved.
Calculation of activities in some gallium-based systems with a miscibility gap
Directory of Open Access Journals (Sweden)
IWAO KATAYAMA
2003-09-01
Full Text Available The calculations of thermodynamic properties in some gallium-based systems with a miscibility gap GaTl, GaHg and GaPb are presented in this paper. The determination of the gallium activities in the mentioned liquid alloys was based on their known phase diagrams using the Zhang-Chou method for calculating activities from phase diagrams involving two liquid or solid coexisting phases. The activities of gallium in GaTl, GaHg and GaPb system were calculated in the 9731273 K, 573873 K and 10001100 K, temperature ranges, respectively. The activities of the other component in all the investigated systems were obtained by the Gibbs-Duhem equation. The results of the calculations are compared with literature data.
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
About calculation of crystal lattice parameters of iron base solid solutions
International Nuclear Information System (INIS)
Lattice parameters of iron base solid solutions (Fe-Be, Fe-Cr, Fe-Co, Fe-Mo, Fe-Nb, Fe-Ni, Fe-Ru, Fe-Ti, Fe-V) are calculated on the basis of previously proposed model with the use of the correction taking into account the chemical interaction between element atoms. calculation results allow the conclusion that the sue of the correction reduced the discrepancy between experimental and calculated data on lattice parameters down tp values comparable with an error of the experiment
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.
Improvement of accuracy of resonance self-shielding calculation based on subgroup method
International Nuclear Information System (INIS)
Based on the neutron self-shielding calculation code SGMOC, which is the combination of subgroup method and characteristics method that developed by ourselves, we studied the two techniques to improve the SGMOC calculation accuracy. The numerical results prove that both techniques have the capability to improve the resonance self-shielding calculation accuracy. The resonance interference effect treatment which uses a new method to obtain the conditional probabilities, has a correction effect about 20∼230 pcm. When the impact of the resonance scattering is considered, the correction effect is about 100 Dcm. When utilizing the above two techniques simultaneously, the correction effect is about 30∼270 pcm. (authors)
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 ...
A transport based one-dimensional perturbation code for reactivity calculations in metal systems
Energy Technology Data Exchange (ETDEWEB)
Wenz, T.R.
1995-02-01
A one-dimensional reactivity calculation code is developed using first order perturbation theory. The reactivity equation is based on the multi-group transport equation using the discrete ordinates method for angular dependence. In addition to the first order perturbation approximations, the reactivity code uses only the isotropic scattering data, but cross section libraries with higher order scattering data can still be used with this code. The reactivity code obtains all the flux, cross section, and geometry data from the standard interface files created by ONEDANT, a discrete ordinates transport code. Comparisons between calculated and experimental reactivities were done with the central reactivity worth data for Lady Godiva, a bare uranium metal assembly. Good agreement is found for isotopes that do not violate the assumptions in the first order approximation. In general for cases where there are large discrepancies, the discretized cross section data is not accurately representing certain resonance regions that coincide with dominant flux groups in the Godiva assembly. Comparing reactivities calculated with first order perturbation theory and a straight {Delta}k/k calculation shows agreement within 10% indicating the perturbation of the calculated fluxes is small enough for first order perturbation theory to be applicable in the modeled system. Computation time comparisons between reactivities calculated with first order perturbation theory and straight {Delta}k/k calculations indicate considerable time can be saved performing a calculation with a perturbation code particularly as the complexity of the modeled problems increase.
A transport based one-dimensional perturbation code for reactivity calculations in metal systems
International Nuclear Information System (INIS)
A one-dimensional reactivity calculation code is developed using first order perturbation theory. The reactivity equation is based on the multi-group transport equation using the discrete ordinates method for angular dependence. In addition to the first order perturbation approximations, the reactivity code uses only the isotropic scattering data, but cross section libraries with higher order scattering data can still be used with this code. The reactivity code obtains all the flux, cross section, and geometry data from the standard interface files created by ONEDANT, a discrete ordinates transport code. Comparisons between calculated and experimental reactivities were done with the central reactivity worth data for Lady Godiva, a bare uranium metal assembly. Good agreement is found for isotopes that do not violate the assumptions in the first order approximation. In general for cases where there are large discrepancies, the discretized cross section data is not accurately representing certain resonance regions that coincide with dominant flux groups in the Godiva assembly. Comparing reactivities calculated with first order perturbation theory and a straight Δk/k calculation shows agreement within 10% indicating the perturbation of the calculated fluxes is small enough for first order perturbation theory to be applicable in the modeled system. Computation time comparisons between reactivities calculated with first order perturbation theory and straight Δk/k calculations indicate considerable time can be saved performing a calculation with a perturbation code particularly as the complexity of the modeled problems increase
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...