Dimensional crossover in fragmentation
Sotolongo-Costa, Oscar; Rodriguez, Arezky H.; Rodgers, G. J.
2000-11-01
Experiments in which thick clay plates and glass rods are fractured have revealed different behavior of fragment mass distribution function in the small and large fragment regions. In this paper we explain this behavior using non-extensive Tsallis statistics and show how the crossover between the two regions is caused by the change in the fragments’ dimensionality during the fracture process. We obtain a physical criterion for the position of this crossover and an expression for the change in the power-law exponent between the small and large fragment regions. These predictions are in good agreement with the experiments on thick clay plates.
Bootstrap embedding: An internally consistent fragment-based method
Energy Technology Data Exchange (ETDEWEB)
Welborn, Matthew; Tsuchimochi, Takashi; Van Voorhis, Troy [Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States)
2016-08-21
Strong correlation poses a difficult problem for electronic structure theory, with computational cost scaling quickly with system size. Fragment embedding is an attractive approach to this problem. By dividing a large complicated system into smaller manageable fragments “embedded” in an approximate description of the rest of the system, we can hope to ameliorate the steep cost of correlated calculations. While appealing, these methods often converge slowly with fragment size because of small errors at the boundary between fragment and bath. We describe a new electronic embedding method, dubbed “Bootstrap Embedding,” a self-consistent wavefunction-in-wavefunction embedding theory that uses overlapping fragments to improve the description of fragment edges. We apply this method to the one dimensional Hubbard model and a translationally asymmetric variant, and find that it performs very well for energies and populations. We find Bootstrap Embedding converges rapidly with embedded fragment size, overcoming the surface-area-to-volume-ratio error typical of many embedding methods. We anticipate that this method may lead to a low-scaling, high accuracy treatment of electron correlation in large molecular systems.
van Agthoven, Maria A; Barrow, Mark P; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O'Connor, Peter B
2015-12-01
Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules. Graphical Abstract ᅟ.
Energy Technology Data Exchange (ETDEWEB)
Gastegger, Michael; Kauffmann, Clemens; Marquetand, Philipp, E-mail: philipp.marquetand@univie.ac.at [Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna (Austria); Behler, Jörg [Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Universitätsstraße 150, Bochum (Germany)
2016-05-21
Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system’s total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy is constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference.
International Nuclear Information System (INIS)
Gastegger, Michael; Kauffmann, Clemens; Marquetand, Philipp; Behler, Jörg
2016-01-01
Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system’s total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy is constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference.
International Nuclear Information System (INIS)
Smith, A.C.; Harmon, J.M.
1987-01-01
The structural organization of the steroid-binding protein of the IM-9 cell glucocorticoid receptor was investigated by using one- and two-dimensional gel electrophoresis of proteolytic receptor fragments. One-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of receptor fragments isolated after trypsin digestion of immunopurified [ 3 H]dexamethasone 21-mesylate ([ 3 H]DM-) labeled receptor revealed the presence of a stable 26.5-kilodalton (kDa) steroid-containing non-DNA-binding fragment, derived from a larger, less stable, 29-kDa fragment. The 26.5-kDa tryptic fragment appeared to be completely contained within a 41-kDa, steroid-containing, DNA-binding species isolated after chymotrypsin digestion of the intact protein. Two-dimensional electrophoretic analysis of the [ 3 H]DM-labeled tryptic fragments resolved two 26.5-kDa and two 29-kDa components. This was the same number of isoforms seen in the intact protein, indicating that the charge heterogeneity of the steroid-binding protein is the result of modification within the steroid-containing, non-DNA-binding, 26.5-kDa tryptic fragment. Two-dimensional analysis of the 41-kDa [ 3 H]DM-labeled chymotryptic species revealed a pattern of isoforms more complex than that seen either in the intact protein or in the steroid-containing tryptic fragments. These results suggest that the 41-kDa [ 3 H]DM-labeled species resolved by one-dimensional SDS-PAGE after chymotrypsin digestion may be composed of several distinct proteolytic fragments
International Nuclear Information System (INIS)
Yi, M.; Au, L.C.; Ichikawa, N.; Ts'o, P.O.
1990-01-01
A probe-free method was developed to detect DNA rearrangement in bacteria based on the electrophoretic separation of twice-digested restriction fragments of genomic DNA into a two-dimensional (2-D) pattern. The first restriction enzyme digestion was done in solution, followed by electrophoresis of the restriction fragments in one dimension. A second restriction enzyme digestion was carried out in situ in the gel, followed by electrophoresis in a second dimension perpendicular to the first electrophoresis. The 2-D pattern provides for the resolution of 300-400 spots, which are defined and indexed by an x,y coordinate system with size markers. This approach has greatly increased the resolution power over conventional one-dimensional (1-D) electrophoresis. To study DNA rearrangement, a 2-D pattern from a test strain was compared with the 2-D pattern from a reference strain. After the first digestion, genomic DNA fragments from the test strain were labeled with 35S, while those from the reference strain were labeled with 32P. This was done to utilize the difference in the energy emission of 35S and 32P isotopes for autoradiography when two x-ray films were exposed simultaneously on top of the gel after the 2-D electrophoresis. The irradiation from the decay of 35S exposed only the lower film, whereas the irradiation from the decay of 32P exposed both the lower and upper films. Different DNA fragments existed in the test DNA compared with the reference DNA can be identified unambiguously by the differential two 2-D patterns produced on two films upon exposure to the 35S and 32P fragments in the same gel. An appropriate photographic procedure further simplified the process, allowing only the difference in DNA fragments between these two patterns to be shown in the map
International Nuclear Information System (INIS)
Lee, Kok Foong; Patterson, Robert I.A.; Wagner, Wolfgang; Kraft, Markus
2015-01-01
Graphical abstract: -- Highlights: •Problems concerning multi-compartment population balance equations are studied. •A class of fragmentation weight transfer functions is presented. •Three stochastic weighted algorithms are compared against the direct simulation algorithm. •The numerical errors of the stochastic solutions are assessed as a function of fragmentation rate. •The algorithms are applied to a multi-dimensional granulation model. -- Abstract: This paper introduces stochastic weighted particle algorithms for the solution of multi-compartment population balance equations. In particular, it presents a class of fragmentation weight transfer functions which are constructed such that the number of computational particles stays constant during fragmentation events. The weight transfer functions are constructed based on systems of weighted computational particles and each of it leads to a stochastic particle algorithm for the numerical treatment of population balance equations. Besides fragmentation, the algorithms also consider physical processes such as coagulation and the exchange of mass with the surroundings. The numerical properties of the algorithms are compared to the direct simulation algorithm and an existing method for the fragmentation of weighted particles. It is found that the new algorithms show better numerical performance over the two existing methods especially for systems with significant amount of large particles and high fragmentation rates.
Energy Technology Data Exchange (ETDEWEB)
Lee, Kok Foong [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA (United Kingdom); Patterson, Robert I.A.; Wagner, Wolfgang [Weierstrass Institute for Applied Analysis and Stochastics, Mohrenstraße 39, 10117 Berlin (Germany); Kraft, Markus, E-mail: mk306@cam.ac.uk [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA (United Kingdom); School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 (Singapore)
2015-12-15
Graphical abstract: -- Highlights: •Problems concerning multi-compartment population balance equations are studied. •A class of fragmentation weight transfer functions is presented. •Three stochastic weighted algorithms are compared against the direct simulation algorithm. •The numerical errors of the stochastic solutions are assessed as a function of fragmentation rate. •The algorithms are applied to a multi-dimensional granulation model. -- Abstract: This paper introduces stochastic weighted particle algorithms for the solution of multi-compartment population balance equations. In particular, it presents a class of fragmentation weight transfer functions which are constructed such that the number of computational particles stays constant during fragmentation events. The weight transfer functions are constructed based on systems of weighted computational particles and each of it leads to a stochastic particle algorithm for the numerical treatment of population balance equations. Besides fragmentation, the algorithms also consider physical processes such as coagulation and the exchange of mass with the surroundings. The numerical properties of the algorithms are compared to the direct simulation algorithm and an existing method for the fragmentation of weighted particles. It is found that the new algorithms show better numerical performance over the two existing methods especially for systems with significant amount of large particles and high fragmentation rates.
Gao, Jian; Guildenbecher, Daniel R; Reu, Phillip L; Kulkarni, Varun; Sojka, Paul E; Chen, Jun
2013-06-01
Quantitative application of digital in-line holography (DIH) to characterize multiphase fragmentation is demonstrated. DIH is applied to record sequential holograms of the breakup of an ethanol droplet in an aerodynamic flow field. Various stages of the breakup process are recorded, including deformation, bag growth, bag breakup, and rim breakup. A recently proposed hybrid method is applied to extract the three-dimensional (3D) location and size of secondary droplets as well as the 3D morphology of the rim. Particle matching between sequential frames is used to determine the velocity. Coincidence with the results obtained from phase Doppler anemometry measurement demonstrates the accuracy of measurement by DIH and the hybrid method.
Route to three-dimensional fragments using diversity-oriented synthesis.
Hung, Alvin W; Ramek, Alex; Wang, Yikai; Kaya, Taner; Wilson, J Anthony; Clemons, Paul A; Young, Damian W
2011-04-26
Fragment-based drug discovery (FBDD) has proven to be an effective means of producing high-quality chemical ligands as starting points for drug-discovery pursuits. The increasing number of clinical candidate drugs developed using FBDD approaches is a testament of the efficacy of this approach. The success of fragment-based methods is highly dependent on the identity of the fragment library used for screening. The vast majority of FBDD has centered on the use of sp(2)-rich aromatic compounds. An expanded set of fragments that possess more 3D character would provide access to a larger chemical space of fragments than those currently used. Diversity-oriented synthesis (DOS) aims to efficiently generate a set of molecules diverse in skeletal and stereochemical properties. Molecules derived from DOS have also displayed significant success in the modulation of function of various "difficult" targets. Herein, we describe the application of DOS toward the construction of a unique set of fragments containing highly sp(3)-rich skeletons for fragment-based screening. Using cheminformatic analysis, we quantified the shapes and physical properties of the new 3D fragments and compared them with a database containing known fragment-like molecules.
Timing characteristics of a two-dimensional multi-wire cathode strip detector for fission fragments
International Nuclear Information System (INIS)
Vind, R.P.; Joshi, B.N.; Jangale, R.V.; Inkar, A.L.; Prajapati, G.K.; John, B.V.; Biswas, D.C.
2014-01-01
In the recent past, a gas filled two-dimensional multi-wire cathode strip detector (MCSD) was developed for the detection of fission fragments (FFs). The position resolution was found to be about 1.0 and 1.5 mm in X and Y directions respectively. The detector has three electrode planes consisting of cathode strip (X-plane), anode wires and split-cathode wires (Y-plane). Each thin wire of the anode plane placed between the two cathode planes is essentially independent and behaves like a proportional counter. The construction of the detector in detail has been given in our earlier paper. The position information has been obtained by employing high impedance discrete delay line read out method for extracting position information in X and Y-directions. In this work, the timing characteristics of MCSD detector are reported to explore the possible use of this detector for the measurement of the mass of the fission fragments produced in heavy ion induced fission reactions
Reconstruction of Banknote Fragments Based on Keypoint Matching Method.
Gwo, Chih-Ying; Wei, Chia-Hung; Li, Yue; Chiu, Nan-Hsing
2015-07-01
Banknotes may be shredded by a scrap machine, ripped up by hand, or damaged in accidents. This study proposes an image registration method for reconstruction of multiple sheets of banknotes. The proposed method first constructs different scale spaces to identify keypoints in the underlying banknote fragments. Next, the features of those keypoints are extracted to represent their local patterns around keypoints. Then, similarity is computed to find the keypoint pairs between the fragment and the reference banknote. The banknote fragments can determine the coordinate and amend the orientation. Finally, an assembly strategy is proposed to piece multiple sheets of banknote fragments together. Experimental results show that the proposed method causes, on average, a deviation of 0.12457 ± 0.12810° for each fragment while the SIFT method deviates 1.16893 ± 2.35254° on average. The proposed method not only reconstructs the banknotes but also decreases the computing cost. Furthermore, the proposed method can estimate relatively precisely the orientation of the banknote fragments to assemble. © 2015 American Academy of Forensic Sciences.
Effective Fragment Potential Method for H-Bonding: How To Obtain Parameters for Nonrigid Fragments.
Dubinets, Nikita; Slipchenko, Lyudmila V
2017-07-20
Accuracy of the effective fragment potential (EFP) method was explored for describing intermolecular interaction energies in three dimers with strong H-bonded interactions, formic acid, formamide, and formamidine dimers, which are a part of HBC6 database of noncovalent interactions. Monomer geometries in these dimers change significantly as a function of intermonomer separation. Several EFP schemes were considered, in which fragment parameters were prepared for a fragment in its gas-phase geometry or recomputed for each unique fragment geometry. Additionally, a scheme in which gas-phase fragment parameters are shifted according to relaxed fragment geometries is introduced and tested. EFP data are compared against the coupled cluster with single, double, and perturbative triple excitations (CCSD(T)) method in a complete basis set (CBS) and the symmetry adapted perturbation theory (SAPT). All considered EFP schemes provide a good agreement with CCSD(T)/CBS for binding energies at equilibrium separations, with discrepancies not exceeding 2 kcal/mol. However, only the schemes that utilize relaxed fragment geometries remain qualitatively correct at shorter than equilibrium intermolecular distances. The EFP scheme with shifted parameters behaves quantitatively similar to the scheme in which parameters are recomputed for each monomer geometry and thus is recommended as a computationally efficient approach for large-scale EFP simulations of flexible systems.
Extension of moment projection method to the fragmentation process
International Nuclear Information System (INIS)
Wu, Shaohua; Yapp, Edward K.Y.; Akroyd, Jethro; Mosbach, Sebastian; Xu, Rong; Yang, Wenming; Kraft, Markus
2017-01-01
The method of moments is a simple but efficient method of solving the population balance equation which describes particle dynamics. Recently, the moment projection method (MPM) was proposed and validated for particle inception, coagulation, growth and, more importantly, shrinkage; here the method is extended to include the fragmentation process. The performance of MPM is tested for 13 different test cases for different fragmentation kernels, fragment distribution functions and initial conditions. Comparisons are made with the quadrature method of moments (QMOM), hybrid method of moments (HMOM) and a high-precision stochastic solution calculated using the established direct simulation algorithm (DSA) and advantages of MPM are drawn.
Extension of moment projection method to the fragmentation process
Energy Technology Data Exchange (ETDEWEB)
Wu, Shaohua [Department of Mechanical Engineering, National University of Singapore, Engineering Block EA, Engineering Drive 1, 117576 (Singapore); Yapp, Edward K.Y.; Akroyd, Jethro; Mosbach, Sebastian [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA (United Kingdom); Xu, Rong [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 (Singapore); Yang, Wenming [Department of Mechanical Engineering, National University of Singapore, Engineering Block EA, Engineering Drive 1, 117576 (Singapore); Kraft, Markus, E-mail: mk306@cam.ac.uk [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA (United Kingdom); School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 (Singapore)
2017-04-15
The method of moments is a simple but efficient method of solving the population balance equation which describes particle dynamics. Recently, the moment projection method (MPM) was proposed and validated for particle inception, coagulation, growth and, more importantly, shrinkage; here the method is extended to include the fragmentation process. The performance of MPM is tested for 13 different test cases for different fragmentation kernels, fragment distribution functions and initial conditions. Comparisons are made with the quadrature method of moments (QMOM), hybrid method of moments (HMOM) and a high-precision stochastic solution calculated using the established direct simulation algorithm (DSA) and advantages of MPM are drawn.
Virtual fragment preparation for computational fragment-based drug design.
Ludington, Jennifer L
2015-01-01
Fragment-based drug design (FBDD) has become an important component of the drug discovery process. The use of fragments can accelerate both the search for a hit molecule and the development of that hit into a lead molecule for clinical testing. In addition to experimental methodologies for FBDD such as NMR and X-ray Crystallography screens, computational techniques are playing an increasingly important role. The success of the computational simulations is due in large part to how the database of virtual fragments is prepared. In order to prepare the fragments appropriately it is necessary to understand how FBDD differs from other approaches and the issues inherent in building up molecules from smaller fragment pieces. The ultimate goal of these calculations is to link two or more simulated fragments into a molecule that has an experimental binding affinity consistent with the additive predicted binding affinities of the virtual fragments. Computationally predicting binding affinities is a complex process, with many opportunities for introducing error. Therefore, care should be taken with the fragment preparation procedure to avoid introducing additional inaccuracies.This chapter is focused on the preparation process used to create a virtual fragment database. Several key issues of fragment preparation which affect the accuracy of binding affinity predictions are discussed. The first issue is the selection of the two-dimensional atomic structure of the virtual fragment. Although the particular usage of the fragment can affect this choice (i.e., whether the fragment will be used for calibration, binding site characterization, hit identification, or lead optimization), general factors such as synthetic accessibility, size, and flexibility are major considerations in selecting the 2D structure. Other aspects of preparing the virtual fragments for simulation are the generation of three-dimensional conformations and the assignment of the associated atomic point charges.
The effective fragment molecular orbital method for fragments connected by covalent bonds.
Directory of Open Access Journals (Sweden)
Casper Steinmann
Full Text Available We extend the effective fragment molecular orbital method (EFMO into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively.
Du, Qi-Shi; Huang, Ri-Bo; Wei, Yu-Tuo; Pang, Zong-Wen; Du, Li-Qin; Chou, Kuo-Chen
2009-01-30
In cooperation with the fragment-based design a new drug design method, the so-called "fragment-based quantitative structure-activity relationship" (FB-QSAR) is proposed. The essence of the new method is that the molecular framework in a family of drug candidates are divided into several fragments according to their substitutes being investigated. The bioactivities of molecules are correlated with the physicochemical properties of the molecular fragments through two sets of coefficients in the linear free energy equations. One coefficient set is for the physicochemical properties and the other for the weight factors of the molecular fragments. Meanwhile, an iterative double least square (IDLS) technique is developed to solve the two sets of coefficients in a training data set alternately and iteratively. The IDLS technique is a feedback procedure with machine learning ability. The standard Two-dimensional quantitative structure-activity relationship (2D-QSAR) is a special case, in the FB-QSAR, when the whole molecule is treated as one entity. The FB-QSAR approach can remarkably enhance the predictive power and provide more structural insights into rational drug design. As an example, the FB-QSAR is applied to build a predictive model of neuraminidase inhibitors for drug development against H5N1 influenza virus. (c) 2008 Wiley Periodicals, Inc.
Velocity distribution of fragments of catastrophic impacts
Takagi, Yasuhiko; Kato, Manabu; Mizutani, Hitoshi
1992-01-01
Three dimensional velocities of fragments produced by laboratory impact experiments were measured for basalts and pyrophyllites. The velocity distribution of fragments obtained shows that the velocity range of the major fragments is rather narrow, at most within a factor of 3 and that no clear dependence of velocity on the fragment mass is observed. The NonDimensional Impact Stress (NDIS) defined by Mizutani et al. (1990) is found to be an appropriate scaling parameter to describe the overall fragment velocity as well as the antipodal velocity.
The dual role of fragments in fragment-assembly methods for de novo protein structure prediction
Handl, Julia; Knowles, Joshua; Vernon, Robert; Baker, David; Lovell, Simon C.
2013-01-01
In fragment-assembly techniques for protein structure prediction, models of protein structure are assembled from fragments of known protein structures. This process is typically guided by a knowledge-based energy function and uses a heuristic optimization method. The fragments play two important roles in this process: they define the set of structural parameters available, and they also assume the role of the main variation operators that are used by the optimiser. Previous analysis has typically focused on the first of these roles. In particular, the relationship between local amino acid sequence and local protein structure has been studied by a range of authors. The correlation between the two has been shown to vary with the window length considered, and the results of these analyses have informed directly the choice of fragment length in state-of-the-art prediction techniques. Here, we focus on the second role of fragments and aim to determine the effect of fragment length from an optimization perspective. We use theoretical analyses to reveal how the size and structure of the search space changes as a function of insertion length. Furthermore, empirical analyses are used to explore additional ways in which the size of the fragment insertion influences the search both in a simulation model and for the fragment-assembly technique, Rosetta. PMID:22095594
Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates.
Wang, Bo; Yang, Ke R; Xu, Xuefei; Isegawa, Miho; Leverentz, Hannah R; Truhlar, Donald G
2014-09-16
Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine
The linearly scaling 3D fragment method for large scale electronic structure calculations
Energy Technology Data Exchange (ETDEWEB)
Zhao Zhengji [National Energy Research Scientific Computing Center (NERSC) (United States); Meza, Juan; Shan Hongzhang; Strohmaier, Erich; Bailey, David; Wang Linwang [Computational Research Division, Lawrence Berkeley National Laboratory (United States); Lee, Byounghak, E-mail: ZZhao@lbl.go [Physics Department, Texas State University (United States)
2009-07-01
The linearly scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) at OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.
ALIS-FLP: Amplified ligation selected fragment-length polymorphism method for microbial genotyping
DEFF Research Database (Denmark)
Brillowska-Dabrowska, A.; Wianecka, M.; Dabrowski, Slawomir
2008-01-01
A DNA fingerprinting method known as ALIS-FLP (amplified ligation selected fragment-length polymorphism) has been developed for selective and specific amplification of restriction fragments from TspRI restriction endonuclease digested genomic DNA. The method is similar to AFLP, but differs...
Hot-stage microscopy for determination of API fragmentation: comparison with other methods.
Šimek, Michal; Grünwaldová, Veronika; Kratochvíl, Bohumil
2016-08-01
Although the fragmentation of the active pharmaceutical ingredient (API) is a phenomenon that is mentioned in many literature sources, no well-suited analytical tools for its investigation are currently known. We used the hot-stage microscopy method, already presented in our previous work, and studied the real fragmentation of the tadalafil particles in model tablets which were prepared under different compaction pressures. The morphology, spectral imaging and evaluation of plastic and elastic energies were also analyzed to support the hot-stage method. The prepared blend of tadalafil and excipients was compacted under a several forces from 5 to 35 kN to reveal the trend of fragmentation. The exact fragmentation of tadalafil with increased compaction pressure was revealed by the hot-stage microscopic method and it was in good agreement with plastic and elastic energies. Conversely, spectral imaging, which is being used for this analysis, was considered to be inaccurate methodology as mainly agglomerates, not individual particles, were measured. The availability of the hot-stage microscopic method equips pharmaceutical scientists with an in vitro assessment technique that will more reliably determine the fragmentation of the API in finished tablets and the behavior of the particles when compacted.
Research on Splicing Method of Digital Relic Fragment Model
Yan, X.; Hu, Y.; Hou, M.
2018-04-01
In the course of archaeological excavation, a large number of pieces of cultural relics were unearthed, and the restoration of these fragments was done manually by traditional arts and crafts experts. In this process, cultural relics experts often try to splice the existing cultural relics, and then use adhesive to stick together the fragments of correct location, which will cause irreversible secondary damage to cultural relics. In order to minimize such damage, the surveyors combine 3D laser scanning with computer technology, and use the method of establishing digital cultural relics fragments model to make virtual splicing of cultural relics. The 3D software on the common market can basically achieve the model translation and rotation, using this two functions can be achieved manually splicing between models, mosaic records after the completion of the specific location of each piece of fragments, so as to effectively reduce the damage to the relics had tried splicing process.
Fragmentation of rotating protostellar clouds
International Nuclear Information System (INIS)
Tohline, J.E.
1980-01-01
We examine, with a three-dimensional hydrodynamic computer code, the behavior of rotating, isothermal gas clouds as they collapse from Jeans unstable configurations, in order to determine whether they are susceptible to fragmentation during the initial dynamic collapse phase of their evolution. We find that a gas cloud will not fragment unless (a) it begins collapsing from a radius much smaller than the Jeans radius (i.e., the cloud initially encloses many Jeans masses) and (b) irregularities in the cloud's initial structure (specifically, density inhomogeneities) enclose more than one Jeans mass of material. Gas pressure smooths out features that are not initially Jeans unstable while rotation plays no direct role in damping inhomogeneities. Instead of fragmenting, most of our models collapse to a ring configuration (as has been observed by other investigators in two-dimensional, axisymmetric models). The rings appear to be less susceptible to gragmentation from arbitrary perturbations in their structure than has previously been indicated in other work. Because our models, which include the effects of gas pressure, do not readily fragment during a phase of dynamic collapse, we suggest that gas clouds in the galactic disk undergo fragmentation only during quasi-equilibrium phases of their evolution
Fragment-based drug discovery using rational design.
Jhoti, H
2007-01-01
Fragment-based drug discovery (FBDD) is established as an alternative approach to high-throughput screening for generating novel small molecule drug candidates. In FBDD, relatively small libraries of low molecular weight compounds (or fragments) are screened using sensitive biophysical techniques to detect their binding to the target protein. A lower absolute affinity of binding is expected from fragments, compared to much higher molecular weight hits detected by high-throughput screening, due to their reduced size and complexity. Through the use of iterative cycles of medicinal chemistry, ideally guided by three-dimensional structural data, it is often then relatively straightforward to optimize these weak binding fragment hits into potent and selective lead compounds. As with most other lead discovery methods there are two key components of FBDD; the detection technology and the compound library. In this review I outline the two main approaches used for detecting the binding of low affinity fragments and also some of the key principles that are used to generate a fragment library. In addition, I describe an example of how FBDD has led to the generation of a drug candidate that is now being tested in clinical trials for the treatment of cancer.
The identification method of the nuclear fragments in emulsions
International Nuclear Information System (INIS)
Jipa, Alexandru; Ocheseanu, Silvia; Caramarcu, Costin; Calin, Marius; Constantin, Florin; Stan, Emil
2003-01-01
The visualization detectors have been successfully used from the beginning of the study of the relativistic nuclear collisions. One of these detectors used in such experiments is the nuclear emulsion. To increase the speed of the passage from pictures to experimental data different methods and tools have been proposed during the time. For identifying the nuclear fragments obtained in the relativistic radioactive beams multiple layers of nuclear emulsions have been exposed in experiments performed at the Synchrophasotron from the JINR Dubna (BECQUEREL Collaboration). The nuclear fragments have been identified using PAVICOM scanning and measuring system. In the present work an identification method based on a real time image processing machine and a reconstruction algorithm based on special conformal transforms is proposed. The results obtained by this method are compared with those obtained using PAVICOM device. Because in this study only pictures have been used, not initial nuclear emulsions, some difficulties in the identification of the nuclear fragments with higher polar angles can appear. Generally, comparable results have been obtained. The authors thank Dr. Pavel Zarubin from JINR Dubna, Laboratory of High Energy Physics, and Dr. Maria Haiduc, Institute of Space Sciences Bucharest-Magurele, for the pictures of the nuclear emulsions exposed in these experiments. (authors)
Thermochemical Fragment Energy Method for Biomolecules: Application to a Collagen Model Peptide.
Suárez, Ernesto; Díaz, Natalia; Suárez, Dimas
2009-06-09
Herein, we first review different methodologies that have been proposed for computing the quantum mechanical (QM) energy and other molecular properties of large systems through a linear combination of subsystem (fragment) energies, which can be computed using conventional QM packages. Particularly, we emphasize the similarities among the different methods that can be considered as variants of the multibody expansion technique. Nevertheless, on the basis of thermochemical arguments, we propose yet another variant of the fragment energy methods, which could be useful for, and readily applicable to, biomolecules using either QM or hybrid quantum mechanical/molecular mechanics methods. The proposed computational scheme is applied to investigate the stability of a triple-helical collagen model peptide. To better address the actual applicability of the fragment QM method and to properly compare with experimental data, we compute average energies by carrying out single-point fragment QM calculations on structures generated by a classical molecular dynamics simulation. The QM calculations are done using a density functional level of theory combined with an implicit solvent model. Other free-energy terms such as attractive dispersion interactions or thermal contributions are included using molecular mechanics. The importance of correcting both the intermolecular and intramolecular basis set superposition error (BSSE) in the QM calculations is also discussed in detail. On the basis of the favorable comparison of our fragment-based energies with experimental data and former theoretical results, we conclude that the fragment QM energy strategy could be an interesting addition to the multimethod toolbox for biomolecular simulations in order to investigate those situations (e.g., interactions with metal clusters) that are beyond the range of applicability of common molecular mechanics methods.
Fragmentation of DNA affects the accuracy of the DNA quantitation by the commonly used methods
Directory of Open Access Journals (Sweden)
Sedlackova Tatiana
2013-02-01
Full Text Available Abstract Background Specific applications and modern technologies, like non-invasive prenatal testing, non-invasive cancer diagnostic and next generation sequencing, are currently in the focus of researchers worldwide. These have common characteristics in use of highly fragmented DNA molecules for analysis. Hence, for the performance of molecular methods, DNA concentration is a crucial parameter; we compared the influence of different levels of DNA fragmentation on the accuracy of DNA concentration measurements. Results In our comparison, the performance of the currently most commonly used methods for DNA concentration measurement (spectrophotometric, fluorometric and qPCR based were tested on artificially fragmented DNA samples. In our comparison, unfragmented and three specifically fragmented DNA samples were used. According to our results, the level of fragmentation did not influence the accuracy of spectrophotometric measurements of DNA concentration, while other methods, fluorometric as well as qPCR-based, were significantly influenced and a decrease in measured concentration was observed with more intensive DNA fragmentation. Conclusions Our study has confirmed that the level of fragmentation of DNA has significant impact on accuracy of DNA concentration measurement with two of three mostly used methods (PicoGreen and qPCR. Only spectrophotometric measurement was not influenced by the level of fragmentation, but sensitivity of this method was lowest among the three tested. Therefore if it is possible the DNA quantification should be performed with use of equally fragmented control DNA.
International Nuclear Information System (INIS)
Truelove, J.K.; Klein, R.I.; McKee, C.F.; Holliman, J.H. II; Truelove, J.K.; McKee, C.F.; Truelove, J.K.; Holliman, J.H. II; Klein, R.I.; Woods, D.T.; McKee, C.F.; Woods, D.T.; Howell, L.H.; Greenough, J.A.
1998-01-01
We describe a new code for numerical solution of three-dimensional self-gravitational hydrodynamics problems. This code utilizes the technique of local adaptive mesh refinement (AMR), employing multiple grids at multiple levels of resolution and automatically and dynamically adding and removing these grids as necessary to maintain adequate resolution. This technology allows solution of problems that would be prohibitively expensive with a code using fixed resolution, and it is more versatile and efficient than competing methods of achieving variable resolution. In particular, we apply this technique to simulate the collapse and fragmentation of a molecular cloud, a key step in star formation. The simulation involves many orders of magnitude of variation in length scale as fragments form at positions that are not a priori discernible from general initial conditions. In this paper, we describe the methodology behind this new code and present several illustrative applications. The criterion that guides the degree of adaptive mesh refinement is critical to the success of the scheme, and, for the isothermal problems considered here, we employ the Jeans condition for this purpose. By maintaining resolution finer than the local Jeans length, we set new benchmarks of accuracy by which to measure other codes on each problem we consider, including the uniform collapse of a finite pressured cloud. We find that the uniformly rotating, spherical clouds treated here first collapse to disks in the equatorial plane and then, in the presence of applied perturbations, form filamentary singularities that do not fragment while isothermal. Our results provide numerical confirmation of recent work by Inutsuka ampersand Miyama on this scenario of isothermal filament formation. copyright copyright 1998. The American Astronomical Society
Isegawa, Miho; Gao, Jiali; Truhlar, Donald G
2011-08-28
Molecular fragmentation algorithms provide a powerful approach to extending electronic structure methods to very large systems. Here we present a method for including charge transfer between molecular fragments in the explicit polarization (X-Pol) fragment method for calculating potential energy surfaces. In the conventional X-Pol method, the total charge of each fragment is preserved, and charge transfer between fragments is not allowed. The description of charge transfer is made possible by treating each fragment as an open system with respect to the number of electrons. To achieve this, we applied Mermin's finite temperature method to the X-Pol wave function. In the application of this method to X-Pol, the fragments are open systems that partially equilibrate their number of electrons through a quasithermodynamics electron reservoir. The number of electrons in a given fragment can take a fractional value, and the electrons of each fragment obey the Fermi-Dirac distribution. The equilibrium state for the electrons is determined by electronegativity equalization with conservation of the total number of electrons. The amount of charge transfer is controlled by re-interpreting the temperature parameter in the Fermi-Dirac distribution function as a coupling strength parameter. We determined this coupling parameter so as to reproduce the charge transfer energy obtained by block localized energy decomposition analysis. We apply the new method to ten systems, and we show that it can yield reasonable approximations to potential energy profiles, to charge transfer stabilization energies, and to the direction and amount of charge transferred. © 2011 American Institute of Physics
Liu, Quansheng; Jiang, Yalong; Wu, Zhijun; Xu, Xiangyu; Liu, Qi
2018-04-01
In this study, a two-dimensional Voronoi element-based numerical manifold method (VE-NMM) is developed to analyze the granite fragmentation process by a single tunnel boring machine (TBM) cutter under different confining stresses. A Voronoi tessellation technique is adopted to generate the polygonal grain assemblage to approximate the microstructure of granite sample from the Gubei colliery of Huainan mining area in China. A modified interface contact model with cohesion and tensile strength is embedded into the numerical manifold method (NMM) to interpret the interactions between the rock grains. Numerical uniaxial compression and Brazilian splitting tests are first conducted to calibrate and validate the VE-NMM models based on the laboratory experiment results using a trial-and-error method. On this basis, numerical simulations of rock fragmentation by a single TBM cutter are conducted. The simulated crack initiation and propagation process as well as the indentation load-penetration depth behaviors in the numerical models accurately predict the laboratory indentation test results. The influence of confining stress on rock fragmentation is also investigated. Simulation results show that radial tensile cracks are more likely to be generated under a low confining stress, eventually coalescing into a major fracture along the loading axis. However, with the increase in confining stress, more side cracks initiate and coalesce, resulting in the formation of rock chips at the upper surface of the model. In addition, the peak indentation load also increases with the increasing confining stress, indicating that a higher thrust force is usually needed during the TBM boring process in deep tunnels.
Aspect Ratio Dependence of Impact Fragmentation
International Nuclear Information System (INIS)
Inaoka, H.; Toyosawa, E.; Takayasu, H.; Inaoka, H.
1997-01-01
A numerical model of three-dimensional impact fragmentation produces a power-law cumulative fragment mass distribution followed by a flat tail. The result is consistent with an experimental result in a recent paper by Meibom and Balslev [Phys. Rev. Lett. 76, 2492 (1996)]. Our numerical simulation also implies that the fragment mass distribution changes from a power law with a flat tail to a power law with a sudden cutoff, depending on the aspect ratio of the fractured object. copyright 1997 The American Physical Society
Prediction of inorganic superconductors with quasi-one-dimensional crystal structure
International Nuclear Information System (INIS)
Volkova, L M; Marinin, D V
2013-01-01
Models of superconductors having a quasi-one-dimensional crystal structure based on the convoluted into a tube Ginzburg sandwich, which comprises a layered dielectric–metal–dielectric structure, have been suggested. The critical crystal chemistry parameters of the Ginzburg sandwich determining the possibility of the emergence of superconductivity and the T c value in layered high-T c cuprates, which could have the same functions in quasi-one-dimensional fragments (sandwich-type tubes), have been examined. The crystal structures of known low-temperature superconductors, in which one can mark out similar quasi-one-dimensional fragments, have been analyzed. Five compounds with quasi-one-dimensional structures, which can be considered as potential parents of new superconductor families, possibly with high transition temperatures, have been suggested. The methods of doping and modification of these compounds are provided. (paper)
Current fragmentation in deep inelastic scattering
International Nuclear Information System (INIS)
Hamer, C.J.
1975-04-01
It is argued that the current fragmentation products in deep inelastic electron scattering will not be distributed in a 'one-dimensional' rapidity plateau as in the parton model picture of Feynman and Bjorken. A reaction mechanism with a multiperipheral topology, but which the above configuration might have been achieved, does not in fact populate the current fragmentation plateau; and unless partons are actually observed in the final state, it cannot lead to Bjorken scaling. The basic reason for this failure is shown to be the fact that when a particle is produced in the current fragmentation plateau, the adjacent momentum transfer in the multiperipheral chain becomes large and negative: such processes are inevitably suppressed. Instead, the current fragmentation products are likely to be generated by a fragmentation, or sequential decay process. (author)
The use of many-body expansions and geometry optimizations in fragment-based methods.
Fedorov, Dmitri G; Asada, Naoya; Nakanishi, Isao; Kitaura, Kazuo
2014-09-16
Conspectus Chemists routinely work with complex molecular systems: solutions, biochemical molecules, and amorphous and composite materials provide some typical examples. The questions one often asks are what are the driving forces for a chemical phenomenon? How reasonable are our views of chemical systems in terms of subunits, such as functional groups and individual molecules? How can one quantify the difference in physicochemical properties of functional units found in a different chemical environment? Are various effects on functional units in molecular systems additive? Can they be represented by pairwise potentials? Are there effects that cannot be represented in a simple picture of pairwise interactions? How can we obtain quantitative values for these effects? Many of these questions can be formulated in the language of many-body effects. They quantify the properties of subunits (fragments), referred to as one-body properties, pairwise interactions (two-body properties), couplings of two-body interactions described by three-body properties, and so on. By introducing the notion of fragments in the framework of quantum chemistry, one obtains two immense benefits: (a) chemists can finally relate to quantum chemistry, which now speaks their language, by discussing chemically interesting subunits and their interactions and (b) calculations become much faster due to a reduced computational scaling. For instance, the somewhat academic sounding question of the importance of three-body effects in water clusters is actually another way of asking how two hydrogen bonds affect each other, when they involve three water molecules. One aspect of this is the many-body charge transfer (CT), because the charge transfers in the two hydrogen bonds are coupled to each other (not independent). In this work, we provide a generalized view on the use of many-body expansions in fragment-based methods, focusing on the general aspects of the property expansion and a contraction of a
A new crystal structure fragment-based pharmacophore method for G protein-coupled receptors
DEFF Research Database (Denmark)
Fidom, Kimberley; Isberg, Vignir; Hauser, Alexander Sebastian
2015-01-01
and receptor residue pairs, from crystal structure complexes. We describe the procedure to collect a library with more than 250 fragments covering 29 residue positions within the generic transmembrane binding pocket. We describe how the library fragments are recombined and inferred to build pharmacophores...... for new targets. A validating retrospective virtual screening of histamine H1 and H3 receptor pharmacophores yielded area-under-the-curves of 0.88 and 0.82, respectively. The fragment-based method has the unique advantage that it can be applied to targets for which no (homologous) crystal structures...... or ligands are known. 47% of the class A G protein-coupled receptors can be targeted with at least four-element pharmacophores. The fragment libraries can also be used to grow known ligands or for rotamer refinement of homology models. Researchers can download the complete fragment library or a subset...
Analysis methods for Kevlar shield response to rotor fragments
Gerstle, J. H.
1977-01-01
Several empirical and analytical approaches to rotor burst shield sizing are compared and principal differences in metal and fabric dynamic behavior are discussed. The application of transient structural response computer programs to predict Kevlar containment limits is described. For preliminary shield sizing, present analytical methods are useful if insufficient test data for empirical modeling are available. To provide other information useful for engineering design, analytical methods require further developments in material characterization, failure criteria, loads definition, and post-impact fragment trajectory prediction.
Bobrovnikov, S. M.; Gorlov, E. V.; Zharkov, V. I.
2018-05-01
A technique for increasing the selectivity of the method of detecting high-energy materials (HEMs) based on laser fragmentation of HEM molecules with subsequent laser excitation of fluorescence of the characteristic NO fragments from the first vibrational level of the ground state is suggested.
Energy Technology Data Exchange (ETDEWEB)
Moeller, Peter [Los Alamos National Laboratory, Theoretical Division, Los Alamos, NM (United States); Ichikawa, Takatoshi [Kyoto University, Yukawa Institute for Theoretical Physics, Kyoto (Japan)
2015-12-15
We propose a method to calculate the two-dimensional (2D) fission-fragment yield Y(Z,N) versus both proton and neutron number, with inclusion of odd-even staggering effects in both variables. The approach is to use the Brownian shape-motion on a macroscopic-microscopic potential-energy surface which, for a particular compound system is calculated versus four shape variables: elongation (quadrupole moment Q{sub 2}), neck d, left nascent fragment spheroidal deformation ε{sub f1}, right nascent fragment deformation ε{sub f2} and two asymmetry variables, namely proton and neutron numbers in each of the two fragments. The extension of previous models 1) introduces a method to calculate this generalized potential-energy function and 2) allows the correlated transfer of nucleon pairs in one step, in addition to sequential transfer. In the previous version the potential energy was calculated as a function of Z and N of the compound system and its shape, including the asymmetry of the shape. We outline here how to generalize the model from the ''compound-system'' model to a model where the emerging fragment proton and neutron numbers also enter, over and above the compound system composition. (orig.)
Two-dimensional collapse calculations of cylindrical clouds
International Nuclear Information System (INIS)
Bastien, P.; Mitalas, R.
1979-01-01
A two-dimensional hydrodynamic computer code has been extensively modified and expanded to study the collapse of non-rotating interstellar clouds. The physics and the numerical methods involved are discussed. The results are presented and discussed in terms of the Jeans number. The critical Jeans number for collapse of non-rotating cylindrical clouds whose length is the same as their diameter is 1.00. No evidence for fragmentation has been found for these clouds, but fragmentation seems quite likely for more elongated cylindrical clouds. (author)
Calculations of three-dimensional collapse and fragmentation
International Nuclear Information System (INIS)
Larson, R.B.
1978-01-01
Calculations of the fragmentation of an isothermally collapsing cloud have been carried out using a method that follows the motion of individual fluid particles and includes pressure and viscosity forces between neighbouring particles. In a cloud or region whose mass is comparable to the Jeans mass, a highly condensed core forms, surrounded by a diffuse envelope that continues to accrete on to the core; in the presence of rotation, the inner part of the envelope becomes essentially an accretion disc. If the mass exceeds the Jeans mass, several such accreting cores are formed, the number being comparable to the initial number of jeans masses in the cloud. Binary systems and hierarchical multiple systems are frequently obtained. The mass of the largest object formed is independent of the Jeans mass but depends on the angular momentum and viscosity of the cloud, and is essentially the maximum mass accretable by a single object. The resulting mass spectrum may be determined by the development of a hierarchy of accreting objects of different sizes, such that each object has several smaller ones associated with it. The hypothesis of a self-similar accretion hierarchy predicts a power-law mass spectrum, which in the limit of inefficient accretion has an exponent x = 1, in reasonable agreement with observations. (author)
Jordan, John B; Whittington, Douglas A; Bartberger, Michael D; Sickmier, E Allen; Chen, Kui; Cheng, Yuan; Judd, Ted
2016-04-28
Fragment-based drug discovery (FBDD) has become a widely used tool in small-molecule drug discovery efforts. One of the most commonly used biophysical methods in detecting weak binding of fragments is nuclear magnetic resonance (NMR) spectroscopy. In particular, FBDD performed with (19)F NMR-based methods has been shown to provide several advantages over (1)H NMR using traditional magnetization-transfer and/or two-dimensional methods. Here, we demonstrate the utility and power of (19)F-based fragment screening by detailing the identification of a second-site fragment through (19)F NMR screening that binds to a specific pocket of the aspartic acid protease, β-secretase (BACE-1). The identification of this second-site fragment allowed the undertaking of a fragment-linking approach, which ultimately yielded a molecule exhibiting a more than 360-fold increase in potency while maintaining reasonable ligand efficiency and gaining much improved selectivity over cathepsin-D (CatD). X-ray crystallographic studies of the molecules demonstrated that the linked fragments exhibited binding modes consistent with those predicted from the targeted screening approach, through-space NMR data, and molecular modeling.
Fragment based drug discovery: practical implementation based on ¹⁹F NMR spectroscopy.
Jordan, John B; Poppe, Leszek; Xia, Xiaoyang; Cheng, Alan C; Sun, Yax; Michelsen, Klaus; Eastwood, Heather; Schnier, Paul D; Nixey, Thomas; Zhong, Wenge
2012-01-26
Fragment based drug discovery (FBDD) is a widely used tool for discovering novel therapeutics. NMR is a powerful means for implementing FBDD, and several approaches have been proposed utilizing (1)H-(15)N heteronuclear single quantum coherence (HSQC) as well as one-dimensional (1)H and (19)F NMR to screen compound mixtures against a target of interest. While proton-based NMR methods of fragment screening (FBS) have been well documented and are widely used, the use of (19)F detection in FBS has been only recently introduced (Vulpetti et al. J. Am. Chem. Soc.2009, 131 (36), 12949-12959) with the aim of targeting "fluorophilic" sites in proteins. Here, we demonstrate a more general use of (19)F NMR-based fragment screening in several areas: as a key tool for rapid and sensitive detection of fragment hits, as a method for the rapid development of structure-activity relationship (SAR) on the hit-to-lead path using in-house libraries and/or commercially available compounds, and as a quick and efficient means of assessing target druggability.
Immobilization of Fab' fragments onto substrate surfaces: A survey of methods and applications.
Crivianu-Gaita, Victor; Thompson, Michael
2015-08-15
Antibody immobilization onto surfaces has widespread applications in many different fields. It is desirable to bind antibodies such that their fragment-antigen-binding (Fab) units are oriented away from the surface in order to maximize analyte binding. The immobilization of only Fab' fragments yields benefits over the more traditional whole antibody immobilization technique. Bound Fab' fragments display higher surface densities, yielding a higher binding capacity for the analyte. The nucleophilic sulfide of the Fab' fragments allows for specific orientations to be achieved. For biosensors, this indicates a higher sensitivity and lower detection limit for a target analyte. The last thirty years have shown tremendous progress in the immobilization of Fab' fragments onto gold, Si-based, polysaccharide-based, plastic-based, magnetic, and inorganic surfaces. This review will show the current scope of Fab' immobilization techniques available and illustrate methods employed to minimize non-specific adsorption of undesirables. Furthermore, a variety of examples will be given to show the versatility of immobilized Fab' fragments in different applications and future directions of the field will be addressed, especially regarding biosensors. Copyright © 2015 Elsevier B.V. All rights reserved.
Sharma, Gaurav; Gn, Kiran Kumar; Khatri, Kavin; Singh, Ravijot; Gamanagatti, Shivanand; Sharma, Vijay
2017-02-01
In this study we describe the morphology of the posteromedial fragment in pertrochanteric fractures using 3D CT scans and answer two questions 1) Do differences exist between the 3D CT appearances of posteromedial fragments and the depictions made in the AO classification 2) Does the posteromedial fragment affect stability in pertrochanteric fractures, in terms of fracture collapse? Preoperative CT scans of eight 31-A1 and fifty 31-A2 fractures were analysed. The presence of PM fragment, its fragmentation, greater trochanter (GT) involvement, lesser trochanter (LT) fragment size (in terms of its posterior and medial extent as well as LT length), LT fragment displacement (in terms of medial displacement and rotation) were determined. All fractures were treated with a DHS. Fracture collapse was determined on postoperative radiographs. The relationship between fracture collapse and patient factors including age, gender, fracture type (A1 versus A2), characteristics of the posteromedial fragment, and the presence of a lateral wall fracture were determined. Three out of eight 31-A1 fractures demonstrated a separate GT fragment (three part fracture). Out of the 50 31-A2 fractures, 12 had a single PM fragment, which included the LT and GT in continuity. The more common four part fractures seem to form by further fragmentation of this basic form. In A2 fractures, the GT was almost always broken and the broken fragment comprised a mean 56% of normal GT. The LT fragment involved an average of 74% of the posterior wall, and an average of 36% of the medial wall of the proximal femur. Larger LT fragments were less displaced as compared to smaller fragments. Univariate regression analyses revealed that fracture collapse was significantly correlated with fracture type (A1 versus A2, p 0.036), GT size (p 0.002) and the presence of a lateral wall fracture (pfragmentation of the posteromedial fragment, nor the size of the lesser trochanter fragment was found to predict stability in
Iterative Two- and One-Dimensional Methods for Three-Dimensional Neutron Diffusion Calculations
International Nuclear Information System (INIS)
Lee, Hyun Chul; Lee, Deokjung; Downar, Thomas J.
2005-01-01
Two methods are proposed for solving the three-dimensional neutron diffusion equation by iterating between solutions of the two-dimensional (2-D) radial and one-dimensional (1-D) axial solutions. In the first method, the 2-D/1-D equations are coupled using a current correction factor (CCF) with the average fluxes of the lower and upper planes and the axial net currents at the plane interfaces. In the second method, an analytic expression for the axial net currents at the interface of the planes is used for planar coupling. A comparison of the new methods is made with two previously proposed methods, which use interface net currents and partial currents for planar coupling. A Fourier convergence analysis of the four methods was performed, and results indicate that the two new methods have at least three advantages over the previous methods. First, the new methods are unconditionally stable, whereas the net current method diverges for small axial mesh size. Second, the new methods provide better convergence performance than the other methods in the range of practical mesh sizes. Third, the spectral radii of the new methods asymptotically approach zero as the mesh size increases, while the spectral radius of the partial current method approaches a nonzero value as the mesh size increases. Of the two new methods proposed here, the analytic method provides a smaller spectral radius than the CCF method, but the CCF method has several advantages over the analytic method in practical applications
Toroidal and rotating bubble nuclei and the nuclear fragmentation
International Nuclear Information System (INIS)
Royer, G.; Fauchard, C.; Haddad, F.; Jouault, B.
1997-01-01
The energy of rotating bubble and toroidal nuclei predicted to be formed in central heavy ion collisions at intermediate energies is calculated within the generalized rotating liquid drop model. Previously, a one-parameter shape sequence has been defined to describe the path leading to pumpkin-like configurations and toroidal shapes. New analytical expressions for the shape dependent functions have been obtained. The potential barriers standing in these exotic deformation paths are compared with the three-dimensional and plane-fragmentation barriers. Metastable bubble-like minima only appear at very high angular momentum and above the three dimensional fragmentation barriers. In the toroidal deformation path of the heaviest systems exists a large potential pocket localized below the plane-fragmentation barriers. This might allow the temporary survival of heavy nuclear toroids before the final clusterization induced by the surface and proximity tension
Mass distribution of fission fragments within the Born-Oppenheimer approximation
Energy Technology Data Exchange (ETDEWEB)
Pomorski, K.; Nerlo-Pomorska, B. [M.C.S. University, Department of Theoretical Physics, Lublin (Poland); Ivanyuk, F.A. [Institute for Nuclear Research, Kiev (Ukraine)
2017-03-15
The fission fragments mass-yield of {sup 236} U is obtained by an approximate solution of the eigenvalue problem of the collective Hamiltonian that describes the dynamics of the fission process whose degrees of freedom are: the fission (elongation), the neck and mass-asymmetry modes. The macroscopic-microscopic method is used to evaluate the potential energy surface. The macroscopic energy part is calculated using the liquid drop model and the microscopic corrections are obtained using a Woods-Saxon single-particle levels. The four-dimensional modified Cassini ovals shape parametrization is used to describe the shape of the fissioning nucleus. The mass tensor is taken within a cranking-type approximation. The final fragment mass distribution is obtained by weighting the adiabatic density distribution in the collective space with the neck-dependent fission probability. The neck degree of freedom is found to play a significant role in determining the final fragment mass distribution. (orig.)
Dijkstra-Tiekstra, M. J.; van der Schoot, C. E.; Pietersz, R. N. I.; Reesink, H. W.
2005-01-01
BACKGROUND AND OBJECTIVES: White blood cell (WBC) fragments in platelet concentrates (PCs) may induce allo-immunization in the recipient. MATERIALS AND METHODS: As the level of WBC fragments can differ between PCs produced using different methods, we compared PCs prepared by using the buffy-coat
Experimental and numerical studies of high-velocity impact fragmentation
Energy Technology Data Exchange (ETDEWEB)
Kipp, M.E.; Grady, D.E.; Swegle, J.W.
1993-08-01
Developments are reported in both experimental and numerical capabilities for characterizing the debris spray produced in penetration events. We have performed a series of high-velocity experiments specifically designed to examine the fragmentation of the projectile during impact. High-strength, well-characterized steel spheres (6.35 mm diameter) were launched with a two-stage light-gas gun to velocities in the range of 3 to 5 km/s. Normal impact with PMMA plates, thicknesses of 0.6 to 11 mm, applied impulsive loads of various amplitudes and durations to the steel sphere. Multiple flash radiography diagnostics and recovery techniques were used to assess size, velocity, trajectory and statistics of the impact-induced fragment debris. Damage modes to the primary target plate (plastic) and to a secondary target plate (aluminum) were also evaluated. Dynamic fragmentation theories, based on energy-balance principles, were used to evaluate local material deformation and fracture state information from CTH, a three-dimensional Eulerian solid dynamics shock wave propagation code. The local fragment characterization of the material defines a weighted fragment size distribution, and the sum of these distributions provides a composite particle size distribution for the steel sphere. The calculated axial and radial velocity changes agree well with experimental data, and the calculated fragment sizes are in qualitative agreement with the radiographic data. A secondary effort involved the experimental and computational analyses of normal and oblique copper ball impacts on steel target plates. High-resolution radiography and witness plate diagnostics provided impact motion and statistical fragment size data. CTH simulations were performed to test computational models and numerical methods.
Hyperion polarization and transverse momentum properties in proton fragmentation
International Nuclear Information System (INIS)
Andersson, B.; Gustafson, G.; Maansson, O.
1982-11-01
A dynamical mechanism for proton interaction in hadronic collisions is presented which provides a verification of the model with an essentially one-dimensional colour force field in the proton fragmentation region, proposed earlier. We include here a discussion of the transverse momentum properties of the final state particles and polarization properties for hyperions in proton fragmentation. (Author)
Three-dimensional display techniques: description and critique of methods
International Nuclear Information System (INIS)
Budinger, T.F.
1982-01-01
The recent advances in non invasive medical imaging of 3 dimensional spatial distribution of radionuclides, X-ray attenuation coefficients, and nuclear magnetic resonance parameters necessitate development of a general method for displaying these data. The objective of this paper is to give a systematic description and comparison of known methods for displaying three dimensional data. The discussion of display methods is divided into two major categories: 1) computer-graphics methods which use a two dimensional display screen; and 2) optical methods (such as holography, stereopsis and vari-focal systems)
Two-dimensional nuclear magnetic resonance spectroscopy
International Nuclear Information System (INIS)
Bax, A.; Lerner, L.
1986-01-01
Great spectral simplification can be obtained by spreading the conventional one-dimensional nuclear magnetic resonance (NMR) spectrum in two independent frequency dimensions. This so-called two-dimensional NMR spectroscopy removes spectral overlap, facilitates spectral assignment, and provides a wealth of additional information. For example, conformational information related to interproton distances is available from resonance intensities in certain types of two-dimensional experiments. Another method generates 1 H NMR spectra of a preselected fragment of the molecule, suppressing resonances from other regions and greatly simplifying spectral appearance. Two-dimensional NMR spectroscopy can also be applied to the study of 13 C and 15 N, not only providing valuable connectivity information but also improving sensitivity of 13 C and 15 N detection by up to two orders of magnitude. 45 references, 10 figures
Vanthomme, Hadrien; Kolowski, Joseph; Nzamba, Brave S; Alonso, Alfonso
2015-10-01
The active field of connectivity conservation has provided numerous methods to identify wildlife corridors with the aim of reducing the ecological effect of fragmentation. Nevertheless, these methods often rely on untested hypotheses of animal movements, usually fail to generate fine-scale predictions of road crossing sites, and do not allow managers to prioritize crossing sites for implementing road fragmentation mitigation measures. We propose a new method that addresses these limitations. We illustrate this method with data from southwestern Gabon (central Africa). We used stratified random transect surveys conducted in two seasons to model the distribution of African forest elephant (Loxodonta cyclotis), forest buffalo (Syncerus caffer nanus), and sitatunga (Tragelaphus spekii) in a mosaic landscape along a 38.5 km unpaved road scheduled for paving. Using a validation data set of recorded crossing locations, we evaluated the performance of three types of models (local suitability, local least-cost movement, and regional least-cost movement) in predicting actual road crossings for each species, and developed a unique and flexible scoring method for prioritizing road sections for the implementation of road fragmentation mitigation measures. With a data set collected in method was able to identify seasonal changes in animal movements for buffalo and sitatunga that shift from a local exploitation of the site in the wet season to movements through the study site in the dry season, whereas elephants use the entire study area in both seasons. These three species highlighted the need to use species- and season-specific modeling of movement. From these movement models, the method ranked road sections for their suitability for implementing fragmentation mitigation efforts, allowing managers to adjust priority thresholds based on budgets and management goals. The method relies on data that can be obtained in a period compatible with environmental impact assessment
Utility of three-dimensional method for diagnosing meniscal lesions
International Nuclear Information System (INIS)
Ohshima, Suguru; Nomura, Kazutoshi; Hirano, Mako; Hashimoto, Noburo; Fukumoto, Tetsuya; Katahira, Kazuhiro
1998-01-01
MRI of the knee is a useful method for diagnosing meniscal tears. Although the spin echo method is usually used for diagnosing meniscal tears, we examined the utility of thin slice scan with the three-dimensional method. We reviewed 70 menisci in which arthroscopic findings were confirmed. In this series, sensitivity was 90.9% for medial meniscal injuries and 68.8% for lateral meniscal injuries. There were 3 meniscal tears in which we could not detect tears on preoperative MRI. We could find tears in two of these cases when re-evaluated using the same MRI. In conclusion, we can get the same diagnostic rate with the three-dimensional method compared with the spin echo method. Scan time of the three-dimensional method is 3 minutes, on the other hand that of spin echo method in 17 minutes. This slice scan with three-dimensional method is useful for screening meniscal injuries before arthroscopy. (author)
A sparse grid based method for generative dimensionality reduction of high-dimensional data
Bohn, Bastian; Garcke, Jochen; Griebel, Michael
2016-03-01
Generative dimensionality reduction methods play an important role in machine learning applications because they construct an explicit mapping from a low-dimensional space to the high-dimensional data space. We discuss a general framework to describe generative dimensionality reduction methods, where the main focus lies on a regularized principal manifold learning variant. Since most generative dimensionality reduction algorithms exploit the representer theorem for reproducing kernel Hilbert spaces, their computational costs grow at least quadratically in the number n of data. Instead, we introduce a grid-based discretization approach which automatically scales just linearly in n. To circumvent the curse of dimensionality of full tensor product grids, we use the concept of sparse grids. Furthermore, in real-world applications, some embedding directions are usually more important than others and it is reasonable to refine the underlying discretization space only in these directions. To this end, we employ a dimension-adaptive algorithm which is based on the ANOVA (analysis of variance) decomposition of a function. In particular, the reconstruction error is used to measure the quality of an embedding. As an application, the study of large simulation data from an engineering application in the automotive industry (car crash simulation) is performed.
Nonlinear transient responses of beams and rings to impulse loading or fragment impact
International Nuclear Information System (INIS)
Witmer, E.A.; Stagliano, T.R.; Rodal, J.J.A.
1977-01-01
Nuclear power plant protective structures may be subjected to various external missiles such as aircraft and tornado-generated missiles: telephone poles, planks, pipes, rods, automobiles, and other blown vehicles. Also, 'internally-generated missiles' such as fragments from powerplant rotors and aircraft engine rotors may impact protective structures. The present paper is concerned with a very limited part of the cited fragment threat; namely, fragments from high speed rotating machinery such as (1) aircraft engine rotors and (2) stationary power plant turbine rotors. Further, it is assumed that the structures intended to contain or control these fragments consist of initially-isotopic elastic-plastic metals. Certain potential containment/control (C/C) structures behave in a planar (or two-dimensional) fashion while other fragment-attacked C/C structures will undergo general three-dimensional deformations. Predictions for only the former category of fragment-attacked structures are discussed in the present paper. Pertinent experimental data discussed on fragment-attacked structures include (a) steel-sphere impact data involving beam targets and (b) engine rotor fragment impact against a steel containment ring. In all of these cases large-deflection, elastic-plastic transient structural responses occur. (Auth.)
Method of dimensionality reduction in contact mechanics and friction
Popov, Valentin L
2015-01-01
This book describes for the first time a simulation method for the fast calculation of contact properties and friction between rough surfaces in a complete form. In contrast to existing simulation methods, the method of dimensionality reduction (MDR) is based on the exact mapping of various types of three-dimensional contact problems onto contacts of one-dimensional foundations. Within the confines of MDR, not only are three dimensional systems reduced to one-dimensional, but also the resulting degrees of freedom are independent from another. Therefore, MDR results in an enormous reduction of the development time for the numerical implementation of contact problems as well as the direct computation time and can ultimately assume a similar role in tribology as FEM has in structure mechanics or CFD methods, in hydrodynamics. Furthermore, it substantially simplifies analytical calculation and presents a sort of “pocket book edition” of the entirety contact mechanics. Measurements of the rheology of bodies in...
On the fragmentation of filaments in a molecular cloud simulation
Chira, R.-A.; Kainulainen, J.; Ibáñez-Mejía, J. C.; Henning, Th.; Mac Low, M.-M.
2018-03-01
Context. The fragmentation of filaments in molecular clouds has attracted a lot of attention recently as there seems to be a close relation between the evolution of filaments and star formation. The study of the fragmentation process has been motivated by simple analytical models. However, only a few comprehensive studies have analysed the evolution of filaments using numerical simulations where the filaments form self-consistently as part of large-scale molecular cloud evolution. Aim. We address the early evolution of parsec-scale filaments that form within individual clouds. In particular, we focus on three questions: How do the line masses of filaments evolve? How and when do the filaments fragment? How does the fragmentation relate to the line masses of the filaments? Methods: We examine three simulated molecular clouds formed in kiloparsec-scale numerical simulations performed with the FLASH adaptive mesh refinement magnetohydrodynamic code. The simulations model a self-gravitating, magnetised, stratified, supernova-driven interstellar medium, including photoelectric heating and radiative cooling. We follow the evolution of the clouds for 6 Myr from the time self-gravity starts to act. We identify filaments using the DisPerSe algorithm, and compare the results to other filament-finding algorithms. We determine the properties of the identified filaments and compare them with the predictions of analytic filament stability models. Results: The average line masses of the identified filaments, as well as the fraction of mass in filamentary structures, increases fairly continuously after the onset of self-gravity. The filaments show fragmentation starting relatively early: the first fragments appear when the line masses lie well below the critical line mass of Ostriker's isolated hydrostatic equilibrium solution ( 16 M⊙ pc-1), commonly used as a fragmentation criterion. The average line masses of filaments identified in three-dimensional volume density cubes
On the effect of grain burnback on STS-SRM fragment velocity
International Nuclear Information System (INIS)
Eck, M.B.; Mukunda, M.
1991-01-01
Concerns raised during the Ulysses Final Safety Analysis Review (FSAR) process called the solid rocket motor (SRM) fragment velocity prediction model into question. The specific area of concern was that there was a section of the SRM casing which was exposed to SRM chamber pressure as the grain (fuel) was consumed. These questions centered on the velocity of fragments which originated from the field joint region given that failure occurred between 37 and 72 seconds mission elapsed time (MET). Two dimensional coupled Eulerian-Lagrangian calculations were performed to assess the hot gas flow field which resulted from SRM casing fragmentation. The fragment to gas interface-pressure time-history obtained from these analyses was reduced to a boundary condition algorithm which was applied to an explicit-time-integration, finite element, three dimensional shell model of the SRM casing and unburned fuel. The results of these calculations showed that the velocity of fragments originating in the field joint was adequately described by the range of velocities given in the Shuttle Data Book (1988). Based on these results, no further analyses were required, and approval was obtained from the Launch Abort Subpanel of the Interagency Nuclear Safety Review Panel to use the SRM fragment velocity environments presented in the Ulysses FSAR (1990)
Verlinde, Christophe L. M. J.; Rudenko, Gabrielle; Hol, Wim G. J.
1992-04-01
A modular method for pursuing structure-based inhibitor design in the framework of a design cycle is presented. The approach entails four stages: (1) a design pathway is defined in the three-dimensional structure of a target protein; (2) this pathway is divided into subregions; (3) complementary building blocks, also called fragments, are designed in each subregion; complementarity is defined in terms of shape, hydrophobicity, hydrogen bond properties and electrostatics; and (4) fragments from different subregions are linked into potential lead compounds. Stages (3) and (4) are qualitatively guided by force-field calculations. In addition, the designed fragments serve as entries for retrieving existing compounds from chemical databases. This linked-fragment approach has been applied in the design of potentially selective inhibitors of triosephosphate isomerase from Trypanosoma brucei, the causative agent of sleeping sickness.
Dimensionality Reduction Methods: Comparative Analysis of methods PCA, PPCA and KPCA
Directory of Open Access Journals (Sweden)
Jorge Arroyo-Hernández
2016-01-01
Full Text Available The dimensionality reduction methods are algorithms mapping the set of data in subspaces derived from the original space, of fewer dimensions, that allow a description of the data at a lower cost. Due to their importance, they are widely used in processes associated with learning machine. This article presents a comparative analysis of PCA, PPCA and KPCA dimensionality reduction methods. A reconstruction experiment of worm-shape data was performed through structures of landmarks located in the body contour, with methods having different number of main components. The results showed that all methods can be seen as alternative processes. Nevertheless, thanks to the potential for analysis in the features space and the method for calculation of its preimage presented, KPCA offers a better method for recognition process and pattern extraction
Fragment-based drug discovery and protein–protein interactions
Directory of Open Access Journals (Sweden)
Turnbull AP
2014-09-01
Full Text Available Andrew P Turnbull,1 Susan M Boyd,2 Björn Walse31CRT Discovery Laboratories, Department of Biological Sciences, Birkbeck, University of London, London, UK; 2IOTA Pharmaceuticals Ltd, Cambridge, UK; 3SARomics Biostructures AB, Lund, SwedenAbstract: Protein–protein interactions (PPIs are involved in many biological processes, with an estimated 400,000 PPIs within the human proteome. There is significant interest in exploiting the relatively unexplored potential of these interactions in drug discovery, driven by the need to find new therapeutic targets. Compared with classical drug discovery against targets with well-defined binding sites, developing small-molecule inhibitors against PPIs where the contact surfaces are frequently more extensive and comparatively flat, with most of the binding energy localized in “hot spots”, has proven far more challenging. However, despite the difficulties associated with targeting PPIs, important progress has been made in recent years with fragment-based drug discovery playing a pivotal role in improving their tractability. Computational and empirical approaches can be used to identify hot-spot regions and assess the druggability and ligandability of new targets, whilst fragment screening campaigns can detect low-affinity fragments that either directly or indirectly perturb the PPI. Once fragment hits have been identified and confirmed using biochemical and biophysical approaches, three-dimensional structural data derived from nuclear magnetic resonance or X-ray crystallography can be used to drive medicinal chemistry efforts towards the development of more potent inhibitors. A small-scale comparison presented in this review of “standard” fragments with those targeting PPIs has revealed that the latter tend to be larger, be more lipophilic, and contain more polar (acid/base functionality, whereas three-dimensional descriptor data indicate that there is little difference in their three-dimensional
Rotating bubble and toroidal nuclei and fragmentation
International Nuclear Information System (INIS)
Royer, G.; Haddad, F.; Jouault, B.
1995-01-01
The energy of rotating bubble and toroidal nuclei predicted to be formed in central heavy-ion collisions at intermediate energies is calculated within the generalized rotating liquid drop model. The potential barriers standing in these exotic deformation paths are compared with the three dimensional and plane fragmentation barriers. In the toroidal deformation path of the heaviest systems exists a large potential pocket localised below the plane fragmentation barriers. This might allow the temporary survival of heavy nuclear toroids before the final clusterization induced by the surface and proximity tension. (author)
DEFF Research Database (Denmark)
Duan, Zhi; Siegumfeldt, Henrik
2010-01-01
We generated monoclonal scFv (single chain variable fragment) antibodies from an antibody phage display library towards three small synthetic peptides derived from the sequence of s1-casein. Key difficulties for selection of scFv-phages against small peptides were addressed. Small peptides do....... The scFvs were sequenced and characterized, and specificity was characterized by ELISA. The methods developed in this study are universally applicable for antibody phage display to efficiently produce antibody fragments against small peptides....
Computational methods for three-dimensional microscopy reconstruction
Frank, Joachim
2014-01-01
Approaches to the recovery of three-dimensional information on a biological object, which are often formulated or implemented initially in an intuitive way, are concisely described here based on physical models of the object and the image-formation process. Both three-dimensional electron microscopy and X-ray tomography can be captured in the same mathematical framework, leading to closely-related computational approaches, but the methodologies differ in detail and hence pose different challenges. The editors of this volume, Gabor T. Herman and Joachim Frank, are experts in the respective methodologies and present research at the forefront of biological imaging and structural biology. Computational Methods for Three-Dimensional Microscopy Reconstruction will serve as a useful resource for scholars interested in the development of computational methods for structural biology and cell biology, particularly in the area of 3D imaging and modeling.
DIAGNOSTIC CHARACTERISTICS OF THE COMPUTER TESTS FORMED BY METHOD OF RESTORED FRAGMENTS
Directory of Open Access Journals (Sweden)
Oleksandr O. Petkov
2013-03-01
Full Text Available Definition of validity and reliability of tests which are formed by a method of restored fragments is considered in the article. The structure of the controlled theoretical material of limit field of knowledge, language expressions that describe the subject of control, and reliability of test, is analyzed. The technique of definition of the most important components of reliability of the considered tests is given: reliability of quantitative determination of coefficient of assimilation and technological reliability. Results of the lead pedagogical experiments have proved, that tests of the given class allow to make the control of mastering of a theoretical material over a level of reproduction in any field of knowledge with high reliability. It is shown, that validity tests with restored fragments basically caused by a degree of structurization and methodical study of a controllable material and can achieve beforehand set parameters, down to a level of absolute validity.
Nonlinear transient responses of beams and rings to impulse loading or fragment impact
International Nuclear Information System (INIS)
Witmer, E.A.; Stagliano, T.R.; Rodal, J.J.A.
1977-01-01
The present paper is concerned with a very limited part of the cited fragment threat; namely, fragments from high speed rotating machinery such as (1) aircraft engine rotors and (2) stationary power plant turbine rotors. Further, it is assumed that the structures intended to contain or control these fragments consist of initially-isotropic elastic-plastic metals. Certain potential containment/control (C/C) structures behave in a planar (or two-dimensional) fashion while other fragment-attacked C/C structures will undergo general three-dimensional deformations. Predictions for only the former category of fragment-attacked structures are discussed in the present paper. Pertinent experimental data discussed here on fragment-attacked structures include (a) steel-sphere impact data involving beam targets and (b) engine rotor fragment impact against a steel containment ring. In all of these cases large-deflection, elastic-plastic transient structural response occur. The governing equations employed are presented in the present analysis to predict the responses of protective (metal) structures to engine-rotor-fragment impact. The protective structure is intended either to contain or to deflect the attacking fragments away from important regions; large-deflection, elasic-plastic structural response is expected because these protective structures must have the least feasible weight. Concise geometric and assumed-displacement-field descriptions of the several types of finite elements to be utilized in subsequent examples are given, together with several categories of strain displacement relations. Both low- and higher-order elements are discussed
TSOM Method for Nanoelectronics Dimensional Metrology
International Nuclear Information System (INIS)
Attota, Ravikiran
2011-01-01
Through-focus scanning optical microscopy (TSOM) is a relatively new method that transforms conventional optical microscopes into truly three-dimensional metrology tools for nanoscale to microscale dimensional analysis. TSOM achieves this by acquiring and analyzing a set of optical images collected at various focus positions going through focus (from above-focus to under-focus). The measurement resolution is comparable to what is possible with typical light scatterometry, scanning electron microscopy (SEM) and atomic force microscopy (AFM). TSOM method is able to identify nanometer scale difference, type of the difference and magnitude of the difference between two nano/micro scale targets using a conventional optical microscope with visible wavelength illumination. Numerous industries could benefit from the TSOM method--such as the semiconductor industry, MEMS, NEMS, biotechnology, nanomanufacturing, data storage, and photonics. The method is relatively simple and inexpensive, has a high throughput, provides nanoscale sensitivity for 3D measurements and could enable significant savings and yield improvements in nanometrology and nanomanufacturing. Potential applications are demonstrated using experiments and simulations.
Rysavy, Steven J; Beck, David AC; Daggett, Valerie
2014-01-01
Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼25–75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments. PMID:25142412
Rysavy, Steven J; Beck, David A C; Daggett, Valerie
2014-11-01
Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼ 25-75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments. © 2014 The Protein Society.
Poltev, V I; Anisimov, V M; Sanchez, C; Deriabina, A; Gonzalez, E; Garcia, D; Rivas, F; Polteva, N A
2016-01-01
It is generally accepted that the important characteristic features of the Watson-Crick duplex originate from the molecular structure of its subunits. However, it still remains to elucidate what properties of each subunit are responsible for the significant characteristic features of the DNA structure. The computations of desoxydinucleoside monophosphates complexes with Na-ions using density functional theory revealed a pivotal role of DNA conformational properties of single-chain minimal fragments in the development of unique features of the Watson-Crick duplex. We found that directionality of the sugar-phosphate backbone and the preferable ranges of its torsion angles, combined with the difference between purines and pyrimidines. in ring bases, define the dependence of three-dimensional structure of the Watson-Crick duplex on nucleotide base sequence. In this work, we extended these density functional theory computations to the minimal' fragments of DNA duplex, complementary desoxydinucleoside monophosphates complexes with Na-ions. Using several computational methods and various functionals, we performed a search for energy minima of BI-conformation for complementary desoxydinucleoside monophosphates complexes with different nucleoside sequences. Two sequences are optimized using ab initio method at the MP2/6-31++G** level of theory. The analysis of torsion angles, sugar ring puckering and mutual base positions of optimized structures demonstrates that the conformational characteristic features of complementary desoxydinucleoside monophosphates complexes with Na-ions remain within BI ranges and become closer to the corresponding characteristic features of the Watson-Crick duplex crystals. Qualitatively, the main characteristic features of each studied complementary desoxydinucleoside monophosphates complex remain invariant when different computational methods are used, although the quantitative values of some conformational parameters could vary lying within the
International Nuclear Information System (INIS)
Arnold, Werner
2002-01-01
Contrary to natural fragmentation, controlled fragmentation offers the possibility to adapt fragment parameters like size and mass to the performance requirements in a very flexible way. Known mechanisms like grooves inside the casing, weaken the structure. This is, however, excluded for applications with high accelerations during launch or piercing requirements for example on a semi armor piercing penetrator. Another method to achieve controlled fragmentation with an additional grid layer is presented with which the required grooves are produced 'just in time' inside the casing during detonation of the high explosive. The process of generating the grooves aided by the grid layer was studied using the hydrocode HULL with respect to varying grid designs and material combinations. Subsequent to this, a large range of these theoretically investigated combinations was contemplated in substantial experimental tests. With an optimised grid design and a suitable material selection, the controlled fragment admits a very flexible adaptation to the set requirements. Additional advantages like the increase of perforation performance or incendiary amplification can be realized with the grid layer
Directory of Open Access Journals (Sweden)
S. C. Oukouomi Noutchie
2014-01-01
Full Text Available We make use of Laplace transform techniques and the method of characteristics to solve fragmentation equations explicitly. Our result is a breakthrough in the analysis of pure fragmentation equations as this is the first instance where an exact solution is provided for the fragmentation evolution equation with general fragmentation rates. This paper is the key for resolving most of the open problems in fragmentation theory including “shattering” and the sudden appearance of infinitely many particles in some systems with initial finite particles number.
Energy Technology Data Exchange (ETDEWEB)
Myagkov, N. N., E-mail: nn-myagkov@mail.ru [Russian Academy of Sciences, Institute of Applied Mechanics (Russian Federation)
2017-01-15
The problem of aluminum projectile fragmentation upon high-velocity impact on a thin aluminum shield is considered. A distinctive feature of this description is that the fragmentation has been numerically simulated using the complete system of equations of deformed solid mechanics by a method of smoothed particle hydrodynamics in three-dimensional setting. The transition from damage to fragmentation is analyzed and scaling relations are derived in terms of the impact velocity (V), ratio of shield thickness to projectile diameter (h/D), and ultimate strength (σ{sub p}) in the criterion of projectile and shield fracture. Analysis shows that the critical impact velocity V{sub c} (separating the damage and fragmentation regions) is a power function of σ{sub p} and h/D. In the supercritical region (V > V{sub c}), the weight-average fragment mass asymptotically tends to a power function of the impact velocity with exponent independent of h/D and σ{sub p}. Mean cumulative fragment mass distributions at the critical point are scale-invariant with respect to parameters h/D and σ{sub p}. Average masses of the largest fragments are also scale-invariant at V > V{sub c}, but only with respect to variable parameter σ{sub p}.
Fujita, Takatoshi; Mochizuki, Yuji
2018-04-19
We developed the fragment-based method for calculating nonlocal excitations in large molecular systems. This method is based on the multilayer fragment molecular orbital method and the configuration interaction single (CIS) wave function using localized molecular orbitals. The excited-state wave function for the whole system is described as a superposition of configuration state functions (CSFs) for intrafragment excitations and for interfragment charge-transfer excitations. The formulation and calculations of singlet excited-state Hamiltonian matrix elements in the fragment CSFs are presented in detail. The efficient approximation schemes for calculating the matrix elements are also presented. The computational efficiency and the accuracy were evaluated using the molecular dimers and molecular aggregates. We confirmed that absolute errors of 50 meV (relative to the conventional calculations) are achievable for the molecular systems in their equilibrium geometries. The perturbative electron correlation correction to the CIS excitation energies is also demonstrated. The present theory can compute a large number of excited states in large molecular systems; in addition, it allows for the systematic derivation of a model exciton Hamiltonian. These features are useful for studying excited-state dynamics in condensed molecular systems based on the ab initio electronic structure theory.
Impact failure and fragmentation properties of metals
Energy Technology Data Exchange (ETDEWEB)
Grady, D.E. [Applied Research Associates, Albuquerque, NM (United States); Kipp, M.E. [Sandia National Labs., Albuquerque, NM (United States)
1998-03-01
In the present study we describe the development of an experimental fracture material property test method specific to dynamic fragmentation. Spherical test samples of the metals of interest are subjected to controlled impulsive stress loads by acceleration to high velocities with a light-gas launcher facility and subsequent normal impact on thin plates. Motion, deformation and fragmentation of the test samples are diagnosed with multiple flash radiography methods. The impact plate materials are selected to be transparent to the x-ray method so that only test metal material is imaged. Through a systematic series of such tests both strain-to-failure and fragmentation resistance properties are determined through this experimental method. Fragmentation property data for several steels, copper, aluminum, tantalum and titanium have been obtained to date. Aspects of the dynamic data have been analyzed with computational methods to achieve a better understanding of the processes leading to failure and fragmentation, and to test an existing computational fragmentation model.
A feasibility study of the use of DNA fragmentation as a method for detecting irradiation of food
International Nuclear Information System (INIS)
Jones, J.L.; Bulford, B.B.
1990-07-01
The main conclusions of the study are: 1. Gamma-irradiation at doses of 1-10 kGy, as recommended for use in food irradiation, causes extensive fragmentation of DNA molecules. The degree of fragmentation increases with increasing doses of irradiation treatment. 2. Irradiation-induced DNA fragments can be rapidly separated from intact DNA using a simple ultra-filtration method. 3. The separated DNA fragments can be detected/quantified rapidly using the simple Invitrogen DNA DipStick procedure. Dot-blot assays based on probes to widely conserved genes (e.g. histone genes) may also prove of value, but will require further development. 4. As DNA is present in a wide range of foods, DNA fragmentation offers a potentially useful marker for the irradiation treatment of foods. The assay now requires assessment with DNA extracts of a variety of foods. (author)
Ternary-fragmentation-driving potential energies of 252Cf
Karthikraj, C.; Ren, Zhongzhou
2017-12-01
Within the framework of a simple macroscopic model, the ternary-fragmentation-driving potential energies of 252Cf are studied. In this work, all possible ternary-fragment combinations of 252Cf are generated by the use of atomic mass evaluation-2016 (AME2016) data and these combinations are minimized by using a two-dimensional minimization approach. This minimization process can be done in two ways: (i) with respect to proton numbers (Z1, Z2, Z3) and (ii) with respect to neutron numbers (N1, N2, N3) of the ternary fragments. In this paper, the driving potential energies for the ternary breakup of 252Cf are presented for both the spherical and deformed as well as the proton-minimized and neutron-minimized ternary fragments. From the proton-minimized spherical ternary fragments, we have obtained different possible ternary configurations with a minimum driving potential, in particular, the experimental expectation of Sn + Ni + Ca ternary fragmentation. However, the neutron-minimized ternary fragments exhibit a driving potential minimum in the true-ternary-fission (TTF) region as well. Further, the Q -value energy systematics of the neutron-minimized ternary fragments show larger values for the TTF fragments. From this, we have concluded that the TTF region fragments with the least driving potential and high Q values have a strong possibility in the ternary fragmentation of 252Cf. Further, the role of ground-state deformations (β2, β3, β4, and β6) in the ternary breakup of 252Cf is also studied. The deformed ternary fragmentation, which involves Z3=12 -19 fragments, possesses the driving potential minimum due to the larger oblate deformations. We also found that the ground-state deformations, particularly β2, strongly influence the driving potential energies and play a major role in determining the most probable fragment combinations in the ternary breakup of 252Cf.
Lessons from hot spot analysis for fragment-based drug discovery
Hall, David R.; Vajda, Sandor
2015-01-01
Analysis of binding energy hot spots at protein surfaces can provide crucial insights into the prospects for successful application of fragment-based drug discovery (FBDD), and whether a fragment hit can be advanced into a high affinity, druglike ligand. The key factor is the strength of the top ranking hot spot, and how well a given fragment complements it. We show that published data are sufficient to provide a sophisticated and quantitative understanding of how hot spots derive from protein three-dimensional structure, and how their strength, number and spatial arrangement govern the potential for a surface site to bind to fragment-sized and larger ligands. This improved understanding provides important guidance for the effective application of FBDD in drug discovery. PMID:26538314
Regnier, D.; Dubray, N.; Schunck, N.; Verrière, M.
2016-05-01
Background: Accurate knowledge of fission fragment yields is an essential ingredient of numerous applications ranging from the formation of elements in the r process to fuel cycle optimization for nuclear energy. The need for a predictive theory applicable where no data are available, together with the variety of potential applications, is an incentive to develop a fully microscopic approach to fission dynamics. Purpose: In this work, we calculate the pre-neutron emission charge and mass distributions of the fission fragments formed in the neutron-induced fission of 239Pu using a microscopic method based on nuclear density functional theory (DFT). Methods: Our theoretical framework is the nuclear energy density functional (EDF) method, where large-amplitude collective motion is treated adiabatically by using the time-dependent generator coordinate method (TDGCM) under the Gaussian overlap approximation (GOA). In practice, the TDGCM is implemented in two steps. First, a series of constrained EDF calculations map the configuration and potential-energy landscape of the fissioning system for a small set of collective variables (in this work, the axial quadrupole and octupole moments of the nucleus). Then, nuclear dynamics is modeled by propagating a collective wave packet on the potential-energy surface. Fission fragment distributions are extracted from the flux of the collective wave packet through the scission line. Results: We find that the main characteristics of the fission charge and mass distributions can be well reproduced by existing energy functionals even in two-dimensional collective spaces. Theory and experiment agree typically within two mass units for the position of the asymmetric peak. As expected, calculations are sensitive to the structure of the initial state and the prescription for the collective inertia. We emphasize that results are also sensitive to the continuity of the collective landscape near scission. Conclusions: Our analysis confirms
New method for solving three-dimensional Schroedinger equation
International Nuclear Information System (INIS)
Melezhik, V.S.
1990-01-01
The method derived recently for solving a multidimensional scattering problem is applied to a three-dimensional Schroedinger equation. As compared with direct three-dimensional calculations of finite elements and finite differences, this approach gives sufficiently accurate upper and lower approximations to the helium-atom binding energy, which demonstrates its efficiency. 15 refs.; 1 fig.; 2 tabs
Fragmentation of sperm DNA using the TUNEL method.
Chenlo, P H; Curi, S M; Pugliese, M N; Ariagno, J I; Sardi-Segovia, M; Furlan, M J; Repetto, H E; Zeitler, E; Cohen, M; Mendeluk, G R
2014-11-01
To establish the validity of the TUNEL assay in determining sperm DNA fragmentation, the relationship between the degree of fragmentation and the seminal parameters and the sample needed to conduct the test. We used semen samples from healthy fertile men (n=33), patients who consulted for infertility with a prescription for the TUNEL assay (n=77) and patients with intracytoplasmic sperm injection failure (n=20), analyzed according to the 2010 WHO. The TUNEL/propidium iodide test was performed by flow cytometry, on baseline and post-swim-up samples. The cutoff value for the TUNEL assay (ROC curves) was 26%, with a sensitivity and specificity of 85% and 89%, respectively. The pre-swim-up and post-swim-up medians of the results from the TUNEL assay showed no significant differences (17.0% vs. 12.9%, respectively). However, 39.1% of the samples showed a difference greater than 15 in absolute value between the results of the baseline and post-swim-up TUNEL assays. The linear correlation study of the morphology, mobility and vitality using the post-swim-up TUNEL assay showed a greater correlation than preselection, with significant results (r: -0.394, P<.0001; r: -0.461, P<.0001; r: -0.526, P<.0001). The TUNEL assay is a valid test for clinical use. DNA fragmentation is a factor independent from traditional semen tests. We found a greater susceptibility to damage generated in the laboratory procedures in the samples with lower quality. The sample of choice for evaluating DNA fragmentation will depend on whether the clinician is treating a natural or assisted fertilization. Copyright © 2014 AEU. Published by Elsevier Espana. All rights reserved.
Crystal structure of an Okazaki fragment at 2-A resolution
Egli, M.; Usman, N.; Zhang, S. G.; Rich, A.
1992-01-01
In DNA replication, Okazaki fragments are formed as double-stranded intermediates during synthesis of the lagging strand. They are composed of the growing DNA strand primed by RNA and the template strand. The DNA oligonucleotide d(GGGTATACGC) and the chimeric RNA-DNA oligonucleotide r(GCG)d(TATACCC) were combined to form a synthetic Okazaki fragment and its three-dimensional structure was determined by x-ray crystallography. The fragment adopts an overall A-type conformation with 11 residues per turn. Although the base-pair geometry, particularly in the central TATA part, is distorted, there is no evidence for a transition from the A- to the B-type conformation at the junction between RNA.DNA hybrid and DNA duplex. The RNA trimer may, therefore, lock the complete fragment in an A-type conformation.
A method of image improvement in three-dimensional imaging
International Nuclear Information System (INIS)
Suto, Yasuzo; Huang, Tewen; Furuhata, Kentaro; Uchino, Masafumi.
1988-01-01
In general, image interpolation is required when the surface configurations of such structures as bones and organs are three-dimensionally constructed from the multi-sliced images obtained by CT. Image interpolation is a processing method whereby an artificial image is inserted between two adjacent slices to make spatial resolution equal to slice resolution in appearance. Such image interpolation makes it possible to increase the image quality of the constructed three-dimensional image. In our newly-developed algorithm, we have converted the presently and subsequently sliced images to distance images, and generated the interpolation images from these two distance images. As a result, compared with the previous method, three-dimensional images with better image quality have been constructed. (author)
Automated building of organometallic complexes from 3D fragments.
Foscato, Marco; Venkatraman, Vishwesh; Occhipinti, Giovanni; Alsberg, Bjørn K; Jensen, Vidar R
2014-07-28
A method for the automated construction of three-dimensional (3D) molecular models of organometallic species in design studies is described. Molecular structure fragments derived from crystallographic structures and accurate molecular-level calculations are used as 3D building blocks in the construction of multiple molecular models of analogous compounds. The method allows for precise control of stereochemistry and geometrical features that may otherwise be very challenging, or even impossible, to achieve with commonly available generators of 3D chemical structures. The new method was tested in the construction of three sets of active or metastable organometallic species of catalytic reactions in the homogeneous phase. The performance of the method was compared with those of commonly available methods for automated generation of 3D models, demonstrating higher accuracy of the prepared 3D models in general, and, in particular, a much wider range with respect to the kind of chemical structures that can be built automatically, with capabilities far beyond standard organic and main-group chemistry.
Energy Technology Data Exchange (ETDEWEB)
Ichikawa, Y., E-mail: yuichikawa@phys.titech.ac.jp [Tokyo Institute of Technology, Department of Physics (Japan); Ueno, H. [RIKEN Nishina Center (Japan); Ishii, Y. [Tokyo Institute of Technology, Department of Physics (Japan); Furukawa, T. [Tokyo Metropolitan University, Department of Physics (Japan); Yoshimi, A. [Okayama University, Research Core for Extreme Quantum World (Japan); Kameda, D.; Watanabe, H.; Aoi, N. [RIKEN Nishina Center (Japan); Asahi, K. [Tokyo Institute of Technology, Department of Physics (Japan); Balabanski, D. L. [Bulgarian Academy of Sciences, Institute for Nuclear Research and Nuclear Energy (Bulgaria); Chevrier, R.; Daugas, J. M. [CEA, DAM, DIF (France); Fukuda, N. [RIKEN Nishina Center (Japan); Georgiev, G. [CSNSM, IN2P3-CNRS, Universite Paris-sud (France); Hayashi, H.; Iijima, H. [Tokyo Institute of Technology, Department of Physics (Japan); Inabe, N. [RIKEN Nishina Center (Japan); Inoue, T. [Tokyo Institute of Technology, Department of Physics (Japan); Ishihara, M.; Kubo, T. [RIKEN Nishina Center (Japan); and others
2013-05-15
A novel method to produce spin-aligned rare-isotope (RI) beam has been developed, that is the two-step projectile fragmentation method with a technique of dispersion matching. The present method was verified in an experiment at the RIKEN RIBF, where an RI beam of {sup 32}Al with spin alignment of 8(1) % was successfully produced from a primary beam of {sup 48}Ca, with {sup 33}Al as an intermediate nucleus. Figure of merit of the present method was found to be improved by a factor larger than 50 compared with a conventional method employing single-step projectile fragmentation.
Predicting "Hot" and "Warm" Spots for Fragment Binding.
Rathi, Prakash Chandra; Ludlow, R Frederick; Hall, Richard J; Murray, Christopher W; Mortenson, Paul N; Verdonk, Marcel L
2017-05-11
Computational fragment mapping methods aim to predict hotspots on protein surfaces where small fragments will bind. Such methods are popular for druggability assessment as well as structure-based design. However, to date researchers developing or using such tools have had no clear way of assessing the performance of these methods. Here, we introduce the first diverse, high quality validation set for computational fragment mapping. The set contains 52 diverse examples of fragment binding "hot" and "warm" spots from the Protein Data Bank (PDB). Additionally, we describe PLImap, a novel protocol for fragment mapping based on the Protein-Ligand Informatics force field (PLIff). We evaluate PLImap against the new fragment mapping test set, and compare its performance to that of simple shape-based algorithms and fragment docking using GOLD. PLImap is made publicly available from https://bitbucket.org/AstexUK/pli .
MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics.
The, Matthew; Käll, Lukas
2016-03-04
Shotgun proteomics experiments generate large amounts of fragment spectra as primary data, normally with high redundancy between and within experiments. Here, we have devised a clustering technique to identify fragment spectra stemming from the same species of peptide. This is a powerful alternative method to traditional search engines for analyzing spectra, specifically useful for larger scale mass spectrometry studies. As an aid in this process, we propose a distance calculation relying on the rarity of experimental fragment peaks, following the intuition that peaks shared by only a few spectra offer more evidence than peaks shared by a large number of spectra. We used this distance calculation and a complete-linkage scheme to cluster data from a recent large-scale mass spectrometry-based study. The clusterings produced by our method have up to 40% more identified peptides for their consensus spectra compared to those produced by the previous state-of-the-art method. We see that our method would advance the construction of spectral libraries as well as serve as a tool for mining large sets of fragment spectra. The source code and Ubuntu binary packages are available at https://github.com/statisticalbiotechnology/maracluster (under an Apache 2.0 license).
Tugnoli, Alessandro; Gubinelli, Gianfilippo; Landucci, Gabriele; Cozzani, Valerio
2014-08-30
The evaluation of the initial direction and velocity of the fragments generated in the fragmentation of a vessel due to internal pressure is an important information in the assessment of damage caused by fragments, in particular within the quantitative risk assessment (QRA) of chemical and process plants. In the present study an approach is proposed to the identification and validation of probability density functions (pdfs) for the initial direction of the fragments. A detailed review of a large number of past accidents provided the background information for the validation procedure. A specific method was developed for the validation of the proposed pdfs. Validated pdfs were obtained for both the vertical and horizontal angles of projection and for the initial velocity of the fragments. Copyright © 2014 Elsevier B.V. All rights reserved.
Mapping enzymatic catalysis using the effective fragment molecular orbital method
DEFF Research Database (Denmark)
Svendsen, Casper Steinmann; Fedorov, Dmitri G.; Jensen, Jan Halborg
2013-01-01
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path...... of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We...
A multi-dimensional sampling method for locating small scatterers
International Nuclear Information System (INIS)
Song, Rencheng; Zhong, Yu; Chen, Xudong
2012-01-01
A multiple signal classification (MUSIC)-like multi-dimensional sampling method (MDSM) is introduced to locate small three-dimensional scatterers using electromagnetic waves. The indicator is built with the most stable part of signal subspace of the multi-static response matrix on a set of combinatorial sampling nodes inside the domain of interest. It has two main advantages compared to the conventional MUSIC methods. First, the MDSM is more robust against noise. Second, it can work with a single incidence even for multi-scatterers. Numerical simulations are presented to show the good performance of the proposed method. (paper)
A DETERMINISTIC METHOD FOR TRANSIENT, THREE-DIMENSIONAL NUETRON TRANSPORT
International Nuclear Information System (INIS)
S. GOLUOGLU, C. BENTLEY, R. DEMEGLIO, M. DUNN, K. NORTON, R. PEVEY I.SUSLOV AND H.L. DODDS
1998-01-01
A deterministic method for solving the time-dependent, three-dimensional Boltzmam transport equation with explicit representation of delayed neutrons has been developed and evaluated. The methodology used in this study for the time variable of the neutron flux is known as the improved quasi-static (IQS) method. The position, energy, and angle-dependent neutron flux is computed deterministically by using the three-dimensional discrete ordinates code TORT. This paper briefly describes the methodology and selected results. The code developed at the University of Tennessee based on this methodology is called TDTORT. TDTORT can be used to model transients involving voided and/or strongly absorbing regions that require transport theory for accuracy. This code can also be used to model either small high-leakage systems, such as space reactors, or asymmetric control rod movements. TDTORT can model step, ramp, step followed by another step, and step followed by ramp type perturbations. It can also model columnwise rod movement can also be modeled. A special case of columnwise rod movement in a three-dimensional model of a boiling water reactor (BWR) with simple adiabatic feedback is also included. TDTORT is verified through several transient one-dimensional, two-dimensional, and three-dimensional benchmark problems. The results show that the transport methodology and corresponding code developed in this work have sufficient accuracy and speed for computing the dynamic behavior of complex multidimensional neutronic systems
Similarity measurement method of high-dimensional data based on normalized net lattice subspace
Institute of Scientific and Technical Information of China (English)
Li Wenfa; Wang Gongming; Li Ke; Huang Su
2017-01-01
The performance of conventional similarity measurement methods is affected seriously by the curse of dimensionality of high-dimensional data.The reason is that data difference between sparse and noisy dimensionalities occupies a large proportion of the similarity, leading to the dissimilarities between any results.A similarity measurement method of high-dimensional data based on normalized net lattice subspace is proposed.The data range of each dimension is divided into several intervals, and the components in different dimensions are mapped onto the corresponding interval.Only the component in the same or adjacent interval is used to calculate the similarity.To validate this meth-od, three data types are used, and seven common similarity measurement methods are compared. The experimental result indicates that the relative difference of the method is increasing with the di-mensionality and is approximately two or three orders of magnitude higher than the conventional method.In addition, the similarity range of this method in different dimensions is [0, 1], which is fit for similarity analysis after dimensionality reduction.
Composition and method for detecting cancer with technetium labeled antibody fragments
International Nuclear Information System (INIS)
Burchiel, S. W.; Crockford, D. R.; Rhodes, B. A.
1984-01-01
F(ab') 2 or Fab fragments of antibodies to: (a) human chorionic gonadotropin (hCG), hCG alpha subunit, hCG beta subunit, or an hCG-like material; or (b) other tumor specific or tumor associated molecules, to include carcinoembryonic antigen (CEA), alpha fetoprotein (AFP), human melanoma associated antigens, human sarcoma associated antigens or other antigens, are radiolabeled with technetium-99m (Tc-99m). When the F(ab') 2 or Fab fragments of antibody to such tumor associated antigens are injected intravenously into a patient, the radiolabeled composition accumulates at tumor sites. The accumulation of the cancer seeking radiopharmaceutical at tumor sites permits detection by external gamma scintigraphy. Thus, the composition is useful in the monitoring, localization and detection of cancer in the body. In an alternative composition, a double antibody approach to tumor localization using radiolabeled F(ab') 2 or Fab fragments is utilized. In this approach, a tumor specific antibody in the form of IgG, F(ab') 2 or Fab is first administered to a patient intravenously. Following a sufficient period of time, a second antibody in the form of F(ab') 2 or Fab is administered. The second antibody is radiolabeled with Tc-99m and has the property that it is reactive with the first antibody. This double antibody method has the advantage over a single antibody approach in that smaller tumors can be localized and detected and that the total amount of radioactive trace localized at the cancer site is increased
Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin.
Floris, Federico; Chiron, Lionel; Lynch, Alice M; Barrow, Mark P; Delsuc, Marc-André; O'Connor, Peter B
2018-06-04
Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about ~23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from ~23% to ~42%. Graphical Abstract Two-dimensional mass spectrometry, when applied to primary fragment ions from the source, allows deep-sequencing of the protein calmodulin.
The dimension split element-free Galerkin method for three-dimensional potential problems
Meng, Z. J.; Cheng, H.; Ma, L. D.; Cheng, Y. M.
2018-02-01
This paper presents the dimension split element-free Galerkin (DSEFG) method for three-dimensional potential problems, and the corresponding formulae are obtained. The main idea of the DSEFG method is that a three-dimensional potential problem can be transformed into a series of two-dimensional problems. For these two-dimensional problems, the improved moving least-squares (IMLS) approximation is applied to construct the shape function, which uses an orthogonal function system with a weight function as the basis functions. The Galerkin weak form is applied to obtain a discretized system equation, and the penalty method is employed to impose the essential boundary condition. The finite difference method is selected in the splitting direction. For the purposes of demonstration, some selected numerical examples are solved using the DSEFG method. The convergence study and error analysis of the DSEFG method are presented. The numerical examples show that the DSEFG method has greater computational precision and computational efficiency than the IEFG method.
A two-dimensional, semi-analytic expansion method for nodal calculations
International Nuclear Information System (INIS)
Palmtag, S.P.
1995-08-01
Most modern nodal methods used today are based upon the transverse integration procedure in which the multi-dimensional flux shape is integrated over the transverse directions in order to produce a set of coupled one-dimensional flux shapes. The one-dimensional flux shapes are then solved either analytically or by representing the flux shape by a finite polynomial expansion. While these methods have been verified for most light-water reactor applications, they have been found to have difficulty predicting the large thermal flux gradients near the interfaces of highly-enriched MOX fuel assemblies. A new method is presented here in which the neutron flux is represented by a non-seperable, two-dimensional, semi-analytic flux expansion. The main features of this method are (1) the leakage terms from the node are modeled explicitly and therefore, the transverse integration procedure is not used, (2) the corner point flux values for each node are directly edited from the solution method, and a corner-point interpolation is not needed in the flux reconstruction, (3) the thermal flux expansion contains hyperbolic terms representing analytic solutions to the thermal flux diffusion equation, and (4) the thermal flux expansion contains a thermal to fast flux ratio term which reduces the number of polynomial expansion functions needed to represent the thermal flux. This new nodal method has been incorporated into the computer code COLOR2G and has been used to solve a two-dimensional, two-group colorset problem containing uranium and highly-enriched MOX fuel assemblies. The results from this calculation are compared to the results found using a code based on the traditional transverse integration procedure
Kutchukian, Peter S; So, Sung-Sau; Fischer, Christian; Waller, Chris L
2015-01-01
Fragment based screening (FBS) has emerged as a mainstream lead discovery strategy in academia, biotechnology start-ups, and large pharma. As a prerequisite of FBS, a structurally diverse library of fragments is desirable in order to identify chemical matter that will interact with the range of diverse target classes that are prosecuted in contemporary screening campaigns. In addition, it is also desirable to offer synthetically amenable starting points to increase the probability of a successful fragment evolution through medicinal chemistry. Herein we describe a method to identify biologically relevant chemical substructures that are missing from an existing fragment library (chemical gaps), and organize these chemical gaps hierarchically so that medicinal chemists can efficiently navigate the prioritized chemical space and subsequently select purchasable fragments for inclusion in an enhanced fragment library.
Three-dimensional compound comparison methods and their application in drug discovery.
Shin, Woong-Hee; Zhu, Xiaolei; Bures, Mark Gregory; Kihara, Daisuke
2015-07-16
Virtual screening has been widely used in the drug discovery process. Ligand-based virtual screening (LBVS) methods compare a library of compounds with a known active ligand. Two notable advantages of LBVS methods are that they do not require structural information of a target receptor and that they are faster than structure-based methods. LBVS methods can be classified based on the complexity of ligand structure information utilized: one-dimensional (1D), two-dimensional (2D), and three-dimensional (3D). Unlike 1D and 2D methods, 3D methods can have enhanced performance since they treat the conformational flexibility of compounds. In this paper, a number of 3D methods will be reviewed. In addition, four representative 3D methods were benchmarked to understand their performance in virtual screening. Specifically, we tested overall performance in key aspects including the ability to find dissimilar active compounds, and computational speed.
Three-dimensional image signals: processing methods
Schiopu, Paul; Manea, Adrian; Craciun, Anca-Ileana; Craciun, Alexandru
2010-11-01
Over the years extensive studies have been carried out to apply coherent optics methods in real-time processing, communications and transmission image. This is especially true when a large amount of information needs to be processed, e.g., in high-resolution imaging. The recent progress in data-processing networks and communication systems has considerably increased the capacity of information exchange. We describe the results of literature investigation research of processing methods for the signals of the three-dimensional images. All commercially available 3D technologies today are based on stereoscopic viewing. 3D technology was once the exclusive domain of skilled computer-graphics developers with high-end machines and software. The images capture from the advanced 3D digital camera can be displayed onto screen of the 3D digital viewer with/ without special glasses. For this is needed considerable processing power and memory to create and render the complex mix of colors, textures, and virtual lighting and perspective necessary to make figures appear three-dimensional. Also, using a standard digital camera and a technique called phase-shift interferometry we can capture "digital holograms." These are holograms that can be stored on computer and transmitted over conventional networks. We present some research methods to process "digital holograms" for the Internet transmission and results.
A NEW METHOD FOR ESTIMATING THE 3D SIZE-DISTRIBUTIONCURVE OF FRAGMENTED ROCKS OUT OF 2D IMAGES
Directory of Open Access Journals (Sweden)
Souhaïl Outal
2011-05-01
Full Text Available Image analysis of rock fragmentation is used in mines and quarries to control the quality of blasting. Obtained information is the particle-size-distribution curve relating volume-proportions to the sizes of fragments. Calculation by image analysis of this particle-size-distribution is carried out in several steps, and each step has its inherent limitations. We will focus in this paper on one of themost crucial steps: reconstructing the volumes (3D. For the 3D-step, we have noticed that, due to the current acquisition method, there is no correlation between the average grey level of surfaces of the fragments and their third dimension. Consequently volumes (3D as well as the sizes (1D has to be calculated indirectly from the extracted projected areas of the visible fragments of images. For this purpose, we have built in laboratory a set of images of fragmented rocks resulting from blasting. Moreover, several tests based on comparisons between image analysis and screening measurements were carried out. A new stereological method, based on the comparison of the densities of probability (histograms of the samemeasurements (with very weak covering and overlappingwas elaborated. It allows us to estimate correctly, for a given type of rock, two intrinsic laws weighing the projected areas distribution in order to predict the volumic distribution.
Energy Technology Data Exchange (ETDEWEB)
Landon, Melissa R.; Lieberman, Raquel L.; Hoang, Quyen Q.; Ju, Shulin; Caaveiro, Jose M.M.; Orwig, Susan D.; Kozakov, Dima; Brenke, Ryan; Chuang, Gwo-Yu; Beglov, Dmitry; Vajda, Sandor; Petsko, Gregory A.; Ringe, Dagmar; (BU-M); (Brandeis); (GIT)
2010-08-04
The identification of hot spots, i.e., binding regions that contribute substantially to the free energy of ligand binding, is a critical step for structure-based drug design. Here we present the application of two fragment-based methods to the detection of hot spots for DJ-1 and glucocerebrosidase (GCase), targets for the development of therapeutics for Parkinson's and Gaucher's diseases, respectively. While the structures of these two proteins are known, binding information is lacking. In this study we employ the experimental multiple solvent crystal structures (MSCS) method and computational fragment mapping (FTMap) to identify regions suitable for the development of pharmacological chaperones for DJ-1 and GCase. Comparison of data derived via MSCS and FTMap also shows that FTMap, a computational method for the identification of fragment binding hot spots, is an accurate and robust alternative to the performance of expensive and difficult crystallographic experiments.
DIAGNOSTIC CHARACTERISTICS OF THE COMPUTER TESTS FORMED BY METHOD OF RESTORED FRAGMENTS
Oleksandr O. Petkov
2013-01-01
Definition of validity and reliability of tests which are formed by a method of restored fragments is considered in the article. The structure of the controlled theoretical material of limit field of knowledge, language expressions that describe the subject of control, and reliability of test, is analyzed. The technique of definition of the most important components of reliability of the considered tests is given: reliability of quantitative determination of coefficient of assimilation and te...
Three-Dimensional Compound Comparison Methods and Their Application in Drug Discovery
Directory of Open Access Journals (Sweden)
Woong-Hee Shin
2015-07-01
Full Text Available Virtual screening has been widely used in the drug discovery process. Ligand-based virtual screening (LBVS methods compare a library of compounds with a known active ligand. Two notable advantages of LBVS methods are that they do not require structural information of a target receptor and that they are faster than structure-based methods. LBVS methods can be classified based on the complexity of ligand structure information utilized: one-dimensional (1D, two-dimensional (2D, and three-dimensional (3D. Unlike 1D and 2D methods, 3D methods can have enhanced performance since they treat the conformational flexibility of compounds. In this paper, a number of 3D methods will be reviewed. In addition, four representative 3D methods were benchmarked to understand their performance in virtual screening. Specifically, we tested overall performance in key aspects including the ability to find dissimilar active compounds, and computational speed.
Fragment approaches in structure-based drug discovery
International Nuclear Information System (INIS)
Hubbard, Roderick E.
2008-01-01
Fragment-based methods are successfully generating novel and selective drug-like inhibitors of protein targets, with a number of groups reporting compounds entering clinical trials. This paper summarizes the key features of the approach as one of the tools in structure-guided drug discovery. There has been considerable interest recently in what is known as 'fragment-based lead discovery'. The novel feature of the approach is to begin with small low-affinity compounds. The main advantage is that a larger potential chemical diversity can be sampled with fewer compounds, which is particularly important for new target classes. The approach relies on careful design of the fragment library, a method that can detect binding of the fragment to the protein target, determination of the structure of the fragment bound to the target, and the conventional use of structural information to guide compound optimization. In this article the methods are reviewed, and experiences in fragment-based discovery of lead series of compounds against kinases such as PDK1 and ATPases such as Hsp90 are discussed. The examples illustrate some of the key benefits and issues of the approach and also provide anecdotal examples of the patterns seen in selectivity and the binding mode of fragments across different protein targets
Guo, Yang; Becker, Ute; Neese, Frank
2018-03-01
Local correlation theories have been developed in two main flavors: (1) "direct" local correlation methods apply local approximation to the canonical equations and (2) fragment based methods reconstruct the correlation energy from a series of smaller calculations on subsystems. The present work serves two purposes. First, we investigate the relative efficiencies of the two approaches using the domain-based local pair natural orbital (DLPNO) approach as the "direct" method and the cluster in molecule (CIM) approach as the fragment based approach. Both approaches are applied in conjunction with second-order many-body perturbation theory (MP2) as well as coupled-cluster theory with single-, double- and perturbative triple excitations [CCSD(T)]. Second, we have investigated the possible merits of combining the two approaches by performing CIM calculations with DLPNO methods serving as the method of choice for performing the subsystem calculations. Our cluster-in-molecule approach is closely related to but slightly deviates from approaches in the literature since we have avoided real space cutoffs. Moreover, the neglected distant pair correlations in the previous CIM approach are considered approximately. Six very large molecules (503-2380 atoms) were studied. At both MP2 and CCSD(T) levels of theory, the CIM and DLPNO methods show similar efficiency. However, DLPNO methods are more accurate for 3-dimensional systems. While we have found only little incentive for the combination of CIM with DLPNO-MP2, the situation is different for CIM-DLPNO-CCSD(T). This combination is attractive because (1) the better parallelization opportunities offered by CIM; (2) the methodology is less memory intensive than the genuine DLPNO-CCSD(T) method and, hence, allows for large calculations on more modest hardware; and (3) the methodology is applicable and efficient in the frequently met cases, where the largest subsystem calculation is too large for the canonical CCSD(T) method.
Fragmentation of suddenly heated liquids in ICF reactors. Revision 1
International Nuclear Information System (INIS)
Blink, J.A.; Hoover, W.G.
1985-01-01
Fragmentation of free liquids in Inertial Confinement Fusion reactors could determine the upper bound on reactor pulse rate because increased surface area will enhance the cooling and condensation of coolant ablated by the fusion x rays. Relaxation from the suddenly (neutron) heated state will move a liquid into the negative pressure region under the liquid-vapor P-V dome. The resulting expansion in a diverging geometry will hydrodynamically force the liquid to fragment, with vapor then forming from the new surfaces to fill the cavities. An energy minimization model is used to determine the fragment size that produces the least amount of non-fragment-center-of-mass energy; i.e., the sum of the surface and dilational kinetic energies. This model predicts fragmentation dependence on original system size and amount of isochoric heating as well as liquid density, Grueneisen parameter, surface tension, and sound speed. A two dimensional molecular dynamics code was developed to test the model at a microscopic scale for the Lennard-Jones fluid with its two adjustable constants chosen to represent lithium
Variational iteration method for one dimensional nonlinear thermoelasticity
International Nuclear Information System (INIS)
Sweilam, N.H.; Khader, M.M.
2007-01-01
This paper applies the variational iteration method to solve the Cauchy problem arising in one dimensional nonlinear thermoelasticity. The advantage of this method is to overcome the difficulty of calculation of Adomian's polynomials in the Adomian's decomposition method. The numerical results of this method are compared with the exact solution of an artificial model to show the efficiency of the method. The approximate solutions show that the variational iteration method is a powerful mathematical tool for solving nonlinear problems
Robust Object Tracking Using Valid Fragments Selection.
Zheng, Jin; Li, Bo; Tian, Peng; Luo, Gang
Local features are widely used in visual tracking to improve robustness in cases of partial occlusion, deformation and rotation. This paper proposes a local fragment-based object tracking algorithm. Unlike many existing fragment-based algorithms that allocate the weights to each fragment, this method firstly defines discrimination and uniqueness for local fragment, and builds an automatic pre-selection of useful fragments for tracking. Then, a Harris-SIFT filter is used to choose the current valid fragments, excluding occluded or highly deformed fragments. Based on those valid fragments, fragment-based color histogram provides a structured and effective description for the object. Finally, the object is tracked using a valid fragment template combining the displacement constraint and similarity of each valid fragment. The object template is updated by fusing feature similarity and valid fragments, which is scale-adaptive and robust to partial occlusion. The experimental results show that the proposed algorithm is accurate and robust in challenging scenarios.
Direct Linear Transformation Method for Three-Dimensional Cinematography
Shapiro, Robert
1978-01-01
The ability of Direct Linear Transformation Method for three-dimensional cinematography to locate points in space was shown to meet the accuracy requirements associated with research on human movement. (JD)
Equilibrium and non equilibrium in fragmentation
International Nuclear Information System (INIS)
Dorso, C.O.; Chernomoretz, A.; Lopez, J.A.
2001-01-01
Full text: In this communication we present recent results regarding the interplay of equilibrium and non equilibrium in the process of fragmentation of excited finite Lennard Jones drops. Because the general features of such a potential resemble the ones of the nuclear interaction (fact that is reinforced by the similarity between the EOS of both systems) these studies are not only relevant from a fundamental point of view but also shed light on the problem of nuclear multifragmentation. We focus on the microscopic analysis of the state of the fragmenting system at fragmentation time. We show that the Caloric Curve (i e. the functional relationship between the temperature of the system and the excitation energy) is of the type rise plateau with no vapor branch. The usual rise plateau rise pattern is only recovered when equilibrium is artificially imposed. This result puts a serious question on the validity of the freeze out hypothesis. This feature is independent of the dimensionality or excitation mechanism. Moreover we explore the behavior of magnitudes which can help us determine the degree of the assumed phase transition. It is found that no clear cut criteria is presently available. (Author)
Directory of Open Access Journals (Sweden)
Wasik Szymon
2010-05-01
Full Text Available Abstract Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA
Method and system for manipulating a digital representation of a three-dimensional object
DEFF Research Database (Denmark)
2010-01-01
A method of manipulating a three-dimensional virtual building block model by means of two-dimensional cursor movements, the virtual building block model including a plurality of virtual building blocks each including a number of connection elements for connecting the virtual building block...... with another virtual building block according to a set of connection rules, the method comprising positioning by means of cursor movements in a computer display area representing a two-dimensional projection of said model, a two-dimensional projection of a first virtual building block to be connected...... to the structure, resulting in a two-dimensional position; determining, from the two-dimensional position, a number of three-dimensional candidate positions of the first virtual building block in the three-dimensional coordinate system; selecting one of said candidate positions based on the connection rules...
International Nuclear Information System (INIS)
Chen, G.S.; Christenson, J.M.
1985-01-01
In this paper, the authors present some initial results from an investigation of the application of a locally one-dimensional (LOD) finite difference method to the solution of the two-dimensional, two-group reactor kinetics equations. Although the LOD method is relatively well known, it apparently has not been previously applied to the space-time kinetics equations. In this investigation, the LOD results were benchmarked against similar computational results (using the same computing environment, the same programming structure, and the same sample problems) obtained by the TWIGL program. For all of the problems considered, the LOD method provided accurate results in one-half to one-eight of the time required by the TWIGL program
The rise of fragment-based drug discovery.
Murray, Christopher W; Rees, David C
2009-06-01
The search for new drugs is plagued by high attrition rates at all stages in research and development. Chemists have an opportunity to tackle this problem because attrition can be traced back, in part, to the quality of the chemical leads. Fragment-based drug discovery (FBDD) is a new approach, increasingly used in the pharmaceutical industry, for reducing attrition and providing leads for previously intractable biological targets. FBDD identifies low-molecular-weight ligands (∼150 Da) that bind to biologically important macromolecules. The three-dimensional experimental binding mode of these fragments is determined using X-ray crystallography or NMR spectroscopy, and is used to facilitate their optimization into potent molecules with drug-like properties. Compared with high-throughput-screening, the fragment approach requires fewer compounds to be screened, and, despite the lower initial potency of the screening hits, offers more efficient and fruitful optimization campaigns. Here, we review the rise of FBDD, including its application to discovering clinical candidates against targets for which other chemistry approaches have struggled.
Mechanics of fragmentation of crocodile skin and other thin films
Qin, Zhao; Pugno, Nicola M.; Buehler, Markus J.
2014-01-01
Fragmentation of thin layers of materials is mediated by a network of cracks on its surface. It is commonly seen in dehydrated paintings or asphalt pavements and even in graphene or other two-dimensional materials, but is also observed in the characteristic polygonal pattern on a crocodile's head. Here, we build a simple mechanical model of a thin film and investigate the generation and development of fragmentation patterns as the material is exposed to various modes of deformation. We find that the characteristic size of fragmentation, defined by the mean diameter of polygons, is strictly governed by mechanical properties of the film material. Our result demonstrates that skin fragmentation on the head of crocodiles is dominated by that it features a small ratio between the fracture energy and Young's modulus, and the patterns agree well with experimental observations. Understanding this mechanics-driven process could be applied to improve the lifetime and reliability of thin film coatings by mimicking crocodile skin. PMID:24862190
Mechanics of fragmentation of crocodile skin and other thin films
Qin, Zhao; Pugno, Nicola M.; Buehler, Markus J.
2014-05-01
Fragmentation of thin layers of materials is mediated by a network of cracks on its surface. It is commonly seen in dehydrated paintings or asphalt pavements and even in graphene or other two-dimensional materials, but is also observed in the characteristic polygonal pattern on a crocodile's head. Here, we build a simple mechanical model of a thin film and investigate the generation and development of fragmentation patterns as the material is exposed to various modes of deformation. We find that the characteristic size of fragmentation, defined by the mean diameter of polygons, is strictly governed by mechanical properties of the film material. Our result demonstrates that skin fragmentation on the head of crocodiles is dominated by that it features a small ratio between the fracture energy and Young's modulus, and the patterns agree well with experimental observations. Understanding this mechanics-driven process could be applied to improve the lifetime and reliability of thin film coatings by mimicking crocodile skin.
Directory of Open Access Journals (Sweden)
SW Kang
2015-02-01
Full Text Available This article introduces an improved non-dimensional dynamic influence function method using a sub-domain method for efficiently extracting the eigenvalues and mode shapes of concave membranes with arbitrary shapes. The non-dimensional dynamic influence function method (non-dimensional dynamic influence function method, which was developed by the authors in 1999, gives highly accurate eigenvalues for membranes, plates, and acoustic cavities, compared with the finite element method. However, it needs the inefficient procedure of calculating the singularity of a system matrix in the frequency range of interest for extracting eigenvalues and mode shapes. To overcome the inefficient procedure, this article proposes a practical approach to make the system matrix equation of the concave membrane of interest into a form of algebraic eigenvalue problem. It is shown by several case studies that the proposed method has a good convergence characteristics and yields very accurate eigenvalues, compared with an exact method and finite element method (ANSYS.
Fragment informatics and computational fragment-based drug design: an overview and update.
Sheng, Chunquan; Zhang, Wannian
2013-05-01
Fragment-based drug design (FBDD) is a promising approach for the discovery and optimization of lead compounds. Despite its successes, FBDD also faces some internal limitations and challenges. FBDD requires a high quality of target protein and good solubility of fragments. Biophysical techniques for fragment screening necessitate expensive detection equipment and the strategies for evolving fragment hits to leads remain to be improved. Regardless, FBDD is necessary for investigating larger chemical space and can be applied to challenging biological targets. In this scenario, cheminformatics and computational chemistry can be used as alternative approaches that can significantly improve the efficiency and success rate of lead discovery and optimization. Cheminformatics and computational tools assist FBDD in a very flexible manner. Computational FBDD can be used independently or in parallel with experimental FBDD for efficiently generating and optimizing leads. Computational FBDD can also be integrated into each step of experimental FBDD and help to play a synergistic role by maximizing its performance. This review will provide critical analysis of the complementarity between computational and experimental FBDD and highlight recent advances in new algorithms and successful examples of their applications. In particular, fragment-based cheminformatics tools, high-throughput fragment docking, and fragment-based de novo drug design will provide the focus of this review. We will also discuss the advantages and limitations of different methods and the trends in new developments that should inspire future research. © 2012 Wiley Periodicals, Inc.
A three-dimensional correlation method for registration of medical images in radiology
Energy Technology Data Exchange (ETDEWEB)
Georgiou, Michalakis; Sfakianakis, George N [Department of Radiology, University of Miami, Jackson Memorial Hospital, Miami, FL 33136 (United States); Nagel, Joachim H [Institute of Biomedical Engineering, University of Stuttgart, Stuttgart 70174 (Germany)
1999-12-31
The availability of methods to register multi-modality images in order to `fuse` them to correlate their information is increasingly becoming an important requirement for various diagnostic and therapeutic procedures. A variety of image registration methods have been developed but they remain limited to specific clinical applications. Assuming rigid body transformation, two images can be registered if their differences are calculated in terms of translation, rotation and scaling. This paper describes the development and testing of a new correlation based approach for three-dimensional image registration. First, the scaling factors introduced by the imaging devices are calculated and compensated for. Then, the two images become translation invariant by computing their three-dimensional Fourier magnitude spectra. Subsequently, spherical coordinate transformation is performed and then the three-dimensional rotation is computed using a novice approach referred to as {sup p}olar Shells{sup .} The method of polar shells maps the three angles of rotation into one rotation and two translations of a two-dimensional function and then proceeds to calculate them using appropriate transformations based on the Fourier invariance properties. A basic assumption in the method is that the three-dimensional rotation is constrained to one large and two relatively small angles. This assumption is generally satisfied in normal clinical settings. The new three-dimensional image registration method was tested with simulations using computer generated phantom data as well as actual clinical data. Performance analysis and accuracy evaluation of the method using computer simulations yielded errors in the sub-pixel range. (authors) 6 refs., 3 figs.
A three-dimensional correlation method for registration of medical images in radiology
International Nuclear Information System (INIS)
Georgiou, Michalakis; Sfakianakis, George N.; Nagel, Joachim H.
1998-01-01
The availability of methods to register multi-modality images in order to 'fuse' them to correlate their information is increasingly becoming an important requirement for various diagnostic and therapeutic procedures. A variety of image registration methods have been developed but they remain limited to specific clinical applications. Assuming rigid body transformation, two images can be registered if their differences are calculated in terms of translation, rotation and scaling. This paper describes the development and testing of a new correlation based approach for three-dimensional image registration. First, the scaling factors introduced by the imaging devices are calculated and compensated for. Then, the two images become translation invariant by computing their three-dimensional Fourier magnitude spectra. Subsequently, spherical coordinate transformation is performed and then the three-dimensional rotation is computed using a novice approach referred to as p olar Shells . The method of polar shells maps the three angles of rotation into one rotation and two translations of a two-dimensional function and then proceeds to calculate them using appropriate transformations based on the Fourier invariance properties. A basic assumption in the method is that the three-dimensional rotation is constrained to one large and two relatively small angles. This assumption is generally satisfied in normal clinical settings. The new three-dimensional image registration method was tested with simulations using computer generated phantom data as well as actual clinical data. Performance analysis and accuracy evaluation of the method using computer simulations yielded errors in the sub-pixel range. (authors)
The stress analysis method for three-dimensional composite materials
Nagai, Kanehiro; Yokoyama, Atsushi; Maekawa, Zen'ichiro; Hamada, Hiroyuki
1994-05-01
This study proposes a stress analysis method for three-dimensionally fiber reinforced composite materials. In this method, the rule-of mixture for composites is successfully applied to 3-D space in which material properties would change 3-dimensionally. The fundamental formulas for Young's modulus, shear modulus, and Poisson's ratio are derived. Also, we discuss a strength estimation and an optimum material design technique for 3-D composite materials. The analysis is executed for a triaxial orthogonally woven fabric, and their results are compared to the experimental data in order to verify the accuracy of this method. The present methodology can be easily understood with basic material mechanics and elementary mathematics, so it enables us to write a computer program of this theory without difficulty. Furthermore, this method can be applied to various types of 3-D composites because of its general-purpose characteristics.
Fragmentation measurement using image processing
Directory of Open Access Journals (Sweden)
Farhang Sereshki
2016-12-01
Full Text Available In this research, first of all, the existing problems in fragmentation measurement are reviewed for the sake of its fast and reliable evaluation. Then, the available methods used for evaluation of blast results are mentioned. The produced errors especially in recognizing the rock fragments in computer-aided methods, and also, the importance of determination of their sizes in the image analysis methods are described. After reviewing the previous work done, an algorithm is proposed for the automated determination of rock particles’ boundary in the Matlab software. This method can determinate automatically the particles boundary in the minimum time. The results of proposed method are compared with those of Split Desktop and GoldSize software in two automated and manual states. Comparing the curves extracted from different methods reveals that the proposed approach is accurately applicable in measuring the size distribution of laboratory samples, while the manual determination of boundaries in the conventional software is very time-consuming, and the results of automated netting of fragments are very different with the real value due to the error in separation of the objects.
Biomedical applications of two- and three-dimensional deterministic radiation transport methods
International Nuclear Information System (INIS)
Nigg, D.W.
1992-01-01
Multidimensional deterministic radiation transport methods are routinely used in support of the Boron Neutron Capture Therapy (BNCT) Program at the Idaho National Engineering Laboratory (INEL). Typical applications of two-dimensional discrete-ordinates methods include neutron filter design, as well as phantom dosimetry. The epithermal-neutron filter for BNCT that is currently available at the Brookhaven Medical Research Reactor (BMRR) was designed using such methods. Good agreement between calculated and measured neutron fluxes was observed for this filter. Three-dimensional discrete-ordinates calculations are used routinely for dose-distribution calculations in three-dimensional phantoms placed in the BMRR beam, as well as for treatment planning verification for live canine subjects. Again, good agreement between calculated and measured neutron fluxes and dose levels is obtained
DEFF Research Database (Denmark)
Svendsen, Casper Steinmann; Jensen, Jan; Fedorov, Dmitri
2013-01-01
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of ...
New method for solving three-dimensional Schroedinger equation
International Nuclear Information System (INIS)
Melezhik, V.S.
1992-01-01
A new method is developed for solving the multidimensional Schroedinger equation without the variable separation. To solve the Schroedinger equation in a multidimensional coordinate space X, a difference grid Ω i (i=1,2,...,N) for some of variables, Ω, from X={R,Ω} is introduced and the initial partial-differential equation is reduced to a system of N differential-difference equations in terms of one of the variables R. The arising multi-channel scattering (or eigenvalue) problem is solved by the algorithm based on a continuous analog of the Newton method. The approach has been successfully tested for several two-dimensional problems (scattering on a nonspherical potential well and 'dipole' scatterer, a hydrogen atom in a homogenous magnetic field) and for a three-dimensional problem of the helium-atom bound states. (author)
Knowledge-based Fragment Binding Prediction
Tang, Grace W.; Altman, Russ B.
2014-01-01
Target-based drug discovery must assess many drug-like compounds for potential activity. Focusing on low-molecular-weight compounds (fragments) can dramatically reduce the chemical search space. However, approaches for determining protein-fragment interactions have limitations. Experimental assays are time-consuming, expensive, and not always applicable. At the same time, computational approaches using physics-based methods have limited accuracy. With increasing high-resolution structural data for protein-ligand complexes, there is now an opportunity for data-driven approaches to fragment binding prediction. We present FragFEATURE, a machine learning approach to predict small molecule fragments preferred by a target protein structure. We first create a knowledge base of protein structural environments annotated with the small molecule substructures they bind. These substructures have low-molecular weight and serve as a proxy for fragments. FragFEATURE then compares the structural environments within a target protein to those in the knowledge base to retrieve statistically preferred fragments. It merges information across diverse ligands with shared substructures to generate predictions. Our results demonstrate FragFEATURE's ability to rediscover fragments corresponding to the ligand bound with 74% precision and 82% recall on average. For many protein targets, it identifies high scoring fragments that are substructures of known inhibitors. FragFEATURE thus predicts fragments that can serve as inputs to fragment-based drug design or serve as refinement criteria for creating target-specific compound libraries for experimental or computational screening. PMID:24762971
Cevizci, Halim
2014-10-01
In this study, the plaster stemming application for blasting at a basalt quarry is studied. Drill cuttings are generally used in open pits and quarries as the most common stemming material since these are most readily available at blast sites. However, dry drill cuttings eject very easily from blastholes without offering much resistance to blast energy. The plaster stemming method has been found to be better than the drill cuttings stemming method due to increased confinement inside the hole and better utilization of blast explosive energy in the rock. The main advantage of the new stemming method is the reduction in the cost of blasting. At a basalt quarry, blasting costs per unit volume of rock were reduced to 15% by increasing burden and spacing distances. In addition, better fragmentation was obtained by using the plaster stemming method. Blast trials showed that plaster stemming produced finer material. In the same blast tests, +30 cm size fragments were reduced to 47.3% of the total, compared to 32.6% in the conventional method of drill cuttings stemming. With this method of stemming, vibration and air shock values increased slightly due to more blast energy being available for rock breakage but generally these increased values were small and stayed under the permitted limit for blast damage criteria unless measuring distance is too close.
Determination of fragment orbitals and LCFO MO's in semiempirical methods with overlap matrices
International Nuclear Information System (INIS)
Konstantinavicius, K.V.; Lazauskas, V.M.
1988-01-01
We propose a technique for a fragment stage solution of the Roothaan equations, allowing us to obtain fragment orbitals (FO's) and to form molecular orbitals (LCFO MO'S) for the molecule from them. As an example, in the Mulliken-Wolfsberg-Helmholtz (MWH) approximation we obtain the orbitals for fragments of the simplest hydrocarbon molecules and we compare them with the FO's found in the CNDO/2 approximation. We discuss the possibilities in perturbation theory for joining the fragments and for study of the properties of the molecules in the FO basis
Vasileiou, Zoe; Barlos, Kostas K; Gatos, Dimitrios; Adermann, Knut; Deraison, Celine; Barlos, Kleomenis
2010-01-01
Proteinase inhibitors are of high pharmaceutical interest and are drug candidates for a variety of indications. Specific kallikrein inhibitors are important for their antitumor activity and their potential application to the treatment of skin diseases. In this study we describe the synthesis of domain 6 of the kallikrein inhibitor Lympho-Epithilial Kazal-Type Inhibitor (LEKTI) by the fragment condensation method and site-directed cystine bridge formation. To obtain the linear LEKTI precursor, the condensation was best performed in solution, coupling the protected fragment 1-22 to 23-68. This method yielded LEKTI domain 6 of high purity and equipotent to the recombinantly produced peptide. (c) 2010 Wiley Periodicals, Inc.
Application of Exp-function method for (2 + 1)-dimensional nonlinear evolution equations
International Nuclear Information System (INIS)
Bekir, Ahmet; Boz, Ahmet
2009-01-01
In this paper, the Exp-function method is used to construct solitary and soliton solutions of (2 + 1)-dimensional nonlinear evolution equations. (2 + 1)-dimensional breaking soliton (Calogero) equation, modified Zakharov-Kuznetsov and Konopelchenko-Dubrovsky equations are chosen to illustrate the effectiveness of the method. The method is straightforward and concise, and its applications are promising. The Exp-function method presents a wider applicability for handling nonlinear wave equations.
A Comparison of Machine Learning Methods in a High-Dimensional Classification Problem
Zekić-Sušac, Marijana; Pfeifer, Sanja; Šarlija, Nataša
2014-01-01
Background: Large-dimensional data modelling often relies on variable reduction methods in the pre-processing and in the post-processing stage. However, such a reduction usually provides less information and yields a lower accuracy of the model. Objectives: The aim of this paper is to assess the high-dimensional classification problem of recognizing entrepreneurial intentions of students by machine learning methods. Methods/Approach: Four methods were tested: artificial neural networks, CART ...
International Nuclear Information System (INIS)
Ye, Yong-jun; Wang, Li-heng; Ding, De-xin; Zhao, Ya-li; Fan, Nan-bin
2014-01-01
The radon diffusion coefficient and the free radon production rate are important parameters for describing radon migration in the fragmented uranium ore. In order to determine the two parameters, the pure diffusion migration equation for radon was firstly established and its analytic solution with the two parameters to be determined was derived. Then, a self manufactured experimental column was used to simulate the pure diffusion of the radon, the improved scintillation cell method was used to measure the pore radon concentrations at different depths of the column loaded with the fragmented uranium ore, and the nonlinear least square algorithm was used to inversely determine the radon diffusion coefficient and the free radon production rate. Finally, the solution with the two inversely determined parameters was used to predict the pore radon concentrations at some depths of the column, and the predicted results were compared with the measured results. The results show that the predicted results are in good agreement with the measured results and the numerical inverse method is applicable to the determination of the radon diffusion coefficient and the free radon production rate for the fragmented uranium ore. - Highlights: • Inverse method for determining two transport parameters of radon is proposed. • A self-made experimental apparatus is used to simulate radon diffusion process. • Sampling volume and position for measuring radon concentration are optimized. • The inverse results of an experimental sample are verified
An Alternative to Conventional Rock Fragmentation Methods Using SCDA: A Review
Directory of Open Access Journals (Sweden)
Radhika Vidanage De Silva
2016-11-01
Full Text Available Global energy and material consumption are expected to rise in exponential proportions during the next few decades, generating huge demands for deep earth energy (oil/gas recovery and mineral processing. Under such circumstances, the continuation of existing methods in rock fragmentation in such applications is questionable due to the proven adverse environmental impacts associated with them. In this regard; the possibility of using more environmentally friendly options as Soundless Chemical Demolition Agents (SCDAs play a vital role in replacing harmful conventional rock fragmentation techniques for gas; oil and mineral recovery. This study reviews up to date research on soundless cracking demolition agent (SCDA application on rock fracturing including its limitations and strengths, possible applications in the petroleum industry and the possibility of using existing rock fragmentation models for SCDA-based rock fragmentation; also known as fracking. Though the expansive properties of SCDAs are currently used in some demolition works, the poor usage guidelines available reflect the insufficient research carried out on its material’s behavior. SCDA is a cementitious powdery substance with quicklime (CaO as its primary ingredient that expands upon contact with water; which results in a huge expansive pressure if this CaO hydration reaction occurs in a confined condition. So, the mechanism can be used for rock fragmentation by injecting the SCDA into boreholes of a rock mass; where the resulting expansive pressure is sufficient to create an effective fracture network in the confined rock mass around the borehole. This expansive pressure development, however, dependent on many factors, where formation water content creates a negative influence on this due to required greater degree of hydration under greater water contents and temperature creates a positive influence by accelerating the reaction. Having a precise understanding of the fracture
Cordero, Chiara; Rubiolo, Patrizia; Reichenbach, Stephen E; Carretta, Andrea; Cobelli, Luigi; Giardina, Matthew; Bicchi, Carlo
2017-01-13
The possibility to transfer methods from thermal to differential-flow modulated comprehensive two-dimensional gas chromatographic (GC×GC) platforms is of high interest to improve GC×GC flexibility and increase the compatibility of results from different platforms. The principles of method translation are here applied to an original method, developed for a loop-type thermal modulated GC×GC-MS/FID system, suitable for quali-quantitative screening of suspected fragrance allergens. The analysis conditions were translated to a reverse-injection differential flow modulated platform (GC×2GC-MS/FID) with a dual-parallel secondary column and dual detection. The experimental results, for a model mixture of suspected volatile allergens and for raw fragrance mixtures of different composition, confirmed the feasibility of translating methods by preserving 1 D elution order, as well as the relative alignment of resulting 2D peak patterns. A correct translation produced several benefits including an effective transfer of metadata (compound names, MS fragmentation pattern, response factors) by automatic template transformation and matching from the original/reference method to its translated counterpart. The correct translation provided: (a) 2D pattern repeatability, (b) MS fragmentation pattern reliability for identity confirmation, and (c) comparable response factors and quantitation accuracy within a concentration range of three orders of magnitude. The adoption of a narrow bore (i.e. 0.1mm d c ) first-dimension column to operate under close-to-optimal conditions with the differential-flow modulation GC×GC platform was also advantageous in halving the total analysis under the translated conditions. Copyright © 2016 Elsevier B.V. All rights reserved.
Neumann, Lars; Ritscher, Allegra; Müller, Gerhard; Hafenbradl, Doris
2009-08-01
For the detection of the precise and unambiguous binding of fragments to a specific binding site on the target protein, we have developed a novel reporter displacement binding assay technology. The application of this technology for the fragment screening as well as the fragment evolution process with a specific modelling based design strategy is demonstrated for inhibitors of the protein kinase p38alpha. In a fragment screening approach seed fragments were identified which were then used to build compounds from the deep-pocket towards the hinge binding area of the protein kinase p38alpha based on a modelling approach. BIRB796 was used as a blueprint for the alignment of the fragments. The fragment evolution of these deep-pocket binding fragments towards the fully optimized inhibitor BIRB796 included the modulation of the residence time as well as the affinity. The goal of our study was to evaluate the robustness and efficiency of our novel fragment screening technology at high fragment concentrations, compare the screening data with biochemical activity data and to demonstrate the evolution of the hit fragments with fast kinetics, into slow kinetic inhibitors in an in silico approach.
Directory of Open Access Journals (Sweden)
Boulund Fredrik
2012-12-01
Full Text Available Abstract Background Broad-spectrum fluoroquinolone antibiotics are central in modern health care and are used to treat and prevent a wide range of bacterial infections. The recently discovered qnr genes provide a mechanism of resistance with the potential to rapidly spread between bacteria using horizontal gene transfer. As for many antibiotic resistance genes present in pathogens today, qnr genes are hypothesized to originate from environmental bacteria. The vast amount of data generated by shotgun metagenomics can therefore be used to explore the diversity of qnr genes in more detail. Results In this paper we describe a new method to identify qnr genes in nucleotide sequence data. We show, using cross-validation, that the method has a high statistical power of correctly classifying sequences from novel classes of qnr genes, even for fragments as short as 100 nucleotides. Based on sequences from public repositories, the method was able to identify all previously reported plasmid-mediated qnr genes. In addition, several fragments from novel putative qnr genes were identified in metagenomes. The method was also able to annotate 39 chromosomal variants of which 11 have previously not been reported in literature. Conclusions The method described in this paper significantly improves the sensitivity and specificity of identification and annotation of qnr genes in nucleotide sequence data. The predicted novel putative qnr genes in the metagenomic data support the hypothesis of a large and uncharacterized diversity within this family of resistance genes in environmental bacterial communities. An implementation of the method is freely available at http://bioinformatics.math.chalmers.se/qnr/.
Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization.
Yang, Jiaoyun; Wang, Haipeng; Ding, Huitong; An, Ning; Alterovitz, Gil
2017-01-19
Visualizing data by dimensionality reduction is an important strategy in Bioinformatics, which could help to discover hidden data properties and detect data quality issues, e.g. data noise, inappropriately labeled data, etc. As crowdsourcing-based synthetic biology databases face similar data quality issues, we propose to visualize biobricks to tackle them. However, existing dimensionality reduction methods could not be directly applied on biobricks datasets. Hereby, we use normalized edit distance to enhance dimensionality reduction methods, including Isomap and Laplacian Eigenmaps. By extracting biobricks from synthetic biology database Registry of Standard Biological Parts, six combinations of various types of biobricks are tested. The visualization graphs illustrate discriminated biobricks and inappropriately labeled biobricks. Clustering algorithm K-means is adopted to quantify the reduction results. The average clustering accuracy for Isomap and Laplacian Eigenmaps are 0.857 and 0.844, respectively. Besides, Laplacian Eigenmaps is 5 times faster than Isomap, and its visualization graph is more concentrated to discriminate biobricks. By combining normalized edit distance with Isomap and Laplacian Eigenmaps, synthetic biology biobircks are successfully visualized in two dimensional space. Various types of biobricks could be discriminated and inappropriately labeled biobricks could be determined, which could help to assess crowdsourcing-based synthetic biology databases' quality, and make biobricks selection.
Dimensional analysis and self-similarity methods for engineers and scientists
Zohuri, Bahman
2015-01-01
This ground-breaking reference provides an overview of key concepts in dimensional analysis, and then pushes well beyond traditional applications in fluid mechanics to demonstrate how powerful this tool can be in solving complex problems across many diverse fields. Of particular interest is the book's coverage of dimensional analysis and self-similarity methods in nuclear and energy engineering. Numerous practical examples of dimensional problems are presented throughout, allowing readers to link the book's theoretical explanations and step-by-step mathematical solutions to practical impleme
A finite-dimensional reduction method for slightly supercritical elliptic problems
Directory of Open Access Journals (Sweden)
Riccardo Molle
2004-01-01
Full Text Available We describe a finite-dimensional reduction method to find solutions for a class of slightly supercritical elliptic problems. A suitable truncation argument allows us to work in the usual Sobolev space even in the presence of supercritical nonlinearities: we modify the supercritical term in such a way to have subcritical approximating problems; for these problems, the finite-dimensional reduction can be obtained applying the methods already developed in the subcritical case; finally, we show that, if the truncation is realized at a sufficiently large level, then the solutions of the approximating problems, given by these methods, also solve the supercritical problems when the parameter is small enough.
Effective method for construction of low-dimensional models for heat transfer process
Energy Technology Data Exchange (ETDEWEB)
Blinov, D.G.; Prokopov, V.G.; Sherenkovskii, Y.V.; Fialko, N.M.; Yurchuk, V.L. [National Academy of Sciences of Ukraine, Kiev (Ukraine). Inst. of Engineering Thermophysics
2004-12-01
A low-dimensional model based on the method of proper orthogonal decomposition (POD) and the method of polyargumental systems (MPS) for thermal conductivity problems with strongly localized source of heat has been presented. The key aspect of these methods is that they enable to avoid weak points of other projection methods, which consists in a priori choice of basis functions. It enables us to use the MPS method and the POD method as convenient means to construct low-dimensional models of heat and mass transfer problems. (Author)
Critical Features of Fragment Libraries for Protein Structure Prediction.
Trevizani, Raphael; Custódio, Fábio Lima; Dos Santos, Karina Baptista; Dardenne, Laurent Emmanuel
2017-01-01
The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction.
Fragment-based approaches to TB drugs.
Marchetti, Chiara; Chan, Daniel S H; Coyne, Anthony G; Abell, Chris
2018-02-01
Tuberculosis is an infectious disease associated with significant mortality and morbidity worldwide, particularly in developing countries. The rise of antibiotic resistance in Mycobacterium tuberculosis (Mtb) urgently demands the development of new drug leads to tackle resistant strains. Fragment-based methods have recently emerged at the forefront of pharmaceutical development as a means to generate more effective lead structures, via the identification of fragment molecules that form weak but high quality interactions with the target biomolecule and subsequent fragment optimization. This review highlights a number of novel inhibitors of Mtb targets that have been developed through fragment-based approaches in recent years.
Renormalization of the fragmentation equation: Exact self-similar solutions and turbulent cascades
Saveliev, V. L.; Gorokhovski, M. A.
2012-12-01
Using an approach developed earlier for renormalization of the Boltzmann collision integral [Saveliev and Nanbu, Phys. Rev. E1539-375510.1103/PhysRevE.65.051205 65, 051205 (2002)], we derive an exact divergence form for the fragmentation operator. Then we reduce the fragmentation equation to the continuity equation in size space, with the flux given explicitly. This allows us to obtain self-similar solutions and to find the integral of motion for these solutions (we call it the bare flux). We show how these solutions can be applied as a description of cascade processes in three- and two-dimensional turbulence. We also suggested an empirical cascade model of impact fragmentation of brittle materials.
Three-dimensional measurement of a tightly focused laser beam
Directory of Open Access Journals (Sweden)
Xiangsheng Xie
2013-02-01
Full Text Available The spatial structure of a tightly focused light field is measured with a double knife-edge scanning method. The measurement method is based on the use of a high-quality double knife-edge fabricated from a right-angled silicon fragment mounted on a photodetector. The reconstruction of the three-dimensional structures of tightly focused spots is carried out with both uniform and partially obstructed linearly polarized incident light beams. The optical field distribution is found to deviate substantially from the input beam profile in the tightly focused region, which is in good agreement with the results of numerical simulations.
Two-Dimensional Impact Reconstruction Method for Rail Defect Inspection
Directory of Open Access Journals (Sweden)
Jie Zhao
2014-01-01
Full Text Available The safety of train operating is seriously menaced by the rail defects, so it is of great significance to inspect rail defects dynamically while the train is operating. This paper presents a two-dimensional impact reconstruction method to realize the on-line inspection of rail defects. The proposed method utilizes preprocessing technology to convert time domain vertical vibration signals acquired by wireless sensor network to space signals. The modern time-frequency analysis method is improved to reconstruct the obtained multisensor information. Then, the image fusion processing technology based on spectrum threshold processing and node color labeling is proposed to reduce the noise, and blank the periodic impact signal caused by rail joints and locomotive running gear. This method can convert the aperiodic impact signals caused by rail defects to partial periodic impact signals, and locate the rail defects. An application indicates that the two-dimensional impact reconstruction method could display the impact caused by rail defects obviously, and is an effective on-line rail defects inspection method.
Irregular grid methods for pricing high-dimensional American options
Berridge, S.J.
2004-01-01
This thesis proposes and studies numerical methods for pricing high-dimensional American options; important examples being basket options, Bermudan swaptions and real options. Four new methods are presented and analysed, both in terms of their application to various test problems, and in terms of
Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi
2017-06-01
The molecular interactions of inhibitors of bromodomains (BRDs) were investigated. BRDs are protein interaction modules that recognizing ε-N-acetyl-lysine (εAc-Lys) motifs found in histone tails and are promising protein-protein interaction (PPI) targets. First, we analyzed a peptide ligand containing εAc-Lys to evaluate native PPIs. We then analyzed tetrahydroquinazoline-6-yl-benzensulfonamide derivatives found by fragment-based drug design (FBDD) and examined their interactions with the protein compared with the peptide ligand in terms of the inter-fragment interaction energy. In addition, we analyzed benzodiazepine derivatives that are high-affinity ligands for BRDs and examined differences in the CH/π interactions of the amino acid residues. We further surveyed changes in the charges of the amino acid residues among individual ligands, performed pair interaction energy decomposition analysis and estimated the water profile within the ligand binding site. Thus, useful insights for drug design were provided. Through these analyses and considerations, we show that the FMO method is a useful drug design tool to evaluate the process of FBDD and to explore PPI inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.
Directory of Open Access Journals (Sweden)
Rong Shen
2015-10-01
Full Text Available The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels, each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good
Fragment emission in relativistic heavy-ion reactions
International Nuclear Information System (INIS)
Csernai, L.P.; Subramanian, P.R.; Buchwald, G.; Graebner, G.; Rosenhauer, A.; Maruhn, J.A.; Greiner, W.
1982-05-01
The authors present a theoretical description of nuclear collisions which consists of a three-dimensional fluid-dynamical model, a chemical equilibrium break-up calculation for local light fragment (i.e. p, n, d, t, 3 He, 4 He) production and a final thermal evaporation of these particles. The light fragment cross section and some properties of the heavy target residues are calculated for the asymmetric systems Ne+U at 400 MeV/N, Ne+Pb at 800 MeV/N and C+Sn at 86 MeV/N. The results of the model calculations are compared with recent experimental data. Several observable signs of the collective hydrodynamical processes are consistent with the present data. An event-by-event analysis of the flow patterns of the various clusters is proposed which can yield deeper insight into collision dynamics. (author)
SCEDS: protein fragments for molecular replacement in Phaser
Energy Technology Data Exchange (ETDEWEB)
McCoy, Airlie J., E-mail: ajm201@cam.ac.uk [University of Cambridge, Hills Road, Cambridge CB2 0XY (United Kingdom); Nicholls, Robert A. [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Schneider, Thomas R. [Hamburg Unit c/o DESY, Notkestrasse 85, 22603 Hamburg (Germany); University of Cambridge, Hills Road, Cambridge CB2 0XY (United Kingdom)
2013-11-01
Protein fragments suitable for use in molecular replacement can be generated by normal-mode perturbation, analysis of the difference distance matrix of the original versus normal-mode perturbed structures, and SCEDS, a score that measures the sphericity, continuity, equality and density of the resulting fragments. A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models. The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model. The unperturbed structure is then compared with each perturbed structure in turn and the structurally invariant regions are identified by analysing the difference distance matrix. These fragments are scored with SCEDS, which is a combined measure of the sphericity of the fragments, the continuity of the fragments with respect to the polypeptide chain, the equality in number of atoms in the fragments and the density of C{sup α} atoms in the triaxial ellipsoid of the fragment extents. The fragment divisions with the highest SCEDS are then used as separate template models for MR. Test cases show that where the protein contains fragments that undergo a change in juxtaposition between template model and target, SCEDS can identify fragments that lead to a lower R factor after ten cycles of all-atom refinement with REFMAC5 than the original template structure. The method has been implemented in the software Phaser.
SCEDS: protein fragments for molecular replacement in Phaser
International Nuclear Information System (INIS)
McCoy, Airlie J.; Nicholls, Robert A.; Schneider, Thomas R.
2013-01-01
Protein fragments suitable for use in molecular replacement can be generated by normal-mode perturbation, analysis of the difference distance matrix of the original versus normal-mode perturbed structures, and SCEDS, a score that measures the sphericity, continuity, equality and density of the resulting fragments. A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models. The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model. The unperturbed structure is then compared with each perturbed structure in turn and the structurally invariant regions are identified by analysing the difference distance matrix. These fragments are scored with SCEDS, which is a combined measure of the sphericity of the fragments, the continuity of the fragments with respect to the polypeptide chain, the equality in number of atoms in the fragments and the density of C α atoms in the triaxial ellipsoid of the fragment extents. The fragment divisions with the highest SCEDS are then used as separate template models for MR. Test cases show that where the protein contains fragments that undergo a change in juxtaposition between template model and target, SCEDS can identify fragments that lead to a lower R factor after ten cycles of all-atom refinement with REFMAC5 than the original template structure. The method has been implemented in the software Phaser
A numerical method for two-dimensional anisotropic transport problem in cylindrical geometry
International Nuclear Information System (INIS)
Du Mingsheng; Feng Tiekai; Fu Lianxiang; Cao Changshu; Liu Yulan
1988-01-01
The authors deal with the triangular mesh-discontinuous finite element method for solving the time-dependent anisotropic neutron transport problem in two-dimensional cylindrical geometry. A prior estimate of the numerical solution is given. Stability is proved. The authors have computed a two dimensional anisotropic neutron transport problem and a Tungsten-Carbide critical assembly problem by using the numerical method. In comparision with DSN method and the experimental results obtained by others both at home and abroad, the method is satisfactory
One-dimensional calculation of flow branching using the method of characteristics
International Nuclear Information System (INIS)
Meier, R.W.; Gido, R.G.
1978-05-01
In one-dimensional flow systems, the flow often branches, such as at a tee or manifold. The study develops a formulation for calculating the flow through branch points with one-dimensional method of characteristics equations. The resultant equations were verified by comparison with experimental measurements
Bedani, F.; Schoenmakers, P.J.; Janssen, H.-G.
2012-01-01
On-line comprehensive two-dimensional liquid chromatography techniques promise to resolve samples that current one-dimensional liquid chromatography methods cannot adequately deal with. To make full use of the potential of two-dimensional liquid chromatography, optimization is required. Optimization
Fragment screening by SPR and advanced application to GPCRs.
Shepherd, Claire A; Hopkins, Andrew L; Navratilova, Iva
2014-01-01
Surface plasmon resonance (SPR) is one of the primary biophysical methods for the screening of low molecular weight 'fragment' libraries, due to its low protein consumption and 'label-free' methodology. SPR biosensor interaction analysis is employed to both screen and confirm the binding of compounds in fragment screening experiments, as it provides accurate information on the affinity and kinetics of molecular interactions. The most advanced application of the use of SPR for fragment screening is against membrane protein drug targets, such G-protein coupled receptors (GPCRs). Biophysical GPCR assays using SPR have been validated with pharmacological measurements approximate to cell-based methods, yet provide the advantage of biophysical methods in their ability to measure the weak affinities of low molecular weight fragments. A number of SPR fragment screens against GPCRs have now been disclosed in the literature. SPR fragment screening is proving versatile to screen both thermostabilised GPCRs and solubilised wild type receptors. In this chapter, we discuss the state-of-the-art in GPCR fragment screening by SPR and the technical considerations in performing such experiments. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.
Fragmentation Energy-Saving Theory of Full Face Rock Tunnel Boring Machine Disc Cutters
Zhang, Zhao-Huang; Gong, Guo-Fang; Gao, Qing-Feng; Sun, Fei
2017-07-01
Attempts to minimize energy consumption of a tunnel boring machine disc cutter during the process of fragmentation have largely focused on optimizing disc-cutter spacing, as determined by the minimum specific energy required for fragmentation; however, indentation tests showed that rock deforms plastically beneath the cutters. Equations for thrust were developed for both the traditional, popularly employed disc cutter and anew design based on three-dimensional theory. The respective energy consumption for penetration, rolling, and side-slip fragmentations were obtained. A change in disc-cutter fragmentation angles resulted in a change in the nature of the interaction between the cutter and rock, which lowered the specific energy of fragmentation. During actual field excavations to the same penetration length, the combined energy consumption for fragmentation using the newly designed cutters was 15% lower than that when using the traditional design. This paper presents a theory for energy saving in tunnel boring machines. Investigation results showed that the disc cutters designed using this theory were more durable than traditional designs, and effectively lowered the energy consumption.
Development of methods to measure hemoglobin adducts by gel electrophoresis - Preliminary results
International Nuclear Information System (INIS)
Sun, J.D.; McBride, S.M.
1988-01-01
Chemical adducts formed on blood hemoglobin may be a useful biomarker for assessing human exposures to these compounds. This paper reports preliminary results in the development of methods to measure such adducts that may be generally applicable for a wide variety of chemicals. Male F344/N rats were intraperitoneally injected with 14 C-BaP dissolved in corn oil. Twenty-four hours later, the rats were sacrificed. Blood samples were collected and globin was isolated. Globin protein was then cleaved into peptide fragments using cyanogen bromide and the fragments separated using 2-dimensional gel electrophoresis. The results showed that the adducted 14 C-globin fragments migrated to different areas of the gel than did unadducted fragments. Further research is being conducted to develop methods that will allow quantitation of separated adducted globin fragments from human blood samples without the use of a radiolabel. (author)
Directory of Open Access Journals (Sweden)
Xiaoni Dong
2016-01-01
Full Text Available Process models and parameters are two critical steps for fault prognosis in the operation of rotating machinery. Due to the requirement for a short and rapid response, it is important to study robust sensor data representation schemes. However, the conventional holospectrum defined by one-dimensional or two-dimensional methods does not sufficiently present this information in both the frequency and time domains. To supply a complete holospectrum model, a new three-dimensional spatial representation method is proposed. This method integrates improved three-dimensional (3D holospectra and 3D filtered orbits, leading to the integration of radial and axial vibration features in one bearing section. The results from simulation and experimental analysis on a complex compressor show that the proposed method can present the real operational status and clearly reveal early faults, thus demonstrating great potential for condition-based maintenance prediction in industrial machinery.
Heart Rate Fragmentation: A Symbolic Dynamical Approach
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Madalena D. Costa
2017-11-01
Full Text Available Background: We recently introduced the concept of heart rate fragmentation along with a set of metrics for its quantification. The term was coined to refer to an increase in the percentage of changes in heart rate acceleration sign, a dynamical marker of a type of anomalous variability. The effort was motivated by the observation that fragmentation, which is consistent with the breakdown of the neuroautonomic-electrophysiologic control system of the sino-atrial node, could confound traditional short-term analysis of heart rate variability.Objective: The objectives of this study were to: (1 introduce a symbolic dynamical approach to the problem of quantifying heart rate fragmentation; (2 evaluate how the distribution of the different dynamical patterns (“words” varied with the participants' age in a group of healthy subjects and patients with coronary artery disease (CAD; and (3 quantify the differences in the fragmentation patterns between the two sample populations.Methods: The symbolic dynamical method employed here was based on a ternary map of the increment NN interval time series and on the analysis of the relative frequency of symbolic sequences (words with a pre-defined set of features. We analyzed annotated, open-access Holter databases of healthy subjects and patients with CAD, provided by the University of Rochester Telemetric and Holter ECG Warehouse (THEW.Results: The degree of fragmentation was significantly higher in older individuals than in their younger counterparts. However, the fragmentation patterns were different in the two sample populations. In healthy subjects, older age was significantly associated with a higher percentage of transitions from acceleration/deceleration to zero acceleration and vice versa (termed “soft” inflection points. In patients with CAD, older age was also significantly associated with higher percentages of frank reversals in heart rate acceleration (transitions from acceleration to
The Fragmentation Criteria in Local Vertically Stratified Self-gravitating Disk Simulations
Energy Technology Data Exchange (ETDEWEB)
Baehr, Hans; Klahr, Hubert [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany); Kratter, Kaitlin M., E-mail: baehr@mpia.de [Steward Observatory, University of Arizona, Tucson, AZ 85721 (United States)
2017-10-10
Massive circumstellar disks are prone to gravitational instabilities, which trigger the formation of spiral arms that can fragment into bound clumps under the right conditions. Two-dimensional simulations of self-gravitating disks are useful starting points for studying fragmentation because they allow high-resolution simulations of thin disks. However, convergence issues can arise in 2D from various sources. One of these sources is the 2D approximation of self-gravity, which exaggerates the effect of self-gravity on small scales when the potential is not smoothed to account for the assumed vertical extent of the disk. This effect is enhanced by increased resolution, resulting in fragmentation at longer cooling timescales β . If true, it suggests that the 3D simulations of disk fragmentation may not have the same convergence problem and could be used to examine the nature of fragmentation without smoothing self-gravity on scales similar to the disk scale height. To that end, we have carried out local 3D self-gravitating disk simulations with simple β cooling with fixed background irradiation to determine if 3D is necessary to properly describe disk fragmentation. Above a resolution of ∼40 grid cells per scale height, we find that our simulations converge with respect to the cooling timescale. This result converges in agreement with analytic expectations which place a fragmentation boundary at β {sub crit} = 3.
Rudashevskaya, Elena L; Breitwieser, Florian P; Huber, Marie L; Colinge, Jacques; Müller, André C; Bennett, Keiryn L
2013-02-05
The identification and validation of cross-linked peptides by mass spectrometry remains a daunting challenge for protein-protein cross-linking approaches when investigating protein interactions. This includes the fragmentation of cross-linked peptides in the mass spectrometer per se and following database searching, the matching of the molecular masses of the fragment ions to the correct cross-linked peptides. The hybrid linear trap quadrupole (LTQ) Orbitrap Velos combines the speed of the tandem mass spectrometry (MS/MS) duty circle with high mass accuracy, and these features were utilized in the current study to substantially improve the confidence in the identification of cross-linked peptides. An MS/MS method termed multiple and sequential data acquisition method (MSDAM) was developed. Preliminary optimization of the MS/MS settings was performed with a synthetic peptide (TP1) cross-linked with bis[sulfosuccinimidyl] suberate (BS(3)). On the basis of these results, MSDAM was created and assessed on the BS(3)-cross-linked bovine serum albumin (BSA) homodimer. MSDAM applies a series of multiple sequential fragmentation events with a range of different normalized collision energies (NCE) to the same precursor ion. The combination of a series of NCE enabled a considerable improvement in the quality of the fragmentation spectra for cross-linked peptides, and ultimately aided in the identification of the sequences of the cross-linked peptides. Concurrently, MSDAM provides confirmatory evidence from the formation of reporter ions fragments, which reduces the false positive rate of incorrectly assigned cross-linked peptides.
Reduced basis ANOVA methods for partial differential equations with high-dimensional random inputs
Energy Technology Data Exchange (ETDEWEB)
Liao, Qifeng, E-mail: liaoqf@shanghaitech.edu.cn [School of Information Science and Technology, ShanghaiTech University, Shanghai 200031 (China); Lin, Guang, E-mail: guanglin@purdue.edu [Department of Mathematics & School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907 (United States)
2016-07-15
In this paper we present a reduced basis ANOVA approach for partial deferential equations (PDEs) with random inputs. The ANOVA method combined with stochastic collocation methods provides model reduction in high-dimensional parameter space through decomposing high-dimensional inputs into unions of low-dimensional inputs. In this work, to further reduce the computational cost, we investigate spatial low-rank structures in the ANOVA-collocation method, and develop efficient spatial model reduction techniques using hierarchically generated reduced bases. We present a general mathematical framework of the methodology, validate its accuracy and demonstrate its efficiency with numerical experiments.
Identifying Interactions that Determine Fragment Binding at Protein Hotspots.
Radoux, Chris J; Olsson, Tjelvar S G; Pitt, Will R; Groom, Colin R; Blundell, Tom L
2016-05-12
Locating a ligand-binding site is an important first step in structure-guided drug discovery, but current methods do little to suggest which interactions within a pocket are the most important for binding. Here we illustrate a method that samples atomic hotspots with simple molecular probes to produce fragment hotspot maps. These maps specifically highlight fragment-binding sites and their corresponding pharmacophores. For ligand-bound structures, they provide an intuitive visual guide within the binding site, directing medicinal chemists where to grow the molecule and alerting them to suboptimal interactions within the original hit. The fragment hotspot map calculation is validated using experimental binding positions of 21 fragments and subsequent lead molecules. The ligands are found in high scoring areas of the fragment hotspot maps, with fragment atoms having a median percentage rank of 97%. Protein kinase B and pantothenate synthetase are examined in detail. In each case, the fragment hotspot maps are able to rationalize a Free-Wilson analysis of SAR data from a fragment-based drug design project.
High-throughput fragment screening by affinity LC-MS.
Duong-Thi, Minh-Dao; Bergström, Maria; Fex, Tomas; Isaksson, Roland; Ohlson, Sten
2013-02-01
Fragment screening, an emerging approach for hit finding in drug discovery, has recently been proven effective by its first approved drug, vemurafenib, for cancer treatment. Techniques such as nuclear magnetic resonance, surface plasmon resonance, and isothemal titration calorimetry, with their own pros and cons, have been employed for screening fragment libraries. As an alternative approach, screening based on high-performance liquid chromatography separation has been developed. In this work, we present weak affinity LC/MS as a method to screen fragments under high-throughput conditions. Affinity-based capillary columns with immobilized thrombin were used to screen a collection of 590 compounds from a fragment library. The collection was divided into 11 mixtures (each containing 35 to 65 fragments) and screened by MS detection. The primary screening was performed in 3500 fragments per day). Thirty hits were defined, which subsequently entered a secondary screening using an active site-blocked thrombin column for confirmation of specificity. One hit showed selective binding to thrombin with an estimated dissociation constant (K (D)) in the 0.1 mM range. This study shows that affinity LC/MS is characterized by high throughput, ease of operation, and low consumption of target and fragments, and therefore it promises to be a valuable method for fragment screening.
Fragmented one dimensional man / El hombre unidimensional fragmentado
Directory of Open Access Journals (Sweden)
Juan Antonio Rodríguez del Pino
2013-10-01
Full Text Available Paraphrase the title of the famous essay by Herbert Marcuse, since the image has traditionally been generated of man, masculinity, has been one-dimensional. I mean, the man was characterized by traits and behaviors established and entrenched since ancient time, considering all other distinguishing signs as mere deviations from the normative improper. But observe that this undeniable reality, as analyzed various researchers through what has come to be called Men's studies, has proven to be a fallacy difficult to maintain throughout history and today turns into fallacious and ineffective against changes in our current existing corporate models.
Binding-site assessment by virtual fragment screening.
Directory of Open Access Journals (Sweden)
Niu Huang
2010-04-01
Full Text Available The accurate prediction of protein druggability (propensity to bind high-affinity drug-like small molecules would greatly benefit the fields of chemical genomics and drug discovery. We have developed a novel approach to quantitatively assess protein druggability by computationally screening a fragment-like compound library. In analogy to NMR-based fragment screening, we dock approximately 11,000 fragments against a given binding site and compute a computational hit rate based on the fraction of molecules that exceed an empirically chosen score cutoff. We perform a large-scale evaluation of the approach on four datasets, totaling 152 binding sites. We demonstrate that computed hit rates correlate with hit rates measured experimentally in a previously published NMR-based screening method. Secondly, we show that the in silico fragment screening method can be used to distinguish known druggable and non-druggable targets, including both enzymes and protein-protein interaction sites. Finally, we explore the sensitivity of the results to different receptor conformations, including flexible protein-protein interaction sites. Besides its original aim to assess druggability of different protein targets, this method could be used to identifying druggable conformations of flexible binding site for lead discovery, and suggesting strategies for growing or joining initial fragment hits to obtain more potent inhibitors.
The power to detect recent fragmentation events using genetic differentiation methods.
Directory of Open Access Journals (Sweden)
Michael W Lloyd
Full Text Available Habitat loss and fragmentation are imminent threats to biological diversity worldwide and thus are fundamental issues in conservation biology. Increased isolation alone has been implicated as a driver of negative impacts in populations associated with fragmented landscapes. Genetic monitoring and the use of measures of genetic divergence have been proposed as means to detect changes in landscape connectivity. Our goal was to evaluate the sensitivity of Wright's F st, Hedrick' G'st , Sherwin's MI, and Jost's D to recent fragmentation events across a range of population sizes and sampling regimes. We constructed an individual-based model, which used a factorial design to compare effects of varying population size, presence or absence of overlapping generations, and presence or absence of population sub-structuring. Increases in population size, overlapping generations, and population sub-structuring each reduced F st, G'st , MI, and D. The signal of fragmentation was detected within two generations for all metrics. However, the magnitude of the change in each was small in all cases, and when N e was >100 individuals it was extremely small. Multi-generational sampling and population estimates are required to differentiate the signal of background divergence from changes in Fst , G'st , MI, and D associated with fragmentation. Finally, the window during which rapid change in Fst , G'st , MI, and D between generations occurs can be small, and if missed would lead to inconclusive results. For these reasons, use of F st, G'st , MI, or D for detecting and monitoring changes in connectivity is likely to prove difficult in real-world scenarios. We advocate use of genetic monitoring only in conjunction with estimates of actual movement among patches such that one could compare current movement with the genetic signature of past movement to determine there has been a change.
An improved algorithm for MFR fragment assembly
International Nuclear Information System (INIS)
Kontaxis, Georg
2012-01-01
A method for generating protein backbone models from backbone only NMR data is presented, which is based on molecular fragment replacement (MFR). In a first step, the PDB database is mined for homologous peptide fragments using experimental backbone-only data i.e. backbone chemical shifts (CS) and residual dipolar couplings (RDC). Second, this fragment library is refined against the experimental restraints. Finally, the fragments are assembled into a protein backbone fold using a rigid body docking algorithm using the RDCs as restraints. For improved performance, backbone nuclear Overhauser effects (NOEs) may be included at that stage. Compared to previous implementations of MFR-derived structure determination protocols this model-building algorithm offers improved stability and reliability. Furthermore, relative to CS-ROSETTA based methods, it provides faster performance and straightforward implementation with the option to easily include further types of restraints and additional energy terms.
Advanced numerical methods for three dimensional two-phase flow calculations
Energy Technology Data Exchange (ETDEWEB)
Toumi, I. [Laboratoire d`Etudes Thermiques des Reacteurs, Gif sur Yvette (France); Caruge, D. [Institut de Protection et de Surete Nucleaire, Fontenay aux Roses (France)
1997-07-01
This paper is devoted to new numerical methods developed for both one and three dimensional two-phase flow calculations. These methods are finite volume numerical methods and are based on the use of Approximate Riemann Solvers concepts to define convective fluxes versus mean cell quantities. The first part of the paper presents the numerical method for a one dimensional hyperbolic two-fluid model including differential terms as added mass and interface pressure. This numerical solution scheme makes use of the Riemann problem solution to define backward and forward differencing to approximate spatial derivatives. The construction of this approximate Riemann solver uses an extension of Roe`s method that has been successfully used to solve gas dynamic equations. As far as the two-fluid model is hyperbolic, this numerical method seems very efficient for the numerical solution of two-phase flow problems. The scheme was applied both to shock tube problems and to standard tests for two-fluid computer codes. The second part describes the numerical method in the three dimensional case. The authors discuss also some improvements performed to obtain a fully implicit solution method that provides fast running steady state calculations. Such a scheme is not implemented in a thermal-hydraulic computer code devoted to 3-D steady-state and transient computations. Some results obtained for Pressurised Water Reactors concerning upper plenum calculations and a steady state flow in the core with rod bow effect evaluation are presented. In practice these new numerical methods have proved to be stable on non staggered grids and capable of generating accurate non oscillating solutions for two-phase flow calculations.
Advanced numerical methods for three dimensional two-phase flow calculations
International Nuclear Information System (INIS)
Toumi, I.; Caruge, D.
1997-01-01
This paper is devoted to new numerical methods developed for both one and three dimensional two-phase flow calculations. These methods are finite volume numerical methods and are based on the use of Approximate Riemann Solvers concepts to define convective fluxes versus mean cell quantities. The first part of the paper presents the numerical method for a one dimensional hyperbolic two-fluid model including differential terms as added mass and interface pressure. This numerical solution scheme makes use of the Riemann problem solution to define backward and forward differencing to approximate spatial derivatives. The construction of this approximate Riemann solver uses an extension of Roe's method that has been successfully used to solve gas dynamic equations. As far as the two-fluid model is hyperbolic, this numerical method seems very efficient for the numerical solution of two-phase flow problems. The scheme was applied both to shock tube problems and to standard tests for two-fluid computer codes. The second part describes the numerical method in the three dimensional case. The authors discuss also some improvements performed to obtain a fully implicit solution method that provides fast running steady state calculations. Such a scheme is not implemented in a thermal-hydraulic computer code devoted to 3-D steady-state and transient computations. Some results obtained for Pressurised Water Reactors concerning upper plenum calculations and a steady state flow in the core with rod bow effect evaluation are presented. In practice these new numerical methods have proved to be stable on non staggered grids and capable of generating accurate non oscillating solutions for two-phase flow calculations
De novo analysis of electron impact mass spectra using fragmentation trees
International Nuclear Information System (INIS)
Hufsky, Franziska; Rempt, Martin; Rasche, Florian; Pohnert, Georg; Böcker, Sebastian
2012-01-01
Highlights: ► We present a method for de novo analysis of accurate mass EI mass spectra of small molecules. ► This method identifies the molecular ion and thus the molecular formula where the molecular ion is present in the spectrum. ► Fragmentation trees are constructed by automated signal extraction and evaluation. ► These trees explain relevant fragmentation reactions. ► This method will be very helpful in the automated analysis of unknown metabolites. - Abstract: The automated fragmentation analysis of high resolution EI mass spectra based on a fragmentation tree algorithm is introduced. Fragmentation trees are constructed from EI spectra by automated signal extraction and evaluation. These trees explain relevant fragmentation reactions and assign molecular formulas to fragments. The method enables the identification of the molecular ion and the molecular formula of a metabolite if the molecular ion is present in the spectrum. These identifications are independent of existing library knowledge and, thus, support assignment and structural elucidation of unknown compounds. The method works even if the molecular ion is of very low abundance or hidden under contaminants with higher masses. We apply the algorithm to a selection of 50 derivatized and underivatized metabolites and demonstrate that in 78% of cases the molecular ion can be correctly assigned. The automatically constructed fragmentation trees correspond very well to published mechanisms and allow the assignment of specific relevant fragments and fragmentation pathways even in the most complex EI-spectra in our dataset. This method will be very helpful in the automated analysis of metabolites that are not included in common libraries and it thus has the potential to support the explorative character of metabolomics studies.
Joshi, Priyanka; Chia, Sean; Habchi, Johnny; Knowles, Tuomas P J; Dobson, Christopher M; Vendruscolo, Michele
2016-03-14
The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.
Brooks–Corey Modeling by One-Dimensional Vertical Infiltration Method
Directory of Open Access Journals (Sweden)
Xuguang Xing
2018-05-01
Full Text Available The laboratory methods used for the soil water retention curve (SWRC construction and parameter estimation is time-consuming. A vertical infiltration method was proposed to estimate parameters α and n and to further construct the SWRC. In the present study, the relationships describing the cumulative infiltration and infiltration rate with the depth of the wetting front were established, and simplified expressions for estimating α and n parameters were proposed. The one-dimensional vertical infiltration experiments of four soils were conducted to verify if the proposed method would accurately estimate α and n. The fitted values of α and n, obtained from the RETC software, were consistent with the calculated values obtained from the infiltration method. The comparison between the measured SWRCs obtained from the centrifuge method and the calculated SWRCs that were based on the infiltration method displayed small values of root mean square error (RMSE, mean absolute percentage error (MAPE, and mean absolute error. SWMS_2D-based simulations of cumulative infiltration, based on the calculated α and n, remained consistent with the measured values due to small RMSE and MAPE values. The experiments verified the proposed one-dimensional vertical infiltration method, which has applications in field hydraulic parameter estimation.
Metabolite identification through multiple kernel learning on fragmentation trees.
Shen, Huibin; Dührkop, Kai; Böcker, Sebastian; Rousu, Juho
2014-06-15
Metabolite identification from tandem mass spectrometric data is a key task in metabolomics. Various computational methods have been proposed for the identification of metabolites from tandem mass spectra. Fragmentation tree methods explore the space of possible ways in which the metabolite can fragment, and base the metabolite identification on scoring of these fragmentation trees. Machine learning methods have been used to map mass spectra to molecular fingerprints; predicted fingerprints, in turn, can be used to score candidate molecular structures. Here, we combine fragmentation tree computations with kernel-based machine learning to predict molecular fingerprints and identify molecular structures. We introduce a family of kernels capturing the similarity of fragmentation trees, and combine these kernels using recently proposed multiple kernel learning approaches. Experiments on two large reference datasets show that the new methods significantly improve molecular fingerprint prediction accuracy. These improvements result in better metabolite identification, doubling the number of metabolites ranked at the top position of the candidates list. © The Author 2014. Published by Oxford University Press.
Calculation of two-dimensional thermal transients by the method of finite elements
International Nuclear Information System (INIS)
Fontoura Rodrigues, J.L.A. da.
1980-08-01
The unsteady linear heat conduction analysis throught anisotropic and/or heterogeneous matter, in either two-dimensional fields with any kind of geometry or three-dimensional fields with axial symmetry is presented. The boundary conditions and the internal heat generation are supposed time - independent. The solution is obtained by modal analysis employing the finite element method under Galerkin formulation. Optionally, it can be used with a reduced resolution method called Stoker Economizing Method wich allows a decrease on the program processing costs. (Author) [pt
A New Ensemble Method with Feature Space Partitioning for High-Dimensional Data Classification
Directory of Open Access Journals (Sweden)
Yongjun Piao
2015-01-01
Full Text Available Ensemble data mining methods, also known as classifier combination, are often used to improve the performance of classification. Various classifier combination methods such as bagging, boosting, and random forest have been devised and have received considerable attention in the past. However, data dimensionality increases rapidly day by day. Such a trend poses various challenges as these methods are not suitable to directly apply to high-dimensional datasets. In this paper, we propose an ensemble method for classification of high-dimensional data, with each classifier constructed from a different set of features determined by partitioning of redundant features. In our method, the redundancy of features is considered to divide the original feature space. Then, each generated feature subset is trained by a support vector machine, and the results of each classifier are combined by majority voting. The efficiency and effectiveness of our method are demonstrated through comparisons with other ensemble techniques, and the results show that our method outperforms other methods.
High efficiency hydrodynamic DNA fragmentation in a bubbling system
Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; Van Den Berg, Albert; Eijkel, Jan C.T.; Shui, Lingling
2017-01-01
DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling
[Fragment-based drug discovery: concept and aim].
Tanaka, Daisuke
2010-03-01
Fragment-Based Drug Discovery (FBDD) has been recognized as a newly emerging lead discovery methodology that involves biophysical fragment screening and chemistry-driven fragment-to-lead stages. Although fragments, defined as structurally simple and small compounds (typically FBDD primarily turns our attention to weakly but specifically binding fragments (hit fragments) as the starting point of medicinal chemistry. Hit fragments are then promoted to more potent lead compounds through linking or merging with another hit fragment and/or attaching functional groups. Another positive aspect of FBDD is ligand efficiency. Ligand efficiency is a useful guide in screening hit selection and hit-to-lead phases to achieve lead-likeness. Owing to these features, a number of successful applications of FBDD to "undruggable targets" (where HTS and other lead identification methods failed to identify useful lead compounds) have been reported. As a result, FBDD is now expected to complement more conventional methodologies. This review, as an introduction of the following articles, will summarize the fundamental concepts of FBDD and will discuss its advantages over other conventional drug discovery approaches.
One-dimensional treatment of polyatomic crystals by the Laplace transform method
International Nuclear Information System (INIS)
Rosato, A.; Santana, P.H.A.
1976-01-01
The one dimensional periodic potential problem is solved using the Laplace transform method and a condensed expression for the relation E x k and effective mass for one electron in a polyatomic structure is determined. Applications related to the effect of the asymmetry of the potential upon the one dimensional band structure are discussed [pt
International Nuclear Information System (INIS)
Yoo, Sung Min; Kim, Yoon Young
2007-01-01
This work is concerned with the topology optimization of three-dimensional cooling fins or heat sinks. Motivated by earlier success of the Internal Element Connectivity Method (I-ECP) method in two dimensional problems, the extension of I-ECP to three-dimensional problems is carried out. The main efforts were made to maintain the numerical trouble-free characteristics of I-ECP for full three-dimensional problems; a serious numerical problem appearing in thermal topology optimization is erroneous temperature undershooting. The effectiveness of the present implementation was checked through the design optimization of three-dimensional fins
A two-dimensional adaptive numerical grids generation method and its realization
International Nuclear Information System (INIS)
Xu Tao; Shui Hongshou
1998-12-01
A two-dimensional adaptive numerical grids generation method and its particular realization is discussed. This method is effective and easy to realize if the control functions are given continuously, and the grids for some regions is showed in this case. For Computational Fluid Dynamics, because the control values of adaptive grids-numerical solution is given in dispersed form, it is needed to interpolate these values to get the continuous control functions. These interpolation techniques are discussed, and some efficient adaptive grids are given. A two-dimensional fluid dynamics example was also given
Development of three-dimensional individual bubble-velocity measurement method by bubble tracking
International Nuclear Information System (INIS)
Kanai, Taizo; Furuya, Masahiro; Arai, Takahiro; Shirakawa, Kenetsu; Nishi, Yoshihisa
2012-01-01
A gas-liquid two-phase flow in a large diameter pipe exhibits a three-dimensional flow structure. Wire-Mesh Sensor (WMS) consists of a pair of parallel wire layers located at the cross section of a pipe. Both the parallel wires cross at 90o with a small gap and each intersection acts as an electrode. The WMS allows the measurement of the instantaneous two-dimensional void-fraction distribution over the cross-section of a pipe, based on the difference between the local instantaneous conductivity of the two-phase flow. Furthermore, the WMS can acquire a phasic-velocity on the basis of the time lag of void signals between two sets of WMS. Previously, the acquired phasic velocity was one-dimensional with time-averaged distributions. The authors propose a method to estimate the three-dimensional bubble-velocity individually WMS data. The bubble velocity is determined by the tracing method. In this tracing method, each bubble is separated from WMS signal, volume and center coordinates of the bubble is acquired. Two bubbles with near volume at two WMS are considered as the same bubble and bubble velocity is estimated from the displacement of the center coordinates of the two bubbles. The validity of this method is verified by a swirl flow. The proposed method can successfully visualize a swirl flow structure and the results of this method agree with the results of cross-correlation analysis. (author)
Development of two dimensional electrophoresis method using single chain DNA
International Nuclear Information System (INIS)
Ikeda, Junichi; Hidaka, So
1998-01-01
By combining a separation method due to molecular weight and a method to distinguish difference of mono-bases, it was aimed to develop a two dimensional single chain DNA labeled with Radioisotope (RI). From electrophoretic pattern difference of parent and variant strands, it was investigated to isolate the root module implantation control gene. At first, a Single Strand Conformation Polymorphism (SSCP) method using concentration gradient gel was investigated. As a result, it was formed that intervals between double chain and single chain DNAs expanded, but intervals of both single chain DNAs did not expand. On next, combination of non-modified acrylic amide electrophoresis method and Denaturing Gradient-Gel Electrophoresis (DGGE) method was examined. As a result, hybrid DNA developed by two dimensional electrophoresis arranged on two lines. But, among them a band of DNA modified by high concentration of urea could not be found. Therefore, in this fiscal year's experiments, no preferable result could be obtained. By the used method, it was thought to be impossible to detect the differences. (G.K.)
Semi-implicit method for three-dimensional compressible MHD simulation
International Nuclear Information System (INIS)
Harned, D.S.; Kerner, W.
1984-03-01
A semi-implicit method for solving the full compressible MHD equations in three dimensions is presented. The method is unconditionally stable with respect to the fast compressional modes. The time step is instead limited by the slower shear Alfven motion. The computing time required for one time step is essentially the same as for explicit methods. Linear stability limits are derived and verified by three-dimensional tests on linear waves in slab geometry. (orig.)
Three-dimensional dynamics of protostellar evolution
International Nuclear Information System (INIS)
Cook, T.L.
1977-06-01
A three-dimensional finite difference numerical methodology was developed for self-gravitating, rotating gaseous systems. The fully nonlinear equations for time-varying fluid dynamics are solved by high speed computer in a cylindrical coordinate system rotating with an instantaneous angular velocity, selected such that the net angular momentum relative to the rotating frame is zero. The time-dependent adiabatic collapse of gravitationally bound, rotating, protostellar clouds is studied for specified uniform and nonuniform initial conditions. Uniform clouds can form axisymmetric, rotating toroidal configurations. If the thermal pressure is high, nonuniform clouds can also collapse to axisymmetric toroids. For low thermal pressures, however, the collapsing cloud is unstable to initial perturbations. The fragmentation of protostellar clouds is investigated by studying the response of rotating, self-gravitating, equilibrium toroids to non-axisymmetric perturbations. The detailed evolution of the fragmenting toroid depends upon a non-dimensional function of the initial entropy, the total mass in the toroid, the angular velocity of rotation, and the number of perturbation wavelengths around the circumference of the toroid. For low and intermediate entropies, the configuration develops into co-rotating components with spiral streamers. In the spiral regions retrograde vortices are observed in some examples. For high levels of entropy, barred spirals can exist as intermediate states of the fragmentation
High dimensional model representation method for fuzzy structural dynamics
Adhikari, S.; Chowdhury, R.; Friswell, M. I.
2011-03-01
Uncertainty propagation in multi-parameter complex structures possess significant computational challenges. This paper investigates the possibility of using the High Dimensional Model Representation (HDMR) approach when uncertain system parameters are modeled using fuzzy variables. In particular, the application of HDMR is proposed for fuzzy finite element analysis of linear dynamical systems. The HDMR expansion is an efficient formulation for high-dimensional mapping in complex systems if the higher order variable correlations are weak, thereby permitting the input-output relationship behavior to be captured by the terms of low-order. The computational effort to determine the expansion functions using the α-cut method scales polynomically with the number of variables rather than exponentially. This logic is based on the fundamental assumption underlying the HDMR representation that only low-order correlations among the input variables are likely to have significant impacts upon the outputs for most high-dimensional complex systems. The proposed method is first illustrated for multi-parameter nonlinear mathematical test functions with fuzzy variables. The method is then integrated with a commercial finite element software (ADINA). Modal analysis of a simplified aircraft wing with fuzzy parameters has been used to illustrate the generality of the proposed approach. In the numerical examples, triangular membership functions have been used and the results have been validated against direct Monte Carlo simulations. It is shown that using the proposed HDMR approach, the number of finite element function calls can be reduced without significantly compromising the accuracy.
Prakash, Celine; Haeseler, Arndt Von
2017-03-01
RNA sequencing (RNA-seq) has emerged as the method of choice for measuring the expression of RNAs in a given cell population. In most RNA-seq technologies, sequencing the full length of RNA molecules requires fragmentation into smaller pieces. Unfortunately, the issue of nonuniform sequencing coverage across a genomic feature has been a concern in RNA-seq and is attributed to biases for certain fragments in RNA-seq library preparation and sequencing. To investigate the expected coverage obtained from fragmentation, we develop a simple fragmentation model that is independent of bias from the experimental method and is not specific to the transcript sequence. Essentially, we enumerate all configurations for maximal placement of a given fragment length, F, on transcript length, T, to represent every possible fragmentation pattern, from which we compute the expected coverage profile across a transcript. We extend this model to incorporate general empirical attributes such as read length, fragment length distribution, and number of molecules of the transcript. We further introduce the fragment starting-point, fragment coverage, and read coverage profiles. We find that the expected profiles are not uniform and that factors such as fragment length to transcript length ratio, read length to fragment length ratio, fragment length distribution, and number of molecules influence the variability of coverage across a transcript. Finally, we explore a potential application of the model where, with simulations, we show that it is possible to correctly estimate the transcript copy number for any transcript in the RNA-seq experiment.
Multi-GPU accelerated three-dimensional FDTD method for electromagnetic simulation.
Nagaoka, Tomoaki; Watanabe, Soichi
2011-01-01
Numerical simulation with a numerical human model using the finite-difference time domain (FDTD) method has recently been performed in a number of fields in biomedical engineering. To improve the method's calculation speed and realize large-scale computing with the numerical human model, we adapt three-dimensional FDTD code to a multi-GPU environment using Compute Unified Device Architecture (CUDA). In this study, we used NVIDIA Tesla C2070 as GPGPU boards. The performance of multi-GPU is evaluated in comparison with that of a single GPU and vector supercomputer. The calculation speed with four GPUs was approximately 3.5 times faster than with a single GPU, and was slightly (approx. 1.3 times) slower than with the supercomputer. Calculation speed of the three-dimensional FDTD method using GPUs can significantly improve with an expanding number of GPUs.
Saitou, Sona; Iijima, Jun; Fujimoto, Mayu; Mochizuki, Yuji; Okuwaki, Koji; Doi, Hideo; Komeiji, Yuto
2018-01-01
We have applied Google's TensorFlow deep learning toolkit to recognize the visualized results of the fragment molecular orbital (FMO) calculations. Typical protein structures of alpha-helix and beta-sheet provide some characteristic patterns in the two-dimensional map of inter-fragment interaction energy termed as IFIE-map (Kurisaki et al., Biophys. Chem. 130 (2007) 1). A thousand of IFIE-map images with labels depending on the existences of alpha-helix and beta-sheet were prepared by employi...
Fragmentation in DNA double-strand breaks
International Nuclear Information System (INIS)
Wei Zhiyong; Suzhou Univ., Suzhou; Zhang Lihui; Li Ming; Fan Wo; Xu Yujie
2005-01-01
DNA double strand breaks are important lesions induced by irradiations. Random breakage model or quantification supported by this concept is suitable to analyze DNA double strand break data induced by low LET radiation, but deviation from random breakage model is more evident in high LET radiation data analysis. In this work we develop a new method, statistical fragmentation model, to analyze the fragmentation process of DNA double strand breaks. After charged particles enter the biological cell, they produce ionizations along their tracks, and transfer their energies to the cells and break the cellular DNA strands into fragments. The probable distribution of the fragments is obtained under the condition in which the entropy is maximum. Under the approximation E≅E 0 + E 1 l + E 2 l 2 , the distribution functions are obtained as exp(αl + βl 2 ). There are two components, the one proportional to exp(βl 2 ), mainly contributes to the low mass fragment yields, the other component, proportional to exp(αl), decreases slowly as the mass of the fragments increases. Numerical solution of the constraint equations provides parameters α and β. Experimental data, especially when the energy deposition is higher, support the statistical fragmentation model. (authors)
A simple three dimensional wide-angle beam propagation method
Ma, Changbao; van Keuren, Edward
2006-05-01
The development of three dimensional (3-D) waveguide structures for chip scale planar lightwave circuits (PLCs) is hampered by the lack of effective 3-D wide-angle (WA) beam propagation methods (BPMs). We present a simple 3-D wide-angle beam propagation method (WA-BPM) using Hoekstra’s scheme along with a new 3-D wave equation splitting method. The applicability, accuracy and effectiveness of our method are demonstrated by applying it to simulations of wide-angle beam propagation and comparing them with analytical solutions.
FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.
Bhattacharya, Debswapna; Adhikari, Badri; Li, Jilong; Cheng, Jianlin
2016-07-01
Speed, accuracy and robustness of building protein fragment library have important implications in de novo protein structure prediction since fragment-based methods are one of the most successful approaches in template-free modeling (FM). Majority of the existing fragment detection methods rely on database-driven search strategies to identify candidate fragments, which are inherently time-consuming and often hinder the possibility to locate longer fragments due to the limited sizes of databases. Also, it is difficult to alleviate the effect of noisy sequence-based predicted features such as secondary structures on the quality of fragment. Here, we present FRAGSION, a database-free method to efficiently generate protein fragment library by sampling from an Input-Output Hidden Markov Model. FRAGSION offers some unique features compared to existing approaches in that it (i) is lightning-fast, consuming only few seconds of CPU time to generate fragment library for a protein of typical length (300 residues); (ii) can generate dynamic-size fragments of any length (even for the whole protein sequence) and (iii) offers ways to handle noise in predicted secondary structure during fragment sampling. On a FM dataset from the most recent Critical Assessment of Structure Prediction, we demonstrate that FGRAGSION provides advantages over the state-of-the-art fragment picking protocol of ROSETTA suite by speeding up computation by several orders of magnitude while achieving comparable performance in fragment quality. Source code and executable versions of FRAGSION for Linux and MacOS is freely available to non-commercial users at http://sysbio.rnet.missouri.edu/FRAGSION/ It is bundled with a manual and example data. chengji@missouri.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Calculation of two-dimensional thermal transients by the finite element method
International Nuclear Information System (INIS)
Fontoura Rodrigues, J.L.A. da; Barcellos, C.S. de
1981-01-01
The linear heat conduction through anisotropic and/or heterogeneous matter, in either two-dimensional fields with any kind of geometry or three-dimensional fields with axial symmetry is analysed. It only accepts time-independent boundary conditions and it is possible to have internal heat generation. The solution is obtained by modal analysis employing the finite element method under Galerkin formulation. (Author) [pt
International Nuclear Information System (INIS)
Montaudon, M.; Laffon, E.; Berger, P.; Corneloup, O.; Latrabe, V.; Laurent, F.
2006-01-01
This study compared a three-dimensional volumetric threshold-based method to a two-dimensional Simpson's rule based short-axis multiplanar method for measuring right (RV) and left ventricular (LV) volumes, stroke volumes, and ejection fraction using electrocardiography-gated multidetector computed tomography (MDCT) data sets. End-diastolic volume (EDV) and end-systolic volume (ESV) of RV and LV were measured independently and blindly by two observers from contrast-enhanced MDCT images using commercial software in 18 patients. For RV and LV the three-dimensionally calculated EDV and ESV values were smaller than those provided by two-dimensional short axis (10%, 5%, 15% and 26% differences respectively). Agreement between the two methods was found for LV (EDV/ESV: r=0.974/0.910, ICC=0.905/0.890) but not for RV (r=0.882/0.930, ICC=0.663/0.544). Measurement errors were significant only for EDV of LV using the two-dimensional method. Similar reproducibility was found for LV measurements, but the three-dimensional method provided greater reproducibility for RV measurements than the two-dimensional. The threshold value supported three-dimensional method provides reproducible cardiac ventricular volume measurements, comparable to those obtained using the short-axis Simpson based method. (orig.)
Directory of Open Access Journals (Sweden)
Virginia H. Garrison
2012-03-01
Full Text Available In response to dramatic losses of reef-building corals and ongoing lack of recovery, a small-scale coral transplant project was initiated in the Caribbean (U.S. Virgin Islands in 1999 and was followed for 12 years. The primary objectives were to (1 identify a source of coral colonies for transplantation that would not result in damage to reefs, (2 test the feasibility of transplanting storm-generated coral fragments, and (3 develop a simple, inexpensive method for transplanting fragments that could be conducted by the local community. The ultimate goal was to enhance abundance of threatened reef-building species on local reefs. Storm-produced coral fragments of two threatened reef-building species [Acropora palmata and A. cervicornis (Acroporidae] and another fast-growing species [Porites porites (Poritidae] were collected from environments hostile to coral fragment survival and transplanted to degraded reefs. Inert nylon cable ties were used to attach transplanted coral fragments to dead coral substrate. Survival of 75 reference colonies and 60 transplants was assessed over 12 years. Only 9% of colonies were alive after 12 years: no A. cervicornis; 3% of A. palmata transplants and 18% of reference colonies; and 13% of P. porites transplants and 7% of reference colonies. Mortality rates for all species were high and were similar for transplant and reference colonies. Physical dislodgement resulted in the loss of 56% of colonies, whereas 35% died in place. Only A. palmata showed a difference between transplant and reference colony survival and that was in the first year only. Location was a factor in survival only for A. palmata reference colonies and after year 10. Even though the tested methods and concepts were proven effective in the field over the 12-year study, they do not present a solution. No coral conservation strategy will be effective until underlying intrinsic and/or extrinsic factors driving high mortality rates are understood and
A Comparison of Methods for Estimating the Determinant of High-Dimensional Covariance Matrix
Hu, Zongliang; Dong, Kai; Dai, Wenlin; Tong, Tiejun
2017-01-01
The determinant of the covariance matrix for high-dimensional data plays an important role in statistical inference and decision. It has many real applications including statistical tests and information theory. Due to the statistical and computational challenges with high dimensionality, little work has been proposed in the literature for estimating the determinant of high-dimensional covariance matrix. In this paper, we estimate the determinant of the covariance matrix using some recent proposals for estimating high-dimensional covariance matrix. Specifically, we consider a total of eight covariance matrix estimation methods for comparison. Through extensive simulation studies, we explore and summarize some interesting comparison results among all compared methods. We also provide practical guidelines based on the sample size, the dimension, and the correlation of the data set for estimating the determinant of high-dimensional covariance matrix. Finally, from a perspective of the loss function, the comparison study in this paper may also serve as a proxy to assess the performance of the covariance matrix estimation.
A Comparison of Methods for Estimating the Determinant of High-Dimensional Covariance Matrix
Hu, Zongliang
2017-09-27
The determinant of the covariance matrix for high-dimensional data plays an important role in statistical inference and decision. It has many real applications including statistical tests and information theory. Due to the statistical and computational challenges with high dimensionality, little work has been proposed in the literature for estimating the determinant of high-dimensional covariance matrix. In this paper, we estimate the determinant of the covariance matrix using some recent proposals for estimating high-dimensional covariance matrix. Specifically, we consider a total of eight covariance matrix estimation methods for comparison. Through extensive simulation studies, we explore and summarize some interesting comparison results among all compared methods. We also provide practical guidelines based on the sample size, the dimension, and the correlation of the data set for estimating the determinant of high-dimensional covariance matrix. Finally, from a perspective of the loss function, the comparison study in this paper may also serve as a proxy to assess the performance of the covariance matrix estimation.
A Comparison of Methods for Estimating the Determinant of High-Dimensional Covariance Matrix.
Hu, Zongliang; Dong, Kai; Dai, Wenlin; Tong, Tiejun
2017-09-21
The determinant of the covariance matrix for high-dimensional data plays an important role in statistical inference and decision. It has many real applications including statistical tests and information theory. Due to the statistical and computational challenges with high dimensionality, little work has been proposed in the literature for estimating the determinant of high-dimensional covariance matrix. In this paper, we estimate the determinant of the covariance matrix using some recent proposals for estimating high-dimensional covariance matrix. Specifically, we consider a total of eight covariance matrix estimation methods for comparison. Through extensive simulation studies, we explore and summarize some interesting comparison results among all compared methods. We also provide practical guidelines based on the sample size, the dimension, and the correlation of the data set for estimating the determinant of high-dimensional covariance matrix. Finally, from a perspective of the loss function, the comparison study in this paper may also serve as a proxy to assess the performance of the covariance matrix estimation.
Searching Fragment Spaces with feature trees.
Lessel, Uta; Wellenzohn, Bernd; Lilienthal, Markus; Claussen, Holger
2009-02-01
Virtual combinatorial chemistry easily produces billions of compounds, for which conventional virtual screening cannot be performed even with the fastest methods available. An efficient solution for such a scenario is the generation of Fragment Spaces, which encode huge numbers of virtual compounds by their fragments/reagents and rules of how to combine them. Similarity-based searches can be performed in such spaces without ever fully enumerating all virtual products. Here we describe the generation of a huge Fragment Space encoding about 5 * 10(11) compounds based on established in-house synthesis protocols for combinatorial libraries, i.e., we encode practically evaluated combinatorial chemistry protocols in a machine readable form, rendering them accessible to in silico search methods. We show how such searches in this Fragment Space can be integrated as a first step in an overall workflow. It reduces the extremely huge number of virtual products by several orders of magnitude so that the resulting list of molecules becomes more manageable for further more elaborated and time-consuming analysis steps. Results of a case study are presented and discussed, which lead to some general conclusions for an efficient expansion of the chemical space to be screened in pharmaceutical companies.
A novel three-dimensional mesh deformation method based on sphere relaxation
International Nuclear Information System (INIS)
Zhou, Xuan; Li, Shuixiang
2015-01-01
In our previous work (2013) [19], we developed a disk relaxation based mesh deformation method for two-dimensional mesh deformation. In this paper, the idea of the disk relaxation is extended to the sphere relaxation for three-dimensional meshes with large deformations. We develop a node based pre-displacement procedure to apply initial movements on nodes according to their layer indices. Afterwards, the nodes are moved locally by the improved sphere relaxation algorithm to transfer boundary deformations and increase the mesh quality. A three-dimensional mesh smoothing method is also adopted to prevent the occurrence of the negative volume of elements, and further improve the mesh quality. Numerical applications in three-dimension including the wing rotation, bending beam and morphing aircraft are carried out. The results demonstrate that the sphere relaxation based approach generates the deformed mesh with high quality, especially regarding complex boundaries and large deformations
A novel three-dimensional mesh deformation method based on sphere relaxation
Energy Technology Data Exchange (ETDEWEB)
Zhou, Xuan [Department of Mechanics & Engineering Science, College of Engineering, Peking University, Beijing, 100871 (China); Institute of Applied Physics and Computational Mathematics, Beijing, 100094 (China); Li, Shuixiang, E-mail: lsx@pku.edu.cn [Department of Mechanics & Engineering Science, College of Engineering, Peking University, Beijing, 100871 (China)
2015-10-01
In our previous work (2013) [19], we developed a disk relaxation based mesh deformation method for two-dimensional mesh deformation. In this paper, the idea of the disk relaxation is extended to the sphere relaxation for three-dimensional meshes with large deformations. We develop a node based pre-displacement procedure to apply initial movements on nodes according to their layer indices. Afterwards, the nodes are moved locally by the improved sphere relaxation algorithm to transfer boundary deformations and increase the mesh quality. A three-dimensional mesh smoothing method is also adopted to prevent the occurrence of the negative volume of elements, and further improve the mesh quality. Numerical applications in three-dimension including the wing rotation, bending beam and morphing aircraft are carried out. The results demonstrate that the sphere relaxation based approach generates the deformed mesh with high quality, especially regarding complex boundaries and large deformations.
LINKAGE ANALYSIS BY 2-DIMENSIONAL DNA TYPING
MEERMAN, GJT; MULLAART, E; VANDERMEULEN, MA; DENDAAS, JHG; MOROLLI, B; UITTERLINDEN, AG; VIJG, J
1993-01-01
In two-dimensional (2-D) DNA typing, genomic DNA fragments are separated, first according to size by electrophoresis in a neutral polyacrylamide gel and second according to sequence by denaturing gradient gel electrophoresis, followed by hybridization analysis using micro- and minisatellite core
Linkage analysis by two-dimensional DNA typing
te Meerman, G J; Mullaart, E; Meulen ,van der Martin; den Daas, J H; Morolli, B; Uitterlinden, A G; Vijg, J
1993-01-01
In two-dimensional (2-D) DNA typing, genomic DNA fragments are separated, first according to size by electrophoresis in a neutral polyacrylamide gel and second according to sequence by denaturing gradient gel electrophoresis, followed by hybridization analysis using micro- and minisatellite core
Revisiting the Lund Fragmentation Model
International Nuclear Information System (INIS)
Andersson, B.; Nilsson, A.
1992-10-01
We present a new method to implement the Lund Model fragmentation distributions for multi-gluon situations. The method of Sjoestrand, implemented in the well-known Monte Carlo simulation program JETSET, is robust and direct and according to his findings there are no observable differences between different ways to implement his scheme. His method can be described as a space-time method because the breakup proper time plays a major role. The method described in this paper is built on energy-momentum space methods. We make use of the χ-curve, which is defined directly from the energy momentum vectors of the partons. We have shown that the χ-curve describes the breakup properties and the final state energy momentum distributions in the mean. We present a method to find the variations around the χ-curve, which also implements the basic Lund Model fragmentation distributions (the area-law and the corresponding iterative cascade). We find differences when comparing the corresponding Monte Carlo implementation REVJET to the JETSET distributions inside the gluon jets. (au)
Girard, Catherine; Dufour, Anne-Béatrice; Charruault, Anne-Lise; Renaud, Sabrina
2018-01-01
Benthic foraminifera have been used as proxies for various paleoenvironmental variables such as food availability, carbon flux from surface waters, microhabitats, and indirectly water depth. Estimating assemblage composition based on morphotypes, as opposed to genus- or species-level identification, potentially loses important ecological information but opens the way to the study of ancient time periods. However, the ability to accurately constrain benthic foraminiferal assemblages has been questioned when the most abundant foraminifera are fragile agglutinated forms, particularly prone to fragmentation. Here we test an alternate method for accurately estimating the composition of fragmented assemblages. The cumulated area per morphotype method is assessed, i.e., the sum of the area of all tests or fragments of a given morphotype in a sample. The percentage of each morphotype is calculated as a portion of the total cumulated area. Percentages of different morphotypes based on counting and cumulated area methods are compared one by one and analyzed using principal component analyses, a co-inertia analysis, and Shannon diversity indices. Morphotype percentages are further compared to an estimate of water depth based on microfacies description. Percentages of the morphotypes are not related to water depth. In all cases, counting and cumulated area methods deliver highly similar results, suggesting that the less time-consuming traditional counting method may provide robust estimates of assemblages. The size of each morphotype may deliver paleobiological information, for instance regarding biomass, but should be considered carefully due to the pervasive issue of fragmentation.
International Nuclear Information System (INIS)
Saxon, D.H.
1985-10-01
The paper reviews studies on jet fragmentation. The subject is discussed under the topic headings: fragmentation models, charged particle multiplicity, bose-einstein correlations, identified hadrons in jets, heavy quark fragmentation, baryon production, gluon and quark jets compared, the string effect, and two successful models. (U.K.)
Jenkins, J A; Draugelis-Dale, R O; Pinkney, A E; Iwanowicz, L R; Blazer, V S
2015-03-15
Declining harvests of yellow perch, Perca flavescens, in urbanized watersheds of Chesapeake Bay have prompted investigations of their reproductive fitness. The purpose of this study was to establish a flow cytometric technique for DNA analysis of fixed samples sent from the field to provide reliable gamete quality measurements. Similar to the sperm chromatin structure assay, measures were made on the susceptibility of nuclear DNA to acid-induced denaturation, but used fixed rather than live or thawed cells. Nuclei were best exposed to the acid treatment for 1 minute at 37 °C followed by the addition of cold (4 °C) propidium iodide staining solution before flow cytometry. The rationale for protocol development is presented graphically through cytograms. Field results collected in 2008 and 2009 revealed DNA fragmentation up to 14.5%. In 2008, DNA fragmentation from the more urbanized watersheds was significantly greater than from reference sites (P = 0.026) and in 2009, higher percentages of haploid testicular cells were noted from the less urbanized watersheds (P = 0.032) indicating better reproductive condition at sites with less urbanization. For both years, total and progressive live sperm motilities by computer-assisted sperm motion analysis ranged from 19.1% to 76.5%, being significantly higher at the less urbanized sites (P < 0.05). This flow cytometric method takes advantage of the propensity of fragmented DNA to be denatured under standard conditions, or 1 minute at 37 °C with 10% buffered formalin-fixed cells. The study of fixed sperm makes possible the restrospective investigation of germplasm fragmentation, spermatogenic ploidy patterns, and chromatin compaction levels from samples translocated over distance and time. The protocol provides an approach that can be modified for other species across taxa. Published by Elsevier Inc.
Missing Fragments: Detecting Cooperative Binding in Fragment-Based Drug Design
2012-01-01
The aim of fragment-based drug design (FBDD) is to identify molecular fragments that bind to alternate subsites within a given binding pocket leading to cooperative binding when linked. In this study, the binding of fragments to human phenylethanolamine N-methyltransferase is used to illustrate how (a) current protocols may fail to detect fragments that bind cooperatively, (b) theoretical approaches can be used to validate potential hits, and (c) apparent false positives obtained when screening against cocktails of fragments may in fact indicate promising leads. PMID:24900472
Moderator feedback effects in two-dimensional nodal methods for pressurized water reactor analysis
International Nuclear Information System (INIS)
Downar, T.J.
1987-01-01
A method was developed for incorporating moderator feedback effects in two-dimensional nodal codes used for pressurized water reactor (PWR) neutronic analysis. Equations for the assembly average quality and density are developed in terms of the assembly power calculated in two dimensions. The method is validated with a Westinghouse PWR using the Electric Power Research Institute code SIMULATE-E. Results show a several percent improvement is achieved in the two-dimensional power distribution prediction compared to methods without moderator feedback
The Validity of Dimensional Regularization Method on Fractal Spacetime
Directory of Open Access Journals (Sweden)
Yong Tao
2013-01-01
Full Text Available Svozil developed a regularization method for quantum field theory on fractal spacetime (1987. Such a method can be applied to the low-order perturbative renormalization of quantum electrodynamics but will depend on a conjectural integral formula on non-integer-dimensional topological spaces. The main purpose of this paper is to construct a fractal measure so as to guarantee the validity of the conjectural integral formula.
DNA fragments assembly based on nicking enzyme system.
Directory of Open Access Journals (Sweden)
Rui-Yan Wang
Full Text Available A couple of DNA ligation-independent cloning (LIC methods have been reported to meet various requirements in metabolic engineering and synthetic biology. The principle of LIC is the assembly of multiple overlapping DNA fragments by single-stranded (ss DNA overlaps annealing. Here we present a method to generate single-stranded DNA overlaps based on Nicking Endonucleases (NEases for LIC, the method was termed NE-LIC. Factors related to cloning efficiency were optimized in this study. This NE-LIC allows generating 3'-end or 5'-end ss DNA overlaps of various lengths for fragments assembly. We demonstrated that the 10 bp/15 bp overlaps had the highest DNA fragments assembling efficiency, while 5 bp/10 bp overlaps showed the highest efficiency when T4 DNA ligase was added. Its advantage over Sequence and Ligation Independent Cloning (SLIC and Uracil-Specific Excision Reagent (USER was obvious. The mechanism can be applied to many other LIC strategies. Finally, the NEases based LIC (NE-LIC was successfully applied to assemble a pathway of six gene fragments responsible for synthesizing microbial poly-3-hydroxybutyrate (PHB.
Evaluation and analysis of geological condition of in-situ fragmentation leaching uranium
International Nuclear Information System (INIS)
Yang Jianming; Tan Kaixuan; Huang Xiaonai
2003-01-01
The ore geological condition, hydrogeological condition, engineering geological condition and technological mineralogical character of in-situ fragmentation leaching uranium are analyzed, and it is considered that the implementation of in-situ fragmentation leaching uranium technology is decided by different geological factor. Previously prospecting and geological condition evaluation of uranium ore is based on traditional mining method. If in-situ fragmentation leaching uranium method is adopted, one must re-evaluate previously prospected deposits before they are mined, or one must evaluate new prospecting deposits according to geological conditions of in-situ fragmentation leaching uranium method. The feasibility evaluation method of uranium deposit by in-situ fragmentation leaching uranium put forward by B. N. Mociniets is introducd, and it is considered that B. N. Mociniets method has guidable significance for geological condition evaluation before uranium deposits are mined. A feasibility study is done by applying B. N. Mociniets method to a uranium deposit. (authors)
Energy Technology Data Exchange (ETDEWEB)
Rao, Laxminarsimha V., E-mail: laxman@iitk.ac.in [Mechanics and Applied Mathematics Group, Department of Mechanical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016 (India); Roy, Subhradeep [Department of Biomedical Engineering and Mechanics (MC 0219), Virginia Tech, 495 Old Turner Street, Blacksburg, VA 24061 (United States); Das, Sovan Lal [Mechanics and Applied Mathematics Group, Department of Mechanical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016 (India)
2017-01-15
We estimate the equilibrium size distribution of cholesterol rich micro-domains on a lipid bilayer by solving Smoluchowski equation for coagulation and fragmentation. Towards this aim, we first derive the coagulation kernels based on the diffusion behaviour of domains moving in a two dimensional membrane sheet, as this represents the reality better. We incorporate three different diffusion scenarios of domain diffusion into our coagulation kernel. Subsequently, we investigate the influence of the parameters in our model on the coagulation and fragmentation behaviour. The observed behaviours of the coagulation and fragmentation kernels are also manifested in the equilibrium domain size distribution and its first moment. Finally, considering the liquid domains diffusing in a supported lipid bilayer, we fit the equilibrium domain size distribution to a benchmark solution.
Simulations of High Speed Fragment Trajectories
Yeh, Peter; Attaway, Stephen; Arunajatesan, Srinivasan; Fisher, Travis
2017-11-01
Flying shrapnel from an explosion are capable of traveling at supersonic speeds and distances much farther than expected due to aerodynamic interactions. Predicting the trajectories and stable tumbling modes of arbitrary shaped fragments is a fundamental problem applicable to range safety calculations, damage assessment, and military technology. Traditional approaches rely on characterizing fragment flight using a single drag coefficient, which may be inaccurate for fragments with large aspect ratios. In our work we develop a procedure to simulate trajectories of arbitrary shaped fragments with higher fidelity using high performance computing. We employ a two-step approach in which the force and moment coefficients are first computed as a function of orientation using compressible computational fluid dynamics. The force and moment data are then input into a six-degree-of-freedom rigid body dynamics solver to integrate trajectories in time. Results of these high fidelity simulations allow us to further understand the flight dynamics and tumbling modes of a single fragment. Furthermore, we use these results to determine the validity and uncertainty of inexpensive methods such as the single drag coefficient model.
Pseudo three-dimensional modeling of particle-fuel packing using distinct element method
International Nuclear Information System (INIS)
Yuki, Daisuke; Takata, Takashi; Yamaguchi, Akira
2007-01-01
Vibration-based packing of sphere-pac fuel is a key technology in a nuclear fuel manufacturing. In the production process of sphere-pac fuel, a Mixed Oxide (MOX) fuel is formed to spherical form and is packed in a cladding tube by adding a vibration force. In the present study, we have developed a numerical simulation method to investigate the behavior of the particles in a vibrated tube using the Distinct Element Method (DEM). In general, the DEM requires a significant computational cost. Therefore we propose a new approach in which a small particle can move through the space between three larger particles even in the two-dimensional simulation. We take into account an equivalent three-dimensional effect in the equations of motion. Thus it is named pseudo three-dimensional modeling. (author)
Varnes, Jeffrey G; Geschwindner, Stefan; Holmquist, Christopher R; Forst, Janet; Wang, Xia; Dekker, Niek; Scott, Clay W; Tian, Gaochao; Wood, Michael W; Albert, Jeffrey S
2016-01-01
Fragment-based drug design (FBDD) relies on direct elaboration of fragment hits and typically requires high resolution structural information to guide optimization. In fragment-assisted drug discovery (FADD), fragments provide information to guide selection and design but do not serve as starting points for elaboration. We describe FADD and high-throughput screening (HTS) campaign strategies conducted in parallel against PDE10A where fragment hit co-crystallography was not available. The fragment screen led to prioritized fragment hits (IC50's ∼500μM), which were used to generate a hypothetical core scaffold. Application of this scaffold as a filter to HTS output afforded a 4μM hit, which, after preparation of a small number of analogs, was elaborated into a 16nM lead. This approach highlights the strength of FADD, as fragment methods were applied despite the absence of co-crystallographical information to efficiently identify a lead compound for further optimization. Copyright © 2015 Elsevier Ltd. All rights reserved.
NMR screening in fragment-based drug design: a practical guide.
Kim, Hai-Young; Wyss, Daniel F
2015-01-01
Fragment-based drug design (FBDD) comprises both fragment-based screening (FBS) to find hits and elaboration of these hits to lead compounds. Typical fragment hits have lower molecular weight (FBDD since it identifies and localizes the binding site of weakly interacting hits on the target protein. Here we describe ligand-based NMR methods for hit identification from fragment libraries and for functional cross-validation of primary hits.
Labeling and stability of radiolabeled antibody fragments by a direct 99mTc-labeling method
International Nuclear Information System (INIS)
Pak, K.Y.; Nedelman, M.A.; Tam, S.H.; Wilson, E.; Daddona, P.E.
1992-01-01
The in vitro labeling and stability of 99m Tc-labeled antibody Fab' fragments prepared by a direct labeling technique were evaluated. Eight antibody fragments derived from murine IgG1 (N = 5), IgG2a (N = 2) and IgG3 (N = 1) isotypes were labeled with a preformed 99m Tc-D-glucarate complex. No loss of radioactivity incorporation was observed for all the 99m Tc-labeled antibody fragments after 24 h incubation at 37 o C. 99m Tc-labeled antibody fragments (IgG1, N = 2; IgG2a, n = 2; IgG3, N = 1) were stable upon challenge with DTPA, EDTA or acidic pH. Using the affinity chromatography technique, two of the 99m Tc-labeled antibody fragments displayed no loss of immunoreactivity after prolonged incubation in phosphate buffer up to 24 h at 37 o C. Bonding between 99m Tc and antibody fragments was elucidated by challenging with a diamide ditholate (N 2 S 2 ) compound. The Fab' with IgG2a isotype displayed tighter binding to 99m Tc in comparison to Fab' from IgG1 and IgG3 isotype in N 2 S 2 challenge and incubation with human plasma. The in vivo biodistribution of five 99m Tc-labeled fragments were evaluated in normal mice. (Author)
Beare, R. A.
2008-01-01
Professional astronomers use specialized software not normally available to students to determine the rotation periods of asteroids from fragmented light curve data. This paper describes a simple yet accurate method based on Microsoft Excel[R] that enables students to find periods in asteroid light curve and other discontinuous time series data of…
Solution of (3+1-Dimensional Nonlinear Cubic Schrodinger Equation by Differential Transform Method
Directory of Open Access Journals (Sweden)
Hassan A. Zedan
2012-01-01
Full Text Available Four-dimensional differential transform method has been introduced and fundamental theorems have been defined for the first time. Moreover, as an application of four-dimensional differential transform, exact solutions of nonlinear system of partial differential equations have been investigated. The results of the present method are compared very well with analytical solution of the system. Differential transform method can easily be applied to linear or nonlinear problems and reduces the size of computational work. With this method, exact solutions may be obtained without any need of cumbersome work, and it is a useful tool for analytical and numerical solutions.
Dynamic fragmentation of laser shock-melted tin: experiment and modelling
Energy Technology Data Exchange (ETDEWEB)
De Resseguier, T. [CNRS ENSMA, Lab Combust and Deton, F-86961 Futuroscope (France); Signor, L.; Dragon, A. [CNRS ENSMA, Mecan and Phys Mat Lab, F-86961 Futuroscope (France); Signor, L.; Roy, G. [CEA Valduc, 21 - Is-sur-Tille (France)
2010-07-01
Dynamic fragmentation of shock-loaded metals is an issue of considerable importance for both basic science and a variety of technological applications, such as pyrotechnics or inertial confinement fusion, the latter involving high energy laser irradiation of thin metallic shells. Whereas spall fracture in solid materials has been extensively studied for many years, little data can be found yet about the evolution of this phenomenon after partial or full melting on compression or on release. Here, we present an investigation of dynamic fragmentation in laser shock-melted tin, from the 'micro-spall' process (ejection of a cloud of fine droplets) occurring upon reflection of the compressive pulse from the target free surface, to the late rupture observed in the un-spalled melted layer (leading to the formation of larger spherical fragments). Experimental results consist of time-resolved velocity measurements and post-shock observations of recovered targets and fragments. They provide original information regarding the loss of tensile strength associated with melting, the cavitation mechanism likely to occur in the melted metal, the sizes of the subsequent fragments and their ejection velocities. A theoretical description based on an energetic approach adapted to the case of a liquid metal is implemented as a failure criterion in a one-dimensional hydro-code including a multi-phase equation of state for tin. The resulting predictions of the micro-spall process are compared with experimental data. In particular, the use of a new experimental technique to quantify the fragment size distributions leads to a much better agreement with theory than previously reported. Finally, a complementary approach focused on cavitation is proposed to evaluate the role of this phenomenon in the fragmentation of the melted metal. (authors)
A probabilistic fragment-based protein structure prediction algorithm.
Directory of Open Access Journals (Sweden)
David Simoncini
Full Text Available Conformational sampling is one of the bottlenecks in fragment-based protein structure prediction approaches. They generally start with a coarse-grained optimization where mainchain atoms and centroids of side chains are considered, followed by a fine-grained optimization with an all-atom representation of proteins. It is during this coarse-grained phase that fragment-based methods sample intensely the conformational space. If the native-like region is sampled more, the accuracy of the final all-atom predictions may be improved accordingly. In this work we present EdaFold, a new method for fragment-based protein structure prediction based on an Estimation of Distribution Algorithm. Fragment-based approaches build protein models by assembling short fragments from known protein structures. Whereas the probability mass functions over the fragment libraries are uniform in the usual case, we propose an algorithm that learns from previously generated decoys and steers the search toward native-like regions. A comparison with Rosetta AbInitio protocol shows that EdaFold is able to generate models with lower energies and to enhance the percentage of near-native coarse-grained decoys on a benchmark of [Formula: see text] proteins. The best coarse-grained models produced by both methods were refined into all-atom models and used in molecular replacement. All atom decoys produced out of EdaFold's decoy set reach high enough accuracy to solve the crystallographic phase problem by molecular replacement for some test proteins. EdaFold showed a higher success rate in molecular replacement when compared to Rosetta. Our study suggests that improving low resolution coarse-grained decoys allows computational methods to avoid subsequent sampling issues during all-atom refinement and to produce better all-atom models. EdaFold can be downloaded from http://www.riken.jp/zhangiru/software.html [corrected].
Huschmann, Franziska U; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S; Mueller, Uwe
2016-05-01
Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.
Huschmann, Franziska U.; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S.; Mueller, Uwe
2016-01-01
Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein–ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin–fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity. PMID:27139825
Towards novel therapeutics for HIV through fragment-based screening and drug design.
Tiefendbrunn, Theresa; Stout, C David
2014-01-01
Fragment-based drug discovery has been applied with varying levels of success to a number of proteins involved in the HIV (Human Immunodeficiency Virus) life cycle. Fragment-based approaches have led to the discovery of novel binding sites within protease, reverse transcriptase, integrase, and gp41. Novel compounds that bind to known pockets within CCR5 have also been identified via fragment screening, and a fragment-based approach to target the TAR-Tat interaction was explored. In the context of HIV-1 reverse transcriptase (RT), fragment-based approaches have yielded fragment hits with mid-μM activity in an in vitro activity assay, as well as fragment hits that are active against drug-resistant variants of RT. Fragment-based drug discovery is a powerful method to elucidate novel binding sites within proteins, and the method has had significant success in the context of HIV proteins.
Forgan, D. H.; Hall, C.; Meru, F.; Rice, W. K. M.
2018-03-01
It is likely that most protostellar systems undergo a brief phase where the protostellar disc is self-gravitating. If these discs are prone to fragmentation, then they are able to rapidly form objects that are initially of several Jupiter masses and larger. The fate of these disc fragments (and the fate of planetary bodies formed afterwards via core accretion) depends sensitively not only on the fragment's interaction with the disc, but also with its neighbouring fragments. We return to and revise our population synthesis model of self-gravitating disc fragmentation and tidal downsizing. Amongst other improvements, the model now directly incorporates fragment-fragment interactions while the disc is still present. We find that fragment-fragment scattering dominates the orbital evolution, even when we enforce rapid migration and inefficient gap formation. Compared to our previous model, we see a small increase in the number of terrestrial-type objects being formed, although their survival under tidal evolution is at best unclear. We also see evidence for disrupted fragments with evolved grain populations - this is circumstantial evidence for the formation of planetesimal belts, a phenomenon not seen in runs where fragment-fragment interactions are ignored. In spite of intense dynamical evolution, our population is dominated by massive giant planets and brown dwarfs at large semimajor axis, which direct imaging surveys should, but only rarely, detect. Finally, disc fragmentation is shown to be an efficient manufacturer of free-floating planetary mass objects, and the typical multiplicity of systems formed via gravitational instability will be low.
International Nuclear Information System (INIS)
Itsubo, Mariko; Kameda, Haruo; Suzuki, Naoki; Okamura, Tetsuo
1989-01-01
The method of three-dimensional display of hepatocellular carcinoma using conventional hepatic arteriogram by computer graphics method was newly exploited and applied in clinical use. Three-dimensional models were reconstructed from contour lines of tumors demonstrated as hypervascular lesions by hepatic arteriography. Although objects were limited by angiographic images in which tumors need to be demonstrated as nodules with hypervascularity, this method of three-dimensional display was not worse on accuracy than that using computed tomographic images. According to this method property of the tumor expressed by vascularity was demonstrated clear and in addition volume of the tumor was calculated easily. When the tumor arose in necrotic changes in which demonstrated as a vascular lesion by hepatic arteriography with reduction of size in usual by conservative treatment such as transcathter arterial embolization therapy, this three-dimensional display was able to demonstrate such changes clear. This preliminary study demonstrates the feasibility and clinical usefulness of three-dimensional display of hepatocellular carcinoma using hepatic arteriogram by computer graphics method. (author)
One-Dimensional Finite Elements An Introduction to the FE Method
Öchsner, Andreas
2013-01-01
This textbook presents finite element methods using exclusively one-dimensional elements. The aim is to present the complex methodology in an easily understandable but mathematically correct fashion. The approach of one-dimensional elements enables the reader to focus on the understanding of the principles of basic and advanced mechanical problems. The reader easily understands the assumptions and limitations of mechanical modeling as well as the underlying physics without struggling with complex mathematics. But although the description is easy it remains scientifically correct. The approach using only one-dimensional elements covers not only standard problems but allows also for advanced topics like plasticity or the mechanics of composite materials. Many examples illustrate the concepts and problems at the end of every chapter help to familiarize with the topics.
Garrison, Virginia H.; Ward, Greg A.
2012-01-01
In response to dramatic losses of reef-building corals and ongoing lack of recovery, a small-scale coral transplant project was initiated in the Caribbean (U.S. Virgin Islands) in 1999 and was followed for 12 years. The primary objectives were to (1) identify a source of coral colonies for transplantation that would not result in damage to reefs, (2) test the feasibility of transplanting storm-generated coral fragments, and (3) develop a simple, inexpensive method for transplanting fragments that could be conducted by the local community. The ultimate goal was to enhance abundance of threatened reef-building species on local reefs. Storm-produced coral fragments of two threatened reef-building species [Acropora palmata and A. cervicornis (Acroporidae)] and another fast-growing species [Porites porites (Poritidae)] were collected from environments hostile to coral fragment survival and transplanted to degraded reefs. Inert nylon cable ties were used to attach transplanted coral fragments to dead coral substrate. Survival of 75 reference colonies and 60 transplants was assessed over 12 years. Only 9% of colonies were alive after 12 years: no A. cervicornis; 3% of A. palmata transplants and 18% of reference colonies; and 13% of P. porites transplants and 7% of reference colonies. Mortality rates for all species were high and were similar for transplant and reference colonies. Physical dislodgement resulted in the loss of 56% of colonies, whereas 35% died in place. Only A. palmata showed a difference between transplant and reference colony survival and that was in the first year only. Location was a factor in survival only for A. palmata reference colonies and after year 10. Even though the tested methods and concepts were proven effective in the field over the 12-year study, they do not present a solution. No coral conservation strategy will be effective until underlying intrinsic and/or extrinsic factors driving high mortality rates are
Energy Technology Data Exchange (ETDEWEB)
Sato, T; Matsuoka, T [Japan Petroleum Exploration Corp., Tokyo (Japan); Saeki, T [Japan National Oil Corp., Tokyo (Japan). Technology Research Center
1997-05-27
Discussed in this report is a wavefield simulation in the 3-dimensional seismic survey. With the level of the object of exploration growing deeper and the object more complicated in structure, the survey method is now turning 3-dimensional. There are several modelling methods for numerical calculation of 3-dimensional wavefields, such as the difference method, pseudospectral method, and the like, all of which demand an exorbitantly large memory and long calculation time, and are costly. Such methods have of late become feasible, however, thanks to the advent of the parallel computer. As compared with the difference method, the pseudospectral method requires a smaller computer memory and shorter computation time, and is more flexible in accepting models. It outputs the result in fullwave just like the difference method, and does not cause wavefield numerical variance. As the computation platform, the parallel computer nCUBE-2S is used. The object domain is divided into the number of the processors, and each of the processors takes care only of its share so that parallel computation as a whole may realize a very high-speed computation. By the use of the pseudospectral method, a 3-dimensional simulation is completed within a tolerable computation time length. 7 refs., 3 figs., 1 tab.
Graph Theory. 1. Fragmentation of Structural Graphs
Directory of Open Access Journals (Sweden)
Lorentz JÄNTSCHI
2002-12-01
Full Text Available The investigation of structural graphs has many fields of applications in engineering, especially in applied sciences like as applied chemistry and physics, computer sciences and automation, electronics and telecommunication. The main subject of the paper is to express fragmentation criteria in graph using a new method of investigation: terminal paths. Using terminal paths are defined most of the fragmentation criteria that are in use in molecular topology, but the fields of applications are more generally than that, as I mentioned before. Graphical examples of fragmentation are given for every fragmentation criteria. Note that all fragmentation is made with a computer program that implements a routine for every criterion.[1] A web routine for tracing all terminal paths in graph can be found at the address: http://vl.academicdirect.ro/molecular_topology/tpaths/ [1] M. V. Diudea, I. Gutman, L. Jäntschi, Molecular Topology, Nova Science, Commack, New York, 2001, 2002.
Development of a three dimensional circulation model based on fractional step method
Directory of Open Access Journals (Sweden)
Mazen Abualtayef
2010-03-01
Full Text Available A numerical model was developed for simulating a three-dimensional multilayer hydrodynamic and thermodynamic model in domains with irregular bottom topography. The model was designed for examining the interactions between flow and topography. The model was based on the three-dimensional Navier-Stokes equations and was solved using the fractional step method, which combines the finite difference method in the horizontal plane and the finite element method in the vertical plane. The numerical techniques were described and the model test and application were presented. For the model application to the northern part of Ariake Sea, the hydrodynamic and thermodynamic results were predicted. The numerically predicted amplitudes and phase angles were well consistent with the field observations.
Improved description of the fragmentation of nuclear collective states
International Nuclear Information System (INIS)
Soloviev, V.G.
1984-01-01
A mathematical method is deveioped for a more accurate description of the fragmentation of one-phonon states forming giant resonances. The method consists in that the one-phonon states already fragmented are used in the two-phonon terms of wave functions. Strength functions are obtained for the exci excitation of collective charge-exchange states ano giant resonances in spherical nuclei
Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.
2012-01-01
We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059
Universal elements of fragmentation
International Nuclear Information System (INIS)
Yanovsky, V. V.; Tur, A. V.; Kuklina, O. V.
2010-01-01
A fragmentation theory is proposed that explains the universal asymptotic behavior of the fragment-size distribution in the large-size range, based on simple physical principles. The basic principles of the theory are the total mass conservation in a fragmentation process and a balance condition for the energy expended in increasing the surface of fragments during their breakup. A flux-based approach is used that makes it possible to supplement the basic principles and develop a minimal theory of fragmentation. Such a supplementary principle is that of decreasing fragment-volume flux with increasing energy expended in fragmentation. It is shown that the behavior of the decreasing flux is directly related to the form of a power-law fragment-size distribution. The minimal theory is used to find universal asymptotic fragment-size distributions and to develop a natural physical classification of fragmentation models. A more general, nonlinear theory of strong fragmentation is also developed. It is demonstrated that solutions to a nonlinear kinetic equation consistent with both basic principles approach a universal asymptotic size distribution. Agreement between the predicted asymptotic fragment-size distributions and experimental observations is discussed.
Four-Dimensional Data Assimilation Using the Adjoint Method
Bao, Jian-Wen
The calculus of variations is used to confirm that variational four-dimensional data assimilation (FDDA) using the adjoint method can be implemented when the numerical model equations have a finite number of first-order discontinuous points. These points represent the on/off switches associated with physical processes, for which the Jacobian matrix of the model equation does not exist. Numerical evidence suggests that, in some situations when the adjoint method is used for FDDA, the temperature field retrieved using horizontal wind data is numerically not unique. A physical interpretation of this type of non-uniqueness of the retrieval is proposed in terms of energetics. The adjoint equations of a numerical model can also be used for model-parameter estimation. A general computational procedure is developed to determine the size and distribution of any internal model parameter. The procedure is then applied to a one-dimensional shallow -fluid model in the context of analysis-nudging FDDA: the weighting coefficients used by the Newtonian nudging technique are determined. The sensitivity of these nudging coefficients to the optimal objectives and constraints is investigated. Experiments of FDDA using the adjoint method are conducted using the dry version of the hydrostatic Penn State/NCAR mesoscale model (MM4) and its adjoint. The minimization procedure converges and the initialization experiment is successful. Temperature-retrieval experiments involving an assimilation of the horizontal wind are also carried out using the adjoint of MM4.
Geotechnical applications of a two-dimensional elastodynamic displacement discontinuity method
CSIR Research Space (South Africa)
Siebrits, E
1993-12-01
Full Text Available A general two-dimensional elastodynamic displacement discontinuity method is used to model a variety of application problems. The plane strain problems are: the elastodynamic motions induced on a cavity by shear slip on a nearby crack; the dynamic...
Method for the manufacture of a thin-layer battery stack on a three-dimensional substrate
2008-01-01
The invention relates to a method for the manufacture of a thin-layer battery stack on a three-dimensional substrate. The invention further relates to a thin-layer battery stack on a three-dimensional substrate obtainable by such a method. Moreover, the invention relates to a device comprising such
2018-01-01
Natural products are well known for their biological relevance, high degree of three-dimensionality, and access to areas of largely unexplored chemical space. To shape our understanding of the interaction between natural products and protein targets in the postgenomic era, we have used native mass spectrometry to investigate 62 potential protein targets for malaria using a natural-product-based fragment library. We reveal here 96 low-molecular-weight natural products identified as binding partners of 32 of the putative malarial targets. Seventy-nine (79) fragments have direct growth inhibition on Plasmodium falciparum at concentrations that are promising for the development of fragment hits against these protein targets. This adds a fragment library to the published HTS active libraries in the public domain. PMID:29436819
Completion of autobuilt protein models using a database of protein fragments
International Nuclear Information System (INIS)
Cowtan, Kevin
2012-01-01
Two developments in the process of automated protein model building in the Buccaneer software are described: the use of a database of protein fragments in improving the model completeness and the assembly of disconnected chain fragments into complete molecules. Two developments in the process of automated protein model building in the Buccaneer software are presented. A general-purpose library for protein fragments of arbitrary size is described, with a highly optimized search method allowing the use of a larger database than in previous work. The problem of assembling an autobuilt model into complete chains is discussed. This involves the assembly of disconnected chain fragments into complete molecules and the use of the database of protein fragments in improving the model completeness. Assembly of fragments into molecules is a standard step in existing model-building software, but the methods have not received detailed discussion in the literature
Wave field restoration using three-dimensional Fourier filtering method.
Kawasaki, T; Takai, Y; Ikuta, T; Shimizu, R
2001-11-01
A wave field restoration method in transmission electron microscopy (TEM) was mathematically derived based on a three-dimensional (3D) image formation theory. Wave field restoration using this method together with spherical aberration correction was experimentally confirmed in through-focus images of amorphous tungsten thin film, and the resolution of the reconstructed phase image was successfully improved from the Scherzer resolution limit to the information limit. In an application of this method to a crystalline sample, the surface structure of Au(110) was observed in a profile-imaging mode. The processed phase image showed quantitatively the atomic relaxation of the topmost layer.
The Chimera Method of Simulation for Unsteady Three-Dimensional Viscous Flow
Meakin, Robert L.
1996-01-01
The Chimera overset grid method is reviewed and discussed in the context of a method of solution and analysis of unsteady three-dimensional viscous flows. The state of maturity of the various pieces of support software required to use the approach is discussed. A variety of recent applications of the method is presented. Current limitations of the approach are defined.
Identification of Histamine H3 Receptor Ligands Using a New Crystal Structure Fragment-based Method
DEFF Research Database (Denmark)
Frandsen, Ida Osborn; Boesgaard, Michael W; Fidom, Kimberley
2017-01-01
Virtual screening offers an efficient alternative to high-throughput screening in the identification of pharmacological tools and lead compounds. Virtual screening is typically based on the matching of target structures or ligand pharmacophores to commercial or in-house compound catalogues....... The complete pharmacophore fragment library is freely available through the GPCR database, GPCRdb, allowing the successful application herein to be repeated for most of the 285 class A GPCR targets. The method could also easily be adapted to other protein families....
International Nuclear Information System (INIS)
Gaimard, J.J.
1990-10-01
In this thesis the experimental results on the cross sections for the production of 36 P in the fragmentation of 403 MeV/u 40 Ar on a carbon target are presented. Furthermore some models of the nuclear fragmentation are elaborated and compared by means of experimental data for the production of gold and cerium isotopes in the reaction 12 C+ 209 Bi at 400 MeV/u, of chlorine, sulfur, aluminium, magnesium, and oxygen isotopes in the reactions 40 Ar+ 12 C at 600 MeV/u and 48 Ca+ 9 Be at 212 MeV/u, and of cobalt, manganese, vanadium, and scandium isotopes together with the charge distributions for A=43 and A=44 in the reactions 40 Ar+ 64 Cu at 2 GeV/u and 56 Fe+ 12 C at 600 MeV/u. (HSI)
An axial calculation method for accurate two-dimensional PWR core simulation
International Nuclear Information System (INIS)
Grimm, P.
1985-02-01
An axial calculation method, which improves the agreement of the multiplication factors determined by two- and three-dimensional PWR neutronic calculations, is presented. The axial buckling is determined at each time point so as to reproduce the increase of the leakage due to the flattening of the axial power distribution and the effect of the axial variation of the group constants of the fuel on the reactivity is taken into account. The results of a test example show that the differences of k-eff and cycle length between two- and three-dimensional calculations, which are unsatisfactorily large if a constant buckling is used, become negligible if the results of the axial calculation are used in the two-dimensional core simulation. (Auth.)
Woods, Lucy A; Dolezal, Olan; Ren, Bin; Ryan, John H; Peat, Thomas S; Poulsen, Sally-Ann
2016-03-10
Fragment-based drug discovery (FBDD) is contingent on the development of analytical methods to identify weak protein-fragment noncovalent interactions. Herein we have combined an underutilized fragment screening method, native state mass spectrometry, together with two proven and popular fragment screening methods, surface plasmon resonance and X-ray crystallography, in a fragment screening campaign against human carbonic anhydrase II (CA II). In an initial fragment screen against a 720-member fragment library (the "CSIRO Fragment Library") seven CA II binding fragments, including a selection of nonclassical CA II binding chemotypes, were identified. A further 70 compounds that comprised the initial hit chemotypes were subsequently sourced from the full CSIRO compound collection and screened. The fragment results were extremely well correlated across the three methods. Our findings demonstrate that there is a tremendous opportunity to apply native state mass spectrometry as a complementary fragment screening method to accelerate drug discovery.
Numerical analysis of fragmentation mechanisms in vapor explosions
Energy Technology Data Exchange (ETDEWEB)
Koshizuka, Seiichi; Ikeda, Hirokazu; Oka, Yoshiaki [Tokyo Univ., Tokai, Ibaraki (Japan). Nuclear Engineering Research Lab.
1998-01-01
Fragmentation of molten metal is the key process in vapor explosions. However this process is so rapid that the mechanisms have not been clarified yet in the experimental studies. Besides, numerical simulation is difficult because we have to analyze water, steam and molten metal simultaneously with evaporation and fragmentation. The authors have been developing a new numerical method, the Moving Particle Semi-implicit (MPS) method, based on moving particles and their interactions. Grids are not necessary. Incompressible flows with fragmentation on free surfaces have been calculated successfully using the MPS method. In the present study numerical simulation of the fragmentation processes using the MPS method is carried out to investigate the mechanisms. A numerical model to calculate evaporation from water to steam is developed. In this model, new particles are generated on water-steam interfaces. Effect of evaporation is also investigated. Growth of the filament is not accelerated when the normal evaporation is considered. This is because the normal evaporation needs a longer time than the moment of the jet impingement, though the filament growth is decided in this moment. Next, rapid evaporation based on spontaneous nucleation is considered. The filament growth is markedly accelerated. This result is consistent with the experimental fact that the spontaneous nucleation temperature is a necessary condition of small-scale vapor explosions. (J.P.N.)
Ma, Jing; Hou, Xiaofang; Zhang, Bing; Wang, Yunan; He, Langchong
2014-03-01
In this study, a new"heart-cutting" two-dimensional liquid chromatography method for the simultaneous determination of carbohydrate contents in milk powder was presented. In this two dimensional liquid chromatography system, a Venusil XBP-C4 analysis column was used in the first dimension ((1)D) as a pre-separation column, a ZORBAX carbohydrates analysis column was used in the second dimension ((2)D) as a final-analysis column. The whole process was completed in less than 35min without a particular sample preparation procedure. The capability of the new two dimensional HPLC method was demonstrated in the determination of carbohydrates in various brands of milk powder samples. A conventional one dimensional chromatography method was also proposed. The two proposed methods were both validated in terms of linearity, limits of detection, accuracy and precision. The comparison between the results obtained with the two methods showed that the new and completely automated two dimensional liquid chromatography method is more suitable for milk powder sample because of its online cleanup effect involved. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.
Nishimoto, Yoshio; Fedorov, Dmitri G.
2018-02-01
The exactly analytic gradient is derived and implemented for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB) using adaptive frozen orbitals. The response contributions which arise from freezing detached molecular orbitals on the border between fragments are computed by solving Z-vector equations. The accuracy of the energy, its gradient, and optimized structures is verified on a set of representative inorganic materials and polypeptides. FMO-DFTB is applied to optimize the structure of a silicon nano-wire, and the results are compared to those of density functional theory and experiment. FMO accelerates the DFTB calculation of a boron nitride nano-ring with 7872 atoms by a factor of 406. Molecular dynamics simulations using FMO-DFTB applied to a 10.7 μm chain of boron nitride nano-rings, consisting of about 1.2 × 106 atoms, reveal the rippling and twisting of nano-rings at room temperature.
Casimir effect in a d-dimensional flat spacetime and the cut-off method
International Nuclear Information System (INIS)
Svaiter, N.F.; Svaiter, B.F.
1989-01-01
The CasiMir efeect in a D-dimensional spacetime produced by a Hermitian massless scalar field in the presence of a pair of perfectly reflecting parallel flat plates is discussed. The exponential cut-off regularization method is employed. The regularized vacuum energy and the Casimir energy of this field are evaluated and a detailed analysis of the divergent terms in the regularized vacuum energy is carried out. The two-dimensional version of the Casimir effect is discussed by means of the same cut-off method. A comparison between the above method and the zeta function regularization procedure is presented in a way which gives the unification between these two methods in the present case. (author) [pt
RAY TRACING RENDER MENGGUNAKAN FRAGMENT ANTI ALIASING
Directory of Open Access Journals (Sweden)
Febriliyan Samopa
2008-07-01
Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Rendering is generating surface and three-dimensional effects on an object displayed on a monitor screen. Ray tracing as a rendering method that traces ray for each image pixel has a drawback, that is, aliasing (jaggies effect. There are some methods for executing anti aliasing. One of those methods is OGSS (Ordered Grid Super Sampling. OGSS is able to perform aliasing well. However, this method requires more computation time since sampling of all pixels in the image will be increased. Fragment Anti Aliasing (FAA is a new alternative method that can cope with the drawback. FAA will check the image when performing rendering to a scene. Jaggies effect is only happened at curve and gradient object. Therefore, only this part of object that will experience sampling magnification. After this sampling magnification and the pixel values are computed, then downsample is performed to retrieve the original pixel values. Experimental results show that the software can implement ray tracing well in order to form images, and it can implement FAA and OGSS technique to perform anti aliasing. In general, rendering using FAA is faster than using OGSS
Crystallization of SHARPIN using an automated two-dimensional grid screen for optimization
International Nuclear Information System (INIS)
Stieglitz, Benjamin; Rittinger, Katrin; Haire, Lesley F.
2012-01-01
The expression, purification and crystallization of an N-terminal fragment of SHARPIN are reported. Diffraction-quality crystals were obtained using a two-dimensional grid-screen seeding technique. An N-terminal fragment of human SHARPIN was recombinantly expressed in Escherichia coli, purified and crystallized. Crystals suitable for X-ray diffraction were obtained by a one-step optimization of seed dilution and protein concentration using a two-dimensional grid screen. The crystals belonged to the primitive tetragonal space group P4 3 2 1 2, with unit-cell parameters a = b = 61.55, c = 222.81 Å. Complete data sets were collected from native and selenomethionine-substituted protein crystals at 100 K to 2.6 and 2.0 Å resolution, respectively
Directory of Open Access Journals (Sweden)
Alejandro Acevedo-Malavé
2012-06-01
Full Text Available Smoothed Particle Hydrodynamics (SPH is a Lagrangian mesh-free formalism and has been useful to model continuous fluid. This formalism is employed to solve the Navier-Stokes equations by replacing the fluid with a set of particles. These particles are interpolation points from which properties of the fluid can be determined. In this study, the SPH method is applied to simulate the hydrodynamics interaction of many drops, showing some settings for the coalescence, fragmentation and flocculation problem of equally sized liquid drops in three-dimensional spaces. For small velocities the drops interact only through their deformed surfaces and the flocculation of the droplets arises. This result is very different if the collision velocity is large enough for the fragmentation of droplets takes place. We observe that for velocities around 15 mm/ms the coalescence of droplets occurs. The velocity vector fields formed inside the drops during the collision process are shown.
Prompt neutrons from {sup 236}U fission fragments
Energy Technology Data Exchange (ETDEWEB)
Boldeman, J W; Musgrove, A.R. de L.; Walsch, R L
1971-03-01
Measurements were made of prompt neutron emission in the thermal neutron fission of {sup 235}U. The mean neutron emission per fragment was obtained for particular values of the fragment mass and total kinetic energy. A direct neutron counting method was employed and a comparison made with data from previous experiments of this type. (author)
New method of three-dimensional reconstruction from two-dimensional MR data sets
International Nuclear Information System (INIS)
Wrazidlo, W.; Schneider, S.; Brambs, H.J.; Richter, G.M.; Kauffmann, G.W.; Geiger, B.; Fischer, C.
1989-01-01
In medical diagnosis and therapy, cross-sectional images are obtained by means of US, CT, or MR imaging. The authors propose a new solution to the problem of constructing a shape over a set of cross-sectional contours from two-dimensional (2D) MR data sets. The authors' method reduces the problem of constructing a shape over the cross sections to one of constructing a sequence of partial shapes, each of them connecting two cross sections lying on adjacent planes. The solution makes use of the Delaunay triangulation, which is isomorphic in that specific situation. The authors compute this Delaunay triangulation. Shape reconstruction is then achieved section by pruning Delaunay triangulations
Fragmentation cross sections outside the limiting-fragmentation regime
Sümmerer, K
2003-01-01
The empirical parametrization of fragmentation cross sections, EPAX, has been successfully applied to estimate fragment production cross sections in reactions of heavy ions at high incident energies. It is checked whether a similar parametrization can be found for proton-induced spallation around 1 GeV, the range of interest for ISOL-type RIB facilities. The validity of EPAX for medium-energy heavy-ion induced reactions is also checked. Only a few datasets are available, but in general EPAX predicts the cross sections rather well, except for fragments close to the projectile, where the experimental cross sections are found to be larger.
Two- and three-dimensional CT analysis of ankle fractures
International Nuclear Information System (INIS)
Magid, D.; Fishman, E.K.; Ney, D.R.; Kuhlman, J.E.
1988-01-01
CT with coronal and sagittal reformatting (two-dimensional CT) and animated volumetric image rendering (three-dimensional CT) was used to assess ankle fractures. Partial volume limits transaxial CT in assessments of horizontally oriented structures. Two-dimensional CT, being orthogonal to the plafond, superior mortise, talar dome, and tibial epiphysis, often provides the most clinically useful images. Two-dimensional CT is most useful in characterizing potentially confusing fractures, such as Tillaux (anterior tubercle), triplane, osteochondral talar dome, or nondisplaced talar neck fractures, and it is the best study to confirm intraarticular fragments. Two-and three-dimensional CT best indicate the percentage of articular surface involvement and best demonstrate postoperative results or complications (hardware migration, residual step-off, delayed union, DJD, AVN, etc). Animated three-dimensional images are the preferred means of integrating the two-dimensional findings for surgical planning, as these images more closely simulate the clinical problem
Finite element method for radiation heat transfer in multi-dimensional graded index medium
International Nuclear Information System (INIS)
Liu, L.H.; Zhang, L.; Tan, H.P.
2006-01-01
In graded index medium, ray goes along a curved path determined by Fermat principle, and curved ray-tracing is very difficult and complex. To avoid the complicated and time-consuming computation of curved ray trajectories, a finite element method based on discrete ordinate equation is developed to solve the radiative transfer problem in a multi-dimensional semitransparent graded index medium. Two particular test problems of radiative transfer are taken as examples to verify this finite element method. The predicted dimensionless net radiative heat fluxes are determined by the proposed method and compared with the results obtained by finite volume method. The results show that the finite element method presented in this paper has a good accuracy in solving the multi-dimensional radiative transfer problem in semitransparent graded index medium
Universality of fragment shapes.
Domokos, Gábor; Kun, Ferenc; Sipos, András Árpád; Szabó, Tímea
2015-03-16
The shape of fragments generated by the breakup of solids is central to a wide variety of problems ranging from the geomorphic evolution of boulders to the accumulation of space debris orbiting Earth. Although the statistics of the mass of fragments has been found to show a universal scaling behavior, the comprehensive characterization of fragment shapes still remained a fundamental challenge. We performed a thorough experimental study of the problem fragmenting various types of materials by slowly proceeding weathering and by rapid breakup due to explosion and hammering. We demonstrate that the shape of fragments obeys an astonishing universality having the same generic evolution with the fragment size irrespective of materials details and loading conditions. There exists a cutoff size below which fragments have an isotropic shape, however, as the size increases an exponential convergence is obtained to a unique elongated form. We show that a discrete stochastic model of fragmentation reproduces both the size and shape of fragments tuning only a single parameter which strengthens the general validity of the scaling laws. The dependence of the probability of the crack plan orientation on the linear extension of fragments proved to be essential for the shape selection mechanism.
Salmingo, Remel A; Tadano, Shigeru; Fujisaki, Kazuhiro; Abe, Yuichiro; Ito, Manabu
2012-05-01
Scoliosis is defined as a spinal pathology characterized as a three-dimensional deformity of the spine combined with vertebral rotation. Treatment for severe scoliosis is achieved when the scoliotic spine is surgically corrected and fixed using implanted rods and screws. Several studies performed biomechanical modeling and corrective forces measurements of scoliosis correction. These studies were able to predict the clinical outcome and measured the corrective forces acting on screws, however, they were not able to measure the intraoperative three-dimensional geometry of the spinal rod. In effect, the results of biomechanical modeling might not be so realistic and the corrective forces during the surgical correction procedure were intra-operatively difficult to measure. Projective geometry has been shown to be successful in the reconstruction of a three-dimensional structure using a series of images obtained from different views. In this study, we propose a new method to measure the three-dimensional geometry of an implant rod using two cameras. The reconstruction method requires only a few parameters, the included angle θ between the two cameras, the actual length of the rod in mm, and the location of points for curve fitting. The implant rod utilized in spine surgery was used to evaluate the accuracy of the current method. The three-dimensional geometry of the rod was measured from the image obtained by a scanner and compared to the proposed method using two cameras. The mean error in the reconstruction measurements ranged from 0.32 to 0.45 mm. The method presented here demonstrated the possibility of intra-operatively measuring the three-dimensional geometry of spinal rod. The proposed method could be used in surgical procedures to better understand the biomechanics of scoliosis correction through real-time measurement of three-dimensional implant rod geometry in vivo.
Two-dimensional semi-analytic nodal method for multigroup pin power reconstruction
International Nuclear Information System (INIS)
Seung Gyou, Baek; Han Gyu, Joo; Un Chul, Lee
2007-01-01
A pin power reconstruction method applicable to multigroup problems involving square fuel assemblies is presented. The method is based on a two-dimensional semi-analytic nodal solution which consists of eight exponential terms and 13 polynomial terms. The 13 polynomial terms represent the particular solution obtained under the condition of a 2-dimensional 13 term source expansion. In order to achieve better approximation of the source distribution, the least square fitting method is employed. The 8 exponential terms represent a part of the analytically obtained homogeneous solution and the 8 coefficients are determined by imposing constraints on the 4 surface average currents and 4 corner point fluxes. The surface average currents determined from a transverse-integrated nodal solution are used directly whereas the corner point fluxes are determined during the course of the reconstruction by employing an iterative scheme that would realize the corner point balance condition. The outgoing current based corner point flux determination scheme is newly introduced. The accuracy of the proposed method is demonstrated with the L336C5 benchmark problem. (authors)
Improving the accuracy of CT dimensional metrology by a novel beam hardening correction method
International Nuclear Information System (INIS)
Zhang, Xiang; Li, Lei; Zhang, Feng; Xi, Xiaoqi; Deng, Lin; Yan, Bin
2015-01-01
Its powerful nondestructive characteristics are attracting more and more research into the study of computed tomography (CT) for dimensional metrology, which offers a practical alternative to the common measurement methods. However, the inaccuracy and uncertainty severely limit the further utilization of CT for dimensional metrology due to many factors, among which the beam hardening (BH) effect plays a vital role. This paper mainly focuses on eliminating the influence of the BH effect in the accuracy of CT dimensional metrology. To correct the BH effect, a novel exponential correction model is proposed. The parameters of the model are determined by minimizing the gray entropy of the reconstructed volume. In order to maintain the consistency and contrast of the corrected volume, a punishment term is added to the cost function, enabling more accurate measurement results to be obtained by the simple global threshold method. The proposed method is efficient, and especially suited to the case where there is a large difference in gray value between material and background. Different spheres with known diameters are used to verify the accuracy of dimensional measurement. Both simulation and real experimental results demonstrate the improvement in measurement precision. Moreover, a more complex workpiece is also tested to show that the proposed method is of general feasibility. (paper)
Inclusive breakup of three-fragment weakly bound nuclei
International Nuclear Information System (INIS)
Carlson, B.V.; Frederico, T.; Hussein, M.S.
2017-01-01
The inclusive breakup of three-fragment projectiles is discussed within a four-body spectator model. Both the elastic breakup and the non-elastic breakup are obtained in a unified framework. Originally developed in the 80's for two-fragment projectiles such as the deuteron, in this paper the theory is successfully generalized to three-fragment projectiles. The expression obtained for the inclusive cross section allows the extraction of the incomplete fusion cross section, and accordingly generalizes the surrogate method to cases such as (t, p) and (t, n) reactions. It is found that two-fragment correlations inside the projectile affect in a conspicuous way the elastic breakup cross section. The inclusive non-elastic breakup cross section is calculated and is found to contain the contribution of a three-body absorption term that is also strongly influenced by the two-fragment correlations. This latter cross section contains the so-called incomplete fusion where more than one compound nuclei are formed. Our theory describes both stable weakly bound three-fragment projectiles and unstable ones such as the Borromean nuclei.
Inclusive breakup of three-fragment weakly bound nuclei
Energy Technology Data Exchange (ETDEWEB)
Carlson, B.V.; Frederico, T. [Instituto Tecnológico de Aeronáutica, DCTA, 12.228-900 São José dos Campos, SP (Brazil); Hussein, M.S., E-mail: hussein@if.usp.br [Instituto Tecnológico de Aeronáutica, DCTA, 12.228-900 São José dos Campos, SP (Brazil); Instituto de Estudos Avançados, Universidade de São Paulo, C.P. 72012, 05508-970 São Paulo, SP (Brazil); Instituto de Física, Universidade de São Paulo, C.P. 66318, 05314-970 São Paulo, SP (Brazil)
2017-04-10
The inclusive breakup of three-fragment projectiles is discussed within a four-body spectator model. Both the elastic breakup and the non-elastic breakup are obtained in a unified framework. Originally developed in the 80's for two-fragment projectiles such as the deuteron, in this paper the theory is successfully generalized to three-fragment projectiles. The expression obtained for the inclusive cross section allows the extraction of the incomplete fusion cross section, and accordingly generalizes the surrogate method to cases such as (t, p) and (t, n) reactions. It is found that two-fragment correlations inside the projectile affect in a conspicuous way the elastic breakup cross section. The inclusive non-elastic breakup cross section is calculated and is found to contain the contribution of a three-body absorption term that is also strongly influenced by the two-fragment correlations. This latter cross section contains the so-called incomplete fusion where more than one compound nuclei are formed. Our theory describes both stable weakly bound three-fragment projectiles and unstable ones such as the Borromean nuclei.
[Detection of UGT1A1*28 Polymorphism Using Fragment Analysis].
Huang, Ying; Su, Jian; Huang, Xiaosui; Lu, Danxia; Xie, Zhi; Yang, Suqing; Guo, Weibang; Lv, Zhiyi; Wu, Hongsui; Zhang, Xuchao
2017-12-20
Uridine-diphosphoglucuronosyl transferase 1A1 (UGT1A1), UGT1A1*28 polymorphism can reduce UGT1A1 enzymatic activity, which may lead to severe toxicities in patients who receive irinotecan. This study tries to build a fragment analysis method to detect UGT1A1*28 polymorphism. A total of 286 blood specimens from the lung cancer patients who were hospitalized in Guangdong General Hospital between April 2014 to May 2015 were detected UGT1A1*28 polymorphism by fragment analysis method. Comparing with Sanger sequencing, precision and accuracy of the fragment analysis method were 100%. Of the 286 patients, 236 (82.5% harbored TA6/6 genotype, 48 (16.8%) TA 6/7 genotype and 2 (0.7%) TA7/7 genotype. Our data suggest hat the fragment analysis method is robust for detecting UGT1A1*28 polymorphism in clinical practice. It's simple, time-saving, and easy-to-carry.
On two flexible methods of 2-dimensional regression analysis
Czech Academy of Sciences Publication Activity Database
Volf, Petr
2012-01-01
Roč. 18, č. 4 (2012), s. 154-164 ISSN 1803-9782 Grant - others:GA ČR(CZ) GAP209/10/2045 Institutional support: RVO:67985556 Keywords : regression analysis * Gordon surface * prediction error * projection pursuit Subject RIV: BB - Applied Statistics, Operational Research http://library.utia.cas.cz/separaty/2013/SI/volf-on two flexible methods of 2-dimensional regression analysis.pdf
Direct-coupled-ray method for design-oriented three-dimensional transport analysis
International Nuclear Information System (INIS)
Bucholz, J.A.; Poncelet, C.G.
1977-01-01
A fast three-dimensional design-oriented transport method has been developed for the solution of both neutron and gamma transport problems. It combines a nodal approach with analytic integral transport to achieve relative speed and accuracy. An analytic solution is obtained for the angular flux in each of the 14 directions defined by the six faces and eight corners of a cubic mesh block. The scheme used to accommodate high-order anisotropic scattering is based on the formulation of ray-to-ray scattering probabilities in an integral sense. A variable mesh approximation has also been introduced to provide greater flexibility. The details of a direct-coupled-ray (DCR) → P 1 conversion technique have been developed but not yet implemented. The DCR method, as implemented in the TRANS3 code, has been used in a number of liquid-metal fast breeder reactor shielding applications. These included a one-dimensional deep penetration configuration and one-, two-, and three dimensional representations of the lower axial shield of the Clinch River Breeder Reactor. Comparisons with ANISN and DOT-III solutions indicated good to excellent agreement in most situations
Fragment screening of cyclin G-associated kinase by weak affinity chromatography.
Meiby, Elinor; Knapp, Stefan; Elkins, Jonathan M; Ohlson, Sten
2012-11-01
Fragment-based drug discovery (FBDD) has become a new strategy for drug discovery where lead compounds are evolved from small molecules. These fragments form low affinity interactions (dissociation constant (K(D)) = mM - μM) with protein targets, which require fragment screening methods of sufficient sensitivity. Weak affinity chromatography (WAC) is a promising new technology for fragment screening based on selective retention of fragments by a drug target. Kinases are a major pharmaceutical target, and FBDD has been successfully applied to several of these targets. In this work, we have demonstrated the potential to use WAC in combination with mass spectrometry (MS) detection for fragment screening of a kinase target-cyclin G-associated kinase (GAK). One hundred seventy fragments were selected for WAC screening by virtual screening of a commercial fragment library against the ATP-binding site of five different proteins. GAK protein was immobilized on a capillary HPLC column, and compound binding was characterized by frontal affinity chromatography. Compounds were screened in sets of 13 or 14, in combination with MS detection for enhanced throughput. Seventy-eight fragments (46 %) with K(D) < 200 μM were detected, including a few highly efficient GAK binders (K(D) of 2 μM; ligand efficiency = 0.51). Of special interest is that chiral screening by WAC may be possible, as two stereoisomeric fragments, which both contained one chiral center, demonstrated twin peaks. This ability, in combination with the robustness, sensitivity, and simplicity of WAC makes it a new method for fragment screening of considerable potential.
Gene prediction in metagenomic fragments: A large scale machine learning approach
Directory of Open Access Journals (Sweden)
Morgenstern Burkhard
2008-04-01
Full Text Available Abstract Background Metagenomics is an approach to the characterization of microbial genomes via the direct isolation of genomic sequences from the environment without prior cultivation. The amount of metagenomic sequence data is growing fast while computational methods for metagenome analysis are still in their infancy. In contrast to genomic sequences of single species, which can usually be assembled and analyzed by many available methods, a large proportion of metagenome data remains as unassembled anonymous sequencing reads. One of the aims of all metagenomic sequencing projects is the identification of novel genes. Short length, for example, Sanger sequencing yields on average 700 bp fragments, and unknown phylogenetic origin of most fragments require approaches to gene prediction that are different from the currently available methods for genomes of single species. In particular, the large size of metagenomic samples requires fast and accurate methods with small numbers of false positive predictions. Results We introduce a novel gene prediction algorithm for metagenomic fragments based on a two-stage machine learning approach. In the first stage, we use linear discriminants for monocodon usage, dicodon usage and translation initiation sites to extract features from DNA sequences. In the second stage, an artificial neural network combines these features with open reading frame length and fragment GC-content to compute the probability that this open reading frame encodes a protein. This probability is used for the classification and scoring of gene candidates. With large scale training, our method provides fast single fragment predictions with good sensitivity and specificity on artificially fragmented genomic DNA. Additionally, this method is able to predict translation initiation sites accurately and distinguishes complete from incomplete genes with high reliability. Conclusion Large scale machine learning methods are well-suited for gene
One New Method to Generate 3-Dimensional Virtual Mannequin
Xiu-jin, Shi; Zhi-jun, Wang; Jia-jin, Le
The personal virtual mannequin is very important in electronic made to measure (eMTM) system. There is one new easy method to generate personal virtual mannequin. First, the characteristic information of customer's body is got from two photos. Secondly, some human body part templates corresponding with the customer are selected from the templates library. Thirdly, these templates are modified and assembled according to certain rules to generate a personalized 3-dimensional human, and then the virtual mannequin is realized. Experimental result shows that the method is easy and feasible.
International Nuclear Information System (INIS)
Karmanov, V.A.
1983-01-01
Experimental data are given, the status of anomalon problem is discussed, theoretical approaches to this problem are outlined. Anomalons are exotic objects formed following fragmentation of nuclei-targets under the effect of nuclei - a beam at the energy of several GeV/nucleon. These nuclear fragments have an anomalously large cross section of interaction and respectively, small free path, considerably shorter than primary nuclei have. The experimental daa are obtained in accelerators following irradiation of nuclear emulsions by 16 O, 56 Fe, 40 Ar beams, as well as propane by 12 C beams. The experimental data testify to dependence of fragment free path on the distance L from the point of the fragment formation. A decrease in the fragment free path is established more reliably than its dependence on L. The problem of the anomalon existence cannot be yet considered resolved. Theoretical models suggested for explanation of anomalously large cross sections of nuclear fragment interaction are variable and rather speculative
DEFF Research Database (Denmark)
Duan, Zhi; Brüggemann, Dagmar Adeline; Siegumfeldt, Henrik
2009-01-01
three small synthetic peptides of the alpha(s1)-casein sequence. These peptides traverse enzymatic cleavage sites of casein during cheese ripening. The specificity of the generated anti-peptide antibodies was determined by ELISA and Western blot. Finally, an immunofluorescent labeling protocol......A novel method to monitor in situ hydrolyzable casein fragments during cheese ripening by using immunofluorescent labeling and confocal laser scanning microscopy (CLSM) was developed. Monoclonal single chain variable fragments of antibody (scFvs) were generated by antibody phage display toward...
Modelling of the PELE fragmentation dynamics
Verreault, J.
2014-05-01
The Penetrator with Enhanced Lateral Effect (PELE) is a type of explosive-free projectile that undergoes radial fragmentation upon an impact with a target plate. This type of projectile is composed of a brittle cylindrical shell (the jacket) filled in its core with a material characterized with a large Poisson's ratio. Upon an impact with a target, the axial compression causes the filling to expand in the radial direction. However, due to the brittleness of the jacket material, very little radial deformation can occur which creates a radial stress between the two materials and a hoop stress in the jacket. Fragmentation of the jacket occurs if the hoop stress exceeds the material's ultimate stress. The PELE fragmentation dynamics is explored via Finite-Element Method (FEM) simulations using the Autodyn explicit dynamics hydrocode. The numerical results are compared with an analytical model based on wave interactions, as well as with the experimental investigation of Paulus and Schirm (1996). The comparison is based on the mechanical stress in the filling and the qualitative fragmentation of the jacket.
Modelling of the PELE fragmentation dynamics
International Nuclear Information System (INIS)
Verreault, J
2014-01-01
The Penetrator with Enhanced Lateral Effect (PELE) is a type of explosive-free projectile that undergoes radial fragmentation upon an impact with a target plate. This type of projectile is composed of a brittle cylindrical shell (the jacket) filled in its core with a material characterized with a large Poisson's ratio. Upon an impact with a target, the axial compression causes the filling to expand in the radial direction. However, due to the brittleness of the jacket material, very little radial deformation can occur which creates a radial stress between the two materials and a hoop stress in the jacket. Fragmentation of the jacket occurs if the hoop stress exceeds the material's ultimate stress. The PELE fragmentation dynamics is explored via Finite-Element Method (FEM) simulations using the Autodyn explicit dynamics hydrocode. The numerical results are compared with an analytical model based on wave interactions, as well as with the experimental investigation of Paulus and Schirm (1996). The comparison is based on the mechanical stress in the filling and the qualitative fragmentation of the jacket.
The fragmentation of proto-globular clusters. I. Thermal instabilities
International Nuclear Information System (INIS)
Murray, S.D.; Lin, D.N.C.
1989-01-01
The metal abundances among the stars within a typical globular cluster are remarkably homogeneous. This indicates that star formation in these systems was a globally coordinated event which occurred over a time span less than or comparable to the collapse time scale of the cluster. This issue is addressed by assuming that the fragmentation of a proto-globular cluster cloud proceeded in two steps. In the first step, thermal instability led to the rapid growth of initial fluctuations. This led to a large contrast in the dynamical time scales between the perturbations and the parent cloud, and the perturbations then underwent gravitational instabilities on short time scales. This process is modeled using one-dimensional hydrodynamic simulations of clouds both with and without external heat sources and self-gravity. The models include the effects of a non-equilibrium H2 abundance. The results indicate that fragmentation can occur on time scales significantly less than the dynamical time scale of the parent cloud. 21 refs
Directory of Open Access Journals (Sweden)
V. V. Zelentsov
2017-01-01
Full Text Available Significant amount of space debris available in the near-Earth space is a reason to protect space vehicles from the fragments of space debris. Existing empirical calculation methods do not allow us to estimate quality of developed protection. Experimental verification of protection requires complex and expensive installations that do not allow having a desirable impact velocity. The article proposes to use the ANSYS AUTODYN software environment – a software complex of the nonlinear dynamic analysis to evaluate quality of developed protection. The ANSYS AUTODYN environment is based on the integration methods of a system of equations of continuum mechanics. The SPH (smoothed particle method method is used as a solver. The SPH method is based on the area of sampling by a finite set of the Lagrangian particles that can be represented as the elementary volumes of the medium. In modeling the targets were under attack of 2 and 3 mm spheres and cylinders with 2 mm in bottom diameter and with generator of 2 and 3 mm. The apheres and cylinders are solid and hollow, with a wall thickness of 0.5 mm. The impact velocity of the particles with a target was assumed to be 7.5 km / s. The number of integration cycles in all cases of calculation was assumed to be 1000. The rate of flying debris fragments of the target material as a function of the h / d ratio (h - the thickness of the target, / d - the diameter of a sphere or a cylinder end is obtained. In simulation the sample picture obtained coincides both with results of experimental study carried out at the Tomsk State Technical University and with results described in the literature.
International Nuclear Information System (INIS)
Roney, A.; Frigon, C.; Larzilliere, M.
1999-01-01
The optical translational spectroscopy technique, based on the principles of fast ion beam laser spectroscopy (FIBLAS) and translational spectroscopy, allows the kinetic energies study of neutral fragments released through free dissociation of a neutral molecule. This method presents interesting features such as near-threshold energy measurements and selection of a specific dissociation limit. The fragments resulting from free dissociation (not induced) of neutral molecules, produced by charge exchange processes with a fast ion beam, are probed by laser radiation. Monitoring of the laser-induced fluorescence allows high-resolution spectra due to the kinematic compression of the velocity spread. Measurements of kinetic energies released to the second limit of dissociation H(1s) + H(2l) of H 2 are put forth and compared with those obtained by means of off-axis translational spectroscopy
Metagenome Fragment Classification Using -Mer Frequency Profiles
Directory of Open Access Journals (Sweden)
Gail Rosen
2008-01-01
Full Text Available A vast amount of microbial sequencing data is being generated through large-scale projects in ecology, agriculture, and human health. Efficient high-throughput methods are needed to analyze the mass amounts of metagenomic data, all DNA present in an environmental sample. A major obstacle in metagenomics is the inability to obtain accuracy using technology that yields short reads. We construct the unique -mer frequency profiles of 635 microbial genomes publicly available as of February 2008. These profiles are used to train a naive Bayes classifier (NBC that can be used to identify the genome of any fragment. We show that our method is comparable to BLAST for small 25 bp fragments but does not have the ambiguity of BLAST's tied top scores. We demonstrate that this approach is scalable to identify any fragment from hundreds of genomes. It also performs quite well at the strain, species, and genera levels and achieves strain resolution despite classifying ubiquitous genomic fragments (gene and nongene regions. Cross-validation analysis demonstrates that species-accuracy achieves 90% for highly-represented species containing an average of 8 strains. We demonstrate that such a tool can be used on the Sargasso Sea dataset, and our analysis shows that NBC can be further enhanced.
Homotopy decomposition method for solving one-dimensional time-fractional diffusion equation
Abuasad, Salah; Hashim, Ishak
2018-04-01
In this paper, we present the homotopy decomposition method with a modified definition of beta fractional derivative for the first time to find exact solution of one-dimensional time-fractional diffusion equation. In this method, the solution takes the form of a convergent series with easily computable terms. The exact solution obtained by the proposed method is compared with the exact solution obtained by using fractional variational homotopy perturbation iteration method via a modified Riemann-Liouville derivative.
A multi-method analysis of forest fragmentation and loss: The case ...
African Journals Online (AJOL)
Lazie
2014-02-01
Feb 1, 2014 ... mented, where the fragmented landscape represents the endpoint of the ... For example, some plants can only be pollinated by a certain kind of bird or ... tropical forests, and of the remainder, temperate and boreal forests ...
The transmission probability method in one-dimensional cylindrical geometry
International Nuclear Information System (INIS)
Rubin, I.E.
1983-01-01
The collision probability method widely used in solving the problems of neutron transpopt in a reactor cell is reliable for simple cells with small number of zones. The increase of the number of zones and also taking into account the anisotropy of scattering greatly increase the scope of calculations. In order to reduce the time of calculation the transmission probability method is suggested to be used for flux calculation in one-dimensional cylindrical geometry taking into account the scattering anisotropy. The efficiency of the suggested method is verified using the one-group calculations for cylindrical cells. The use of the transmission probability method allows to present completely angular and spatial dependences is neutrons distributions without the increase in the scope of calculations. The method is especially effective in solving the multi-group problems
A new method for information retrieval in two-dimensional grating-based X-ray phase contrast imaging
International Nuclear Information System (INIS)
Wang Zhi-Li; Gao Kun; Chen Jian; Ge Xin; Tian Yang-Chao; Wu Zi-Yu; Zhu Pei-Ping
2012-01-01
Grating-based X-ray phase contrast imaging has been demonstrated to be an extremely powerful phase-sensitive imaging technique. By using two-dimensional (2D) gratings, the observable contrast is extended to two refraction directions. Recently, we have developed a novel reverse-projection (RP) method, which is capable of retrieving the object information efficiently with one-dimensional (1D) grating-based phase contrast imaging. In this contribution, we present its extension to the 2D grating-based X-ray phase contrast imaging, named the two-dimensional reverse-projection (2D-RP) method, for information retrieval. The method takes into account the nonlinear contributions of two refraction directions and allows the retrieval of the absorption, the horizontal and the vertical refraction images. The obtained information can be used for the reconstruction of the three-dimensional phase gradient field, and for an improved phase map retrieval and reconstruction. Numerical experiments are carried out, and the results confirm the validity of the 2D-RP method
Telomere Restriction Fragment (TRF) Analysis.
Mender, Ilgen; Shay, Jerry W
2015-11-20
While telomerase is expressed in ~90% of primary human tumors, most somatic tissue cells except transiently proliferating stem-like cells do not have detectable telomerase activity (Shay and Wright, 1996; Shay and Wright, 2001). Telomeres progressively shorten with each cell division in normal cells, including proliferating stem-like cells, due to the end replication (lagging strand synthesis) problem and other causes such as oxidative damage, therefore all somatic cells have limited cell proliferation capacity (Hayflick limit) (Hayflick and Moorhead, 1961; Olovnikov, 1973). The progressive telomere shortening eventually leads to growth arrest in normal cells, which is known as replicative senescence (Shay et al. , 1991). Once telomerase is activated in cancer cells, telomere length is stabilized by the addition of TTAGGG repeats to the end of chromosomes, thus enabling the limitless continuation of cell division (Shay and Wright, 1996; Shay and Wright, 2001). Therefore, the link between aging and cancer can be partially explained by telomere biology. There are many rapid and convenient methods to study telomere biology such as Telomere Restriction Fragment (TRF), Telomere Repeat Amplification Protocol (TRAP) (Mender and Shay, 2015b) and Telomere dysfunction Induced Foci (TIF) analysis (Mender and Shay, 2015a). In this protocol paper we describe Telomere Restriction Fragment (TRF) analysis to determine average telomeric length of cells. Telomeric length can be indirectly measured by a technique called Telomere Restriction Fragment analysis (TRF). This technique is a modified Southern blot, which measures the heterogeneous range of telomere lengths in a cell population using the length distribution of the terminal restriction fragments (Harley et al. , 1990; Ouellette et al. , 2000). This method can be used in eukaryotic cells. The description below focuses on the measurement of human cancer cells telomere length. The principle of this method relies on the lack of
Directory of Open Access Journals (Sweden)
Krystal Cole
Full Text Available High throughput screening technologies such as acoustic droplet ejection (ADE greatly increase the rate at which X-ray diffraction data can be acquired from crystals. One promising high throughput screening application of ADE is to rapidly combine protein crystals with fragment libraries. In this approach, each fragment soaks into a protein crystal either directly on data collection media or on a moving conveyor belt which then delivers the crystals to the X-ray beam. By simultaneously handling multiple crystals combined with fragment specimens, these techniques relax the automounter duty-cycle bottleneck that currently prevents optimal exploitation of third generation synchrotrons. Two factors limit the speed and scope of projects that are suitable for fragment screening using techniques such as ADE. Firstly, in applications where the high throughput screening apparatus is located inside the X-ray station (such as the conveyor belt system described above, the speed of data acquisition is limited by the time required for each fragment to soak into its protein crystal. Secondly, in applications where crystals are combined with fragments directly on data acquisition media (including both of the ADE methods described above, the maximum time that fragments have to soak into crystals is limited by evaporative dehydration of the protein crystals during the fragment soak. Here we demonstrate that both of these problems can be minimized by using small crystals, because the soak time required for a fragment hit to attain high occupancy depends approximately linearly on crystal size.
A new method for three-dimensional laparoscopic ultrasound model reconstruction
DEFF Research Database (Denmark)
Fristrup, C W; Pless, T; Durup, J
2004-01-01
BACKGROUND: Laparoscopic ultrasound is an important modality in the staging of gastrointestinal tumors. Correct staging depends on good spatial understanding of the regional tumor infiltration. Three-dimensional (3D) models may facilitate the evaluation of tumor infiltration. The aim of the study...... accuracy of the new method was tested ex vivo, and the clinical feasibility was tested on a small series of patients. RESULTS: Both electromagnetic tracked reconstructions and the new 3D method gave good volumetric information with no significant difference. Clinical use of the new 3D method showed...
Production of a phage-displayed single chain variable fragment ...
African Journals Online (AJOL)
Purpose: To develop specific single chain variable fragments (scFv) against infectious bursal disease virus (IBDV) via phage display technology. Methods: Purified viruses were initially applied for iterative panning rounds of scFv phage display libraries. The binding ability of the selected scFv antibody fragments against the ...
Thomas, Thaddeus P.; Anderson, Donald D.; Willis, Andrew R.; Liu, Pengcheng; Frank, Matthew C.; Marsh, J. Lawrence; Brown, Thomas D.
2011-01-01
Reconstructing highly comminuted articular fractures poses a difficult surgical challenge, akin to solving a complicated three-dimensional (3D) puzzle. Pre-operative planning using CT is critically important, given the desirability of less invasive surgical approaches. The goal of this work is to advance 3D puzzle solving methods toward use as a pre-operative tool for reconstructing these complex fractures. Methodology for generating typical fragmentation/dispersal patterns was developed. Five identical replicas of human distal tibia anatomy, were machined from blocks of high-density polyetherurethane foam (bone fragmentation surrogate), and were fractured using an instrumented drop tower. Pre- and post-fracture geometries were obtained using laser scans and CT. A semi-automatic virtual reconstruction computer program aligned fragment native (non-fracture) surfaces to a pre-fracture template. The tibias were precisely reconstructed with alignment accuracies ranging from 0.03-0.4mm. This novel technology has potential to significantly enhance surgical techniques for reconstructing comminuted intra-articular fractures, as illustrated for a representative clinical case. PMID:20924863
Dynamics and instabilities in nuclear fragmentation
International Nuclear Information System (INIS)
Colonna, M.; Guarnera, A.; Di Toro, M.; Latora, V.; Smerzi, A.; Catania Univ.
1993-01-01
A general procedure to identify instability regions which lead to multifragmentation events is presented. The method covers all possible sources of dynamical instabilities. Informations on the instability point, like the time when the nuclear system enters the critical region, the most unstable modes and the time constant of the exponential growing of the relative variances, are deduced without any numerical bias. Important memory effects in the fragmentation pattern are revealed. Some hints towards a fully dynamical picture of fragmentation processes are finally suggested. (author) 7 refs., 3 figs
Gene Prediction in Metagenomic Fragments with Deep Learning
Directory of Open Access Journals (Sweden)
Shao-Wu Zhang
2017-01-01
Full Text Available Next generation sequencing technologies used in metagenomics yield numerous sequencing fragments which come from thousands of different species. Accurately identifying genes from metagenomics fragments is one of the most fundamental issues in metagenomics. In this article, by fusing multifeatures (i.e., monocodon usage, monoamino acid usage, ORF length coverage, and Z-curve features and using deep stacking networks learning model, we present a novel method (called Meta-MFDL to predict the metagenomic genes. The results with 10 CV and independent tests show that Meta-MFDL is a powerful tool for identifying genes from metagenomic fragments.
A GPU-based calculation using the three-dimensional FDTD method for electromagnetic field analysis.
Nagaoka, Tomoaki; Watanabe, Soichi
2010-01-01
Numerical simulations with the numerical human model using the finite-difference time domain (FDTD) method have recently been performed frequently in a number of fields in biomedical engineering. However, the FDTD calculation runs too slowly. We focus, therefore, on general purpose programming on the graphics processing unit (GPGPU). The three-dimensional FDTD method was implemented on the GPU using Compute Unified Device Architecture (CUDA). In this study, we used the NVIDIA Tesla C1060 as a GPGPU board. The performance of the GPU is evaluated in comparison with the performance of a conventional CPU and a vector supercomputer. The results indicate that three-dimensional FDTD calculations using a GPU can significantly reduce run time in comparison with that using a conventional CPU, even a native GPU implementation of the three-dimensional FDTD method, while the GPU/CPU speed ratio varies with the calculation domain and thread block size.
New method of 2-dimensional metrology using mask contouring
Matsuoka, Ryoichi; Yamagata, Yoshikazu; Sugiyama, Akiyuki; Toyoda, Yasutaka
2008-10-01
We have developed a new method of accurately profiling and measuring of a mask shape by utilizing a Mask CD-SEM. The method is intended to realize high accuracy, stability and reproducibility of the Mask CD-SEM adopting an edge detection algorithm as the key technology used in CD-SEM for high accuracy CD measurement. In comparison with a conventional image processing method for contour profiling, this edge detection method is possible to create the profiles with much higher accuracy which is comparable with CD-SEM for semiconductor device CD measurement. This method realizes two-dimensional metrology for refined pattern that had been difficult to measure conventionally by utilizing high precision contour profile. In this report, we will introduce the algorithm in general, the experimental results and the application in practice. As shrinkage of design rule for semiconductor device has further advanced, an aggressive OPC (Optical Proximity Correction) is indispensable in RET (Resolution Enhancement Technology). From the view point of DFM (Design for Manufacturability), a dramatic increase of data processing cost for advanced MDP (Mask Data Preparation) for instance and surge of mask making cost have become a big concern to the device manufacturers. This is to say, demands for quality is becoming strenuous because of enormous quantity of data growth with increasing of refined pattern on photo mask manufacture. In the result, massive amount of simulated error occurs on mask inspection that causes lengthening of mask production and inspection period, cost increasing, and long delivery time. In a sense, it is a trade-off between the high accuracy RET and the mask production cost, while it gives a significant impact on the semiconductor market centered around the mask business. To cope with the problem, we propose the best method of a DFM solution using two-dimensional metrology for refined pattern.
FragIt: a tool to prepare input files for fragment based quantum chemical calculations.
Directory of Open Access Journals (Sweden)
Casper Steinmann
Full Text Available Near linear scaling fragment based quantum chemical calculations are becoming increasingly popular for treating large systems with high accuracy and is an active field of research. However, it remains difficult to set up these calculations without expert knowledge. To facilitate the use of such methods, software tools need to be available to support these methods and help to set up reasonable input files which will lower the barrier of entry for usage by non-experts. Previous tools relies on specific annotations in structure files for automatic and successful fragmentation such as residues in PDB files. We present a general fragmentation methodology and accompanying tools called FragIt to help setup these calculations. FragIt uses the SMARTS language to locate chemically appropriate fragments in large structures and is applicable to fragmentation of any molecular system given suitable SMARTS patterns. We present SMARTS patterns of fragmentation for proteins, DNA and polysaccharides, specifically for D-galactopyranose for use in cyclodextrins. FragIt is used to prepare input files for the Fragment Molecular Orbital method in the GAMESS program package, but can be extended to other computational methods easily.
Computational Methods for Inviscid and Viscous Two-and-Three-Dimensional Flow Fields.
1975-01-01
Difference Equations Over a Network, Watson Sei. Comput. Lab. Report, 19U9. 173- Isaacson, E. and Keller, H. B., Analaysis of Numerical Methods...element method has given a new impulse to the old mathematical theory of multivariate interpolation. We first study the one-dimensional case, which
Newton-sor iterative method for solving the two-dimensional porous ...
African Journals Online (AJOL)
In this paper, we consider the application of the Newton-SOR iterative method in obtaining the approximate solution of the two-dimensional porous medium equation (2D PME). The nonlinear finite difference approximation equation to the 2D PME is derived by using the implicit finite difference scheme. The developed ...
International Nuclear Information System (INIS)
Chung, K.C.
1989-01-01
An introduction to nuclear fragmentation, with emphasis in percolation ideas, is presented. The main theoretical models are discussed and as an application, the uniform expansion approximation is presented and the statistical multifragmentation model is used to calculate the fragment energy spectra. (L.C.)
International Nuclear Information System (INIS)
Lee, Gil Soo
2006-02-01
To describe power distribution and multiplication factor of a reactor core accurately, it is necessary to perform calculations based on neutron transport equation considering heterogeneous geometry and scattering angles. These calculations require very heavy calculations and were nearly impossible with computers of old days. From the limitation of computing power, traditional approach of reactor core design consists of heterogeneous transport calculation in fuel assembly level and whole core diffusion nodal calculation with assembly homogenized properties, resulting from fuel assembly transport calculation. This approach may be effective in computation time, but it gives less accurate results for highly heterogeneous problems. As potential for whole core heterogeneous transport calculation became more feasible owing to rapid development of computing power during last several years, the interests in two and three dimensional whole core heterogeneous transport calculations by deterministic method are increased. For two dimensional calculation, there were several successful approaches using even parity transport equation with triangular meshes, S N method with refined rectangular meshes, the method of characteristics (MOC) with unstructured meshes, and so on. The work in this thesis originally started from the two dimensional whole core heterogeneous transport calculation by using MOC. After successful achievement in two dimensional calculation, there were efforts in three-dimensional whole-core heterogeneous transport calculation using MOC. Since direct extension to three dimensional calculation of MOC requires too much computing power, indirect approach to three dimensional calculation was considered.Thus, 2D/1D fusion method for three dimensional heterogeneous transport calculation was developed and successfully implemented in a computer code. The 2D/1D fusion method is synergistic combination of the MOC for radial 2-D calculation and S N -like methods for axial 1
Directory of Open Access Journals (Sweden)
Chih-Hao Lu
2015-01-01
Full Text Available We developed a computational method to identify NAD- and FAD-binding sites in proteins. First, we extracted from the Protein Data Bank structures of proteins that bind to at least one of these ligands. NAD-/FAD-binding residue templates were then constructed by identifying binding residues through the ligand-binding database BioLiP. The fragment transformation method was used to identify structures within query proteins that resembled the ligand-binding templates. By comparing residue types and their relative spatial positions, potential binding sites were identified and a ligand-binding potential for each residue was calculated. Setting the false positive rate at 5%, our method predicted NAD- and FAD-binding sites at true positive rates of 67.1% and 68.4%, respectively. Our method provides excellent results for identifying FAD- and NAD-binding sites in proteins, and the most important is that the requirement of conservation of residue types and local structures in the FAD- and NAD-binding sites can be verified.
Krasilenko, Vladimir G.; Lazarev, Alexander A.; Nikitovich, Diana V.
2018-03-01
The biologically-motivated self-learning equivalence-convolutional recurrent-multilayer neural structures (BLM_SL_EC_RMNS) for fragments images clustering and recognition will be discussed. We shall consider these neural structures and their spatial-invariant equivalental models (SIEMs) based on proposed equivalent two-dimensional functions of image similarity and the corresponding matrix-matrix (or tensor) procedures using as basic operations of continuous logic and nonlinear processing. These SIEMs can simply describe the signals processing during the all training and recognition stages and they are suitable for unipolar-coding multilevel signals. The clustering efficiency in such models and their implementation depends on the discriminant properties of neural elements of hidden layers. Therefore, the main models and architecture parameters and characteristics depends on the applied types of non-linear processing and function used for image comparison or for adaptive-equivalent weighing of input patterns. We show that these SL_EC_RMNSs have several advantages, such as the self-study and self-identification of features and signs of the similarity of fragments, ability to clustering and recognize of image fragments with best efficiency and strong mutual correlation. The proposed combined with learning-recognition clustering method of fragments with regard to their structural features is suitable not only for binary, but also color images and combines self-learning and the formation of weight clustered matrix-patterns. Its model is constructed and designed on the basis of recursively continuous logic and nonlinear processing algorithms and to k-average method or method the winner takes all (WTA). The experimental results confirmed that fragments with a large numbers of elements may be clustered. For the first time the possibility of generalization of these models for space invariant case is shown. The experiment for an images of different dimensions (a reference
Advanced numerical methods for three dimensional two-phase flow calculations in PWR
International Nuclear Information System (INIS)
Toumi, I.; Gallo, D.; Royer, E.
1997-01-01
This paper is devoted to new numerical methods developed for three dimensional two-phase flow calculations. These methods are finite volume numerical methods. They are based on an extension of Roe's approximate Riemann solver to define convective fluxes versus mean cell quantities. To go forward in time, a linearized conservative implicit integrating step is used, together with a Newton iterative method. We also present here some improvements performed to obtain a fully implicit solution method that provides fast running steady state calculations. This kind of numerical method, which is widely used for fluid dynamic calculations, is proved to be very efficient for the numerical solution to two-phase flow problems. This numerical method has been implemented for the three dimensional thermal-hydraulic code FLICA-4 which is mainly dedicated to core thermal-hydraulic transient and steady-state analysis. Hereafter, we will also find some results obtained for the EPR reactor running in a steady-state at 60% of nominal power with 3 pumps out of 4, and a thermal-hydraulic core analysis for a 1300 MW PWR at low flow steam-line-break conditions. (author)
Production and characterization of anti-human IgG F(ab')2 antibody fragment.
Valedkarimi, Zahra; Nasiri, Hadi; Aghebati-Maleki, Leili; Abdolalizadeh, Jalal; Esparvarinha, Mojghan; Majidi, Jafar
2018-04-10
In present study an optimized protocol for the separation of antibodies into antigen-binding fragments F(ab')2 using pepsin digestion was investigated. The production of these fragments is a consequential step in the development of medical research, treatment and diagnosis. For production of polyclonal antibody rabbit received antigen in four steps. The rabbit serum at 1/128000 dilution showed high absorbance in reaction with human IgG at the designed ELISA method. Rabbit IgG was purified by Ion-Exchange Chromatography (IEC) method. Purity was assessed by SDS-PAGE method. In non-reduced condition only one band was seen in about 150 kDa MW position and in reduced form, two bands were seen in 50 and 25 kDa MW positions. Rabbit IgG was digested by pepsin enzyme. The antibody fragments solution was applied to Gel filtration column to isolate the F(ab')2. Non-reduced SDS-PAGE for determining the purity of F(ab')2 fragment resulted in one band in 100 kDa corresponds to F(ab')2 fragment and a band in 150 kDa MW position corresponds to undigested IgG antibodies. The activities of FITC conjugated F(ab')2 fragment and commercial ones were compared using flowcytometry method. The activity results implied that the FITC conjugated- anti human F(ab')2 fragment worked as efficiently as the commercial one.
Advances in fragment-based drug discovery platforms.
Orita, Masaya; Warizaya, Masaichi; Amano, Yasushi; Ohno, Kazuki; Niimi, Tatsuya
2009-11-01
Fragment-based drug discovery (FBDD) has been established as a powerful alternative and complement to traditional high-throughput screening techniques for identifying drug leads. At present, this technique is widely used among academic groups as well as small biotech and large pharmaceutical companies. In recent years, > 10 new compounds developed with FBDD have entered clinical development, and more and more attention in the drug discovery field is being focused on this technique. Under the FBDD approach, a fragment library of relatively small compounds (molecular mass = 100 - 300 Da) is screened by various methods and the identified fragment hits which normally weakly bind to the target are used as starting points to generate more potent drug leads. Because FBDD is still a relatively new drug discovery technology, further developments and optimizations in screening platforms and fragment exploitation can be expected. This review summarizes recent advances in FBDD platforms and discusses the factors important for the successful application of this technique. Under the FBDD approach, both identifying the starting fragment hit to be developed and generating the drug lead from that starting fragment hit are important. Integration of various techniques, such as computational technology, X-ray crystallography, NMR, surface plasmon resonance, isothermal titration calorimetry, mass spectrometry and high-concentration screening, must be applied in a situation-appropriate manner.
Extraction of Phrase-Structure Fragments with a Linear Average Time Tree-Kernel
van Cranenburgh, Andreas
2014-01-01
We present an algorithm and implementation for extracting recurring fragments from treebanks. Using a tree-kernel method the largest common fragments are extracted from each pair of trees. The algorithm presented achieves a thirty-fold speedup over the previously available method on the Wall Street
BcL-xL Conformational Changes upon Fragment Binding Revealed by NMR
Aguirre, Clémentine; ten Brink, Tim; Walker, Olivier; Guillière, Florence; Davesne, Dany; Krimm, Isabelle
2013-01-01
Protein-protein interactions represent difficult but increasingly important targets for the design of therapeutic compounds able to interfere with biological processes. Recently, fragment-based strategies have been proposed as attractive approaches for the elaboration of protein-protein surface inhibitors from fragment-like molecules. One major challenge in targeting protein-protein interactions is related to the structural adaptation of the protein surface upon molecular recognition. Methods capable of identifying subtle conformational changes of proteins upon fragment binding are therefore required at the early steps of the drug design process. In this report we present a fast NMR method able to probe subtle conformational changes upon fragment binding. The approach relies on the comparison of experimental fragment-induced Chemical Shift Perturbation (CSP) of amine protons to CSP simulated for a set of docked fragment poses, considering the ring-current effect from fragment binding. We illustrate the method by the retrospective analysis of the complex between the anti-apoptotic Bcl-xL protein and the fragment 4′-fluoro-[1,1′-biphenyl]-4-carboxylic acid that was previously shown to bind one of the Bcl-xL hot spots. The CSP-based approach shows that the protein undergoes a subtle conformational rearrangement upon interaction, for residues located in helices 2, 3 and the very beginning of 5. Our observations are corroborated by residual dipolar coupling measurements performed on the free and fragment-bound forms of the Bcl-xL protein. These NMR-based results are in total agreement with previous molecular dynamic calculations that evidenced a high flexibility of Bcl-xL around the binding site. Here we show that CSP of protein amine protons are useful and reliable structural probes. Therefore, we propose to use CSP simulation to assess protein conformational changes upon ligand binding in the fragment-based drug design approach. PMID:23717610
A Monte Carlo Green's function method for three-dimensional neutron transport
International Nuclear Information System (INIS)
Gamino, R.G.; Brown, F.B.; Mendelson, M.R.
1992-01-01
This paper describes a Monte Carlo transport kernel capability, which has recently been incorporated into the RACER continuous-energy Monte Carlo code. The kernels represent a Green's function method for neutron transport from a fixed-source volume out to a particular volume of interest. This method is very powerful transport technique. Also, since kernels are evaluated numerically by Monte Carlo, the problem geometry can be arbitrarily complex, yet exact. This method is intended for problems where an ex-core neutron response must be determined for a variety of reactor conditions. Two examples are ex-core neutron detector response and vessel critical weld fast flux. The response is expressed in terms of neutron transport kernels weighted by a core fission source distribution. In these types of calculations, the response must be computed for hundreds of source distributions, but the kernels only need to be calculated once. The advance described in this paper is that the kernels are generated with a highly accurate three-dimensional Monte Carlo transport calculation instead of an approximate method such as line-of-sight attenuation theory or a synthesized three-dimensional discrete ordinates solution
Some comments on jet fragmentation models and sup(α)s determinations
International Nuclear Information System (INIS)
Sjoestrand, T.
1984-03-01
A number of interrelated topics on jet properties in e + e - annihilation is discussed. The need for different αsub(s) values in different fragmentation models is explained, with particular emphasis on the sensitivity to the choice of momentum conservation scheme in independent fragmentation models. Also other factors leading to a broad range of experimental αsub(s) values are discussed. Old and new methods to distinguish different fragmentation models are presented, with particular emphasis on gluon jet fragmentation properties. (orig.)
Three-dimensional protein structure prediction: Methods and computational strategies.
Dorn, Márcio; E Silva, Mariel Barbachan; Buriol, Luciana S; Lamb, Luis C
2014-10-12
A long standing problem in structural bioinformatics is to determine the three-dimensional (3-D) structure of a protein when only a sequence of amino acid residues is given. Many computational methodologies and algorithms have been proposed as a solution to the 3-D Protein Structure Prediction (3-D-PSP) problem. These methods can be divided in four main classes: (a) first principle methods without database information; (b) first principle methods with database information; (c) fold recognition and threading methods; and (d) comparative modeling methods and sequence alignment strategies. Deterministic computational techniques, optimization techniques, data mining and machine learning approaches are typically used in the construction of computational solutions for the PSP problem. Our main goal with this work is to review the methods and computational strategies that are currently used in 3-D protein prediction. Copyright © 2014 Elsevier Ltd. All rights reserved.
Sun, HongGuang; Liu, Xiaoting; Zhang, Yong; Pang, Guofei; Garrard, Rhiannon
2017-09-01
Fractional-order diffusion equations (FDEs) extend classical diffusion equations by quantifying anomalous diffusion frequently observed in heterogeneous media. Real-world diffusion can be multi-dimensional, requiring efficient numerical solvers that can handle long-term memory embedded in mass transport. To address this challenge, a semi-discrete Kansa method is developed to approximate the two-dimensional spatiotemporal FDE, where the Kansa approach first discretizes the FDE, then the Gauss-Jacobi quadrature rule solves the corresponding matrix, and finally the Mittag-Leffler function provides an analytical solution for the resultant time-fractional ordinary differential equation. Numerical experiments are then conducted to check how the accuracy and convergence rate of the numerical solution are affected by the distribution mode and number of spatial discretization nodes. Applications further show that the numerical method can efficiently solve two-dimensional spatiotemporal FDE models with either a continuous or discrete mixing measure. Hence this study provides an efficient and fast computational method for modeling super-diffusive, sub-diffusive, and mixed diffusive processes in large, two-dimensional domains with irregular shapes.
Development of three-dimensional transport code by the double finite element method
International Nuclear Information System (INIS)
Fujimura, Toichiro
1985-01-01
Development of a three-dimensional neutron transport code by the double finite element method is described. Both of the Galerkin and variational methods are adopted to solve the problem, and then the characteristics of them are compared. Computational results of the collocation method, developed as a technique for the vaviational one, are illustrated in comparison with those of an Ssub(n) code. (author)
A Comparison of Machine Learning Methods in a High-Dimensional Classification Problem
Directory of Open Access Journals (Sweden)
Zekić-Sušac Marijana
2014-09-01
Full Text Available Background: Large-dimensional data modelling often relies on variable reduction methods in the pre-processing and in the post-processing stage. However, such a reduction usually provides less information and yields a lower accuracy of the model. Objectives: The aim of this paper is to assess the high-dimensional classification problem of recognizing entrepreneurial intentions of students by machine learning methods. Methods/Approach: Four methods were tested: artificial neural networks, CART classification trees, support vector machines, and k-nearest neighbour on the same dataset in order to compare their efficiency in the sense of classification accuracy. The performance of each method was compared on ten subsamples in a 10-fold cross-validation procedure in order to assess computing sensitivity and specificity of each model. Results: The artificial neural network model based on multilayer perceptron yielded a higher classification rate than the models produced by other methods. The pairwise t-test showed a statistical significance between the artificial neural network and the k-nearest neighbour model, while the difference among other methods was not statistically significant. Conclusions: Tested machine learning methods are able to learn fast and achieve high classification accuracy. However, further advancement can be assured by testing a few additional methodological refinements in machine learning methods.
Gamma Radiation from Fission Fragments Experimental Apparatus-Mass Spectrum Resolution
Energy Technology Data Exchange (ETDEWEB)
Higbie, Jack
1969-08-15
The gamma-radiation from fission fragments was studied as a function of the fragment mass. The mass was determined from the fragment energies using solid state detectors. The mass resolution which can be achieved by this method is treated in detail. The average initial fragment mass and the initial mass resolution is calculated as a function of the measured (apparent) mass yield for three different thicknesses of the fissile material deposit. This treatment gives a clear indication of those factors most important for good mass resolution work. A detailed description of the experimental apparatus is given in the appendices.
A Generic multi-dimensional feature extraction method using multiobjective genetic programming.
Zhang, Yang; Rockett, Peter I
2009-01-01
In this paper, we present a generic feature extraction method for pattern classification using multiobjective genetic programming. This not only evolves the (near-)optimal set of mappings from a pattern space to a multi-dimensional decision space, but also simultaneously optimizes the dimensionality of that decision space. The presented framework evolves vector-to-vector feature extractors that maximize class separability. We demonstrate the efficacy of our approach by making statistically-founded comparisons with a wide variety of established classifier paradigms over a range of datasets and find that for most of the pairwise comparisons, our evolutionary method delivers statistically smaller misclassification errors. At very worst, our method displays no statistical difference in a few pairwise comparisons with established classifier/dataset combinations; crucially, none of the misclassification results produced by our method is worse than any comparator classifier. Although principally focused on feature extraction, feature selection is also performed as an implicit side effect; we show that both feature extraction and selection are important to the success of our technique. The presented method has the practical consequence of obviating the need to exhaustively evaluate a large family of conventional classifiers when faced with a new pattern recognition problem in order to attain a good classification accuracy.
String fragmentation; La fragmentation des cordes
Energy Technology Data Exchange (ETDEWEB)
Drescher, H.J.; Werner, K. [Laboratoire de Physique Subatomique et des Technologies Associees - SUBATECH, Centre National de la Recherche Scientifique, 44 - Nantes (France)
1997-10-01
The classical string model is used in VENUS as a fragmentation model. For the soft domain simple 2-parton strings were sufficient, whereas for higher energies up to LHC, the perturbative regime of the QCD gives additional soft gluons, which are mapped on the string as so called kinks, energy singularities between the leading partons. The kinky string model is chosen to handle fragmentation of these strings by application of the Lorentz invariant area law. The `kinky strings` model, corresponding to the perturbative gluons coming from pQCD, takes into consideration this effect by treating the partons and gluons on the same footing. The decay law is always the Artru-Menessier area law which is the most realistic since it is invariant to the Lorentz and gauge transformations. For low mass strings a manipulation of the rupture point is necessary if the string corresponds already to an elementary particle determined by the mass and the flavor content. By means of the fragmentation model it will be possible to simulate the data from future experiments at LHC and RHIC 3 refs.
Method for coupling two-dimensional to three-dimensional discrete ordinates calculations
International Nuclear Information System (INIS)
Thompson, J.L.; Emmett, M.B.; Rhoades, W.A.; Dodds, H.L. Jr.
1985-01-01
A three-dimensional (3-D) discrete ordinates transport code, TORT, has been developed at the Oak Ridge National Laboratory for radiation penetration studies. It is not feasible to solve some 3-D penetration problems with TORT, such as a building located a large distance from a point source, because (a) the discretized 3-D problem is simply too big to fit on the computer or (b) the computing time (and corresponding cost) is prohibitive. Fortunately, such problems can be solved with a hybrid approach by coupling a two-dimensional (2-D) description of the point source, which is assumed to be azimuthally symmetric, to a 3-D description of the building, the region of interest. The purpose of this paper is to describe this hybrid methodology along with its implementation and evaluation in the DOTTOR (Discrete Ordinates to Three-dimensional Oak Ridge Transport) code
Fragment separator momentum compression schemes
Energy Technology Data Exchange (ETDEWEB)
Bandura, Laura, E-mail: bandura@anl.gov [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); National Superconducting Cyclotron Lab, Michigan State University, 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Erdelyi, Bela [Argonne National Laboratory, Argonne, IL 60439 (United States); Northern Illinois University, DeKalb, IL 60115 (United States); Hausmann, Marc [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Kubo, Toshiyuki [RIKEN Nishina Center, RIKEN, Wako (Japan); Nolen, Jerry [Argonne National Laboratory, Argonne, IL 60439 (United States); Portillo, Mauricio [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Sherrill, Bradley M. [National Superconducting Cyclotron Lab, Michigan State University, 1 Cyclotron, East Lansing, MI 48824-1321 (United States)
2011-07-21
We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.
Fragment separator momentum compression schemes
International Nuclear Information System (INIS)
Bandura, Laura; Erdelyi, Bela; Hausmann, Marc; Kubo, Toshiyuki; Nolen, Jerry; Portillo, Mauricio; Sherrill, Bradley M.
2011-01-01
We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.
Moving Least Squares Method for a One-Dimensional Parabolic Inverse Problem
Directory of Open Access Journals (Sweden)
Baiyu Wang
2014-01-01
Full Text Available This paper investigates the numerical solution of a class of one-dimensional inverse parabolic problems using the moving least squares approximation; the inverse problem is the determination of an unknown source term depending on time. The collocation method is used for solving the equation; some numerical experiments are presented and discussed to illustrate the stability and high efficiency of the method.
Building a better fragment library for de novo protein structure prediction.
Directory of Open Access Journals (Sweden)
Saulo H P de Oliveira
Full Text Available Fragment-based approaches are the current standard for de novo protein structure prediction. These approaches rely on accurate and reliable fragment libraries to generate good structural models. In this work, we describe a novel method for structure fragment library generation and its application in fragment-based de novo protein structure prediction. The importance of correct testing procedures in assessing the quality of fragment libraries is demonstrated. In particular, the exclusion of homologs to the target from the libraries to correctly simulate a de novo protein structure prediction scenario, something which surprisingly is not always done. We demonstrate that fragments presenting different predominant predicted secondary structures should be treated differently during the fragment library generation step and that exhaustive and random search strategies should both be used. This information was used to develop a novel method, Flib. On a validation set of 41 structurally diverse proteins, Flib libraries presents both a higher precision and coverage than two of the state-of-the-art methods, NNMake and HHFrag. Flib also achieves better precision and coverage on the set of 275 protein domains used in the two previous experiments of the the Critical Assessment of Structure Prediction (CASP9 and CASP10. We compared Flib libraries against NNMake libraries in a structure prediction context. Of the 13 cases in which a correct answer was generated, Flib models were more accurate than NNMake models for 10. "Flib is available for download at: http://www.stats.ox.ac.uk/research/proteins/resources".
Building a Better Fragment Library for De Novo Protein Structure Prediction
de Oliveira, Saulo H. P.; Shi, Jiye; Deane, Charlotte M.
2015-01-01
Fragment-based approaches are the current standard for de novo protein structure prediction. These approaches rely on accurate and reliable fragment libraries to generate good structural models. In this work, we describe a novel method for structure fragment library generation and its application in fragment-based de novo protein structure prediction. The importance of correct testing procedures in assessing the quality of fragment libraries is demonstrated. In particular, the exclusion of homologs to the target from the libraries to correctly simulate a de novo protein structure prediction scenario, something which surprisingly is not always done. We demonstrate that fragments presenting different predominant predicted secondary structures should be treated differently during the fragment library generation step and that exhaustive and random search strategies should both be used. This information was used to develop a novel method, Flib. On a validation set of 41 structurally diverse proteins, Flib libraries presents both a higher precision and coverage than two of the state-of-the-art methods, NNMake and HHFrag. Flib also achieves better precision and coverage on the set of 275 protein domains used in the two previous experiments of the the Critical Assessment of Structure Prediction (CASP9 and CASP10). We compared Flib libraries against NNMake libraries in a structure prediction context. Of the 13 cases in which a correct answer was generated, Flib models were more accurate than NNMake models for 10. “Flib is available for download at: http://www.stats.ox.ac.uk/research/proteins/resources”. PMID:25901595
International Nuclear Information System (INIS)
Blaise, Philippe
1998-01-01
The aim of this thesis is to study metallic sodium clusters by numerical simulation. We have developed two ab initio molecular dynamics programs within the formalism of density functional theory. The first is based on the semi-classical extended Thomas-Fermi approach. We use a real-space grid and a Car-Parrinello-like scheme. The computational cost is O(N), and we have built a pseudopotential that speeds up the calculations. By neglecting quantum shell effects, we are able to study a very large set of clusters. We show that sodium cluster energies fit well a liquid drop formula, by adjusting a few parameters. We have investigated breathing modes, surface oscillations and the net charge density. We have shown that the surface energy varies strongly with temperature, and that clusters have a lower melting point than bulk material. We have calculated fission barriers by a constraint method. The second program is based on the quantum Kohn-Sham approach. We use a real-space grid, and combine a generalized Broyden scheme for assuring self-consistency with an iterative Davidson-Lanczos algorithm for solving the Eigen-problem. The cost of the method is much higher. First of all, we have calculated some stable structures for small clusters and their energetics. We obtained very good agreement with previous works. Then, we have investigated highly charged cluster dynamics. We have identified a chaotic fission process. For high fissility systems, we observe a multi-fragmentation dynamics and we find preferential emission of monomers on a characteristic time scale less than a pico-second. This has been simulated for the first time, with the help of our adaptive grid method which follows each fragment as they move apart during the fragmentation. (author)
Experiences in fragment-based drug discovery.
Murray, Christopher W; Verdonk, Marcel L; Rees, David C
2012-05-01
Fragment-based drug discovery (FBDD) has become established in both industry and academia as an alternative approach to high-throughput screening for the generation of chemical leads for drug targets. In FBDD, specialised detection methods are used to identify small chemical compounds (fragments) that bind to the drug target, and structural biology is usually employed to establish their binding mode and to facilitate their optimisation. In this article, we present three recent and successful case histories in FBDD. We then re-examine the key concepts and challenges of FBDD with particular emphasis on recent literature and our own experience from a substantial number of FBDD applications. Our opinion is that careful application of FBDD is living up to its promise of delivering high quality leads with good physical properties and that in future many drug molecules will be derived from fragment-based approaches. Copyright © 2012 Elsevier Ltd. All rights reserved.
Fission fragment angular momentum
International Nuclear Information System (INIS)
Frenne, D. De
1991-01-01
Most of the energy released in fission is converted into translational kinetic energy of the fragments. The remaining excitation energy will be distributed among neutrons and gammas. An important parameter characterizing the scission configuration is the primary angular momentum of the nascent fragments. Neutron emission is not expected to decrease the spin of the fragments by more than one unit of angular momentum and is as such of less importance in the determination of the initial fragment spins. Gamma emission is a suitable tool in studying initial fragment spins because the emission time, number, energy, and multipolarity of the gammas strongly depend on the value of the primary angular momentum. The main conclusions of experiments on gamma emission were that the initial angular momentum of the fragments is large compared to the ground state spin and oriented perpendicular to the fission axis. Most of the recent information concerning initial fragment spin distributions comes from the measurement of isomeric ratios for isomeric pairs produced in fission. Although in nearly every mass chain isomers are known, only a small number are suitable for initial fission fragment spin studies. Yield and half-life considerations strongly limit the number of candidates. This has the advantage that the behavior of a specific isomeric pair can be investigated for a number of fissioning systems at different excitation energies of the fragments and fissioning nuclei. Because most of the recent information on primary angular momenta comes from measurements of isomeric ratios, the global deexcitation process of the fragments and the calculation of the initial fragment spin distribution from measured isomeric ratios are discussed here. The most important results on primary angular momentum determinations are reviewed and some theoretical approaches are given. 45 refs., 7 figs., 2 tabs
The discrete cones method for two-dimensional neutron transport calculations
International Nuclear Information System (INIS)
Watanabe, Y.; Maynard, C.W.
1986-01-01
A novel method, the discrete cones method (DC/sub N/), is proposed as an alternative to the discrete ordinates method (S/sub N/) for solutions of the two-dimensional neutron transport equation. The new method utilizes a new concept, discrete cones, which are made by partitioning a unit spherical surface that the direction vector of particles covers. In this method particles in a cone are simultaneously traced instead of those in discrete directions so that an anomaly of the S/sub N/ method, the ray effects, can be eliminated. The DC/sub N/ method has been formulated for X-Y geometry and a program has been creaed by modifying the standard S/sub N/ program TWOTRAN-II. Our sample calculations demonstrate a strong mitigation of the ray effects without a computing cost penalty
A finite element method for calculating the 3-dimensional magnetic fields of cyclotron
International Nuclear Information System (INIS)
Zhao Xiaofeng
1986-01-01
A series of formula of the finite element method (scalar potential) for calculating the three-dimensional magnetic field of the main magnet of a sector focused cyclotron, and the realization method of the periodic boundary conditions in the code are given
Protein-Templated Fragment Ligations-From Molecular Recognition to Drug Discovery.
Jaegle, Mike; Wong, Ee Lin; Tauber, Carolin; Nawrotzky, Eric; Arkona, Christoph; Rademann, Jörg
2017-06-19
Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") utilizing a protein's surface as a reaction vessel to catalyze the formation of a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. In this way, chemical synthesis and bioassay are integrated in one single step. This Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products. The chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System.
Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; van den Berg, Albert; Eijkel, Jan C T; Shui, Lingling
2017-01-18
DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling system. We expect that hydrodynamic forces generated during the bubbling process shear the DNA molecules, extending and breaking them at the points where shearing forces are larger than the strength of the phosphate backbone. Factors of applied pressure, bubbling time and temperature have been investigated. Genomic DNA could be fragmented down to controllable 1-10 Kbp fragment lengths with a yield of 75.30-91.60%. We demonstrate that the ends of the genomic DNAs generated from hydrodynamic shearing can be ligated by T4 ligase and the fragmented DNAs can be used as templates for polymerase chain reaction. Therefore, in the bubbling system, DNAs could be hydrodynamically sheared to achieve smaller pieces in dsDNAs available for further processes. It could potentially serve as a DNA sample pretreatment technique in the future.
Azimuthal Anisotropies in Nuclear Fragmentation
International Nuclear Information System (INIS)
Dabrowska, A.; Szarska, M.; Trzupek, A.; Wolter, W.; Wosiek, B.
2002-01-01
The directed and elliptic flow of fragments emitted from the excited projectile nuclei has been observed for 158 AGeV Pb collisions with the lead and plastic targets. For comparison the flow analysis has been performed for 10.6 AGeV Au collisions with the emulsion target. The strong directed flow of heaviest fragments is found. Light fragments exhibit directed flow opposite to that of heavy fragments. The elliptic flow for all multiply charged fragments is positive and increases with the charge of the fragment. The observed flow patterns in the fragmentation of the projectile nucleus are practically independent of the mass of the target nucleus and the collision energy. Emission of fragments in nuclear multifragmentation shows similar, although weaker, flow effects. (author)
Analysis of fission-fragment mass distribution within the quantum-mechanical fragmentation theory
Energy Technology Data Exchange (ETDEWEB)
Singh, Pardeep; Kaur, Harjeet [Guru Nanak Dev University, Department of Physics, Amritsar (India)
2016-11-15
The fission-fragment mass distribution is analysed for the {sup 208}Pb({sup 18}O, f) reaction within the quantum-mechanical fragmentation theory (QMFT). The reaction potential has been calculated by taking the binding energies, Coulomb potential and proximity potential of all possible decay channels and a stationary Schroedinger equation has been solved numerically to calculate the fission-fragment yield. The overall results for mass distribution are compared with those obtained in experiment. Fine structure dips in yield, corresponding to fragment shell closures at Z = 50 and N=82, which are observed by Bogachev et al., are reproduced successfully in the present calculations. These calculations will help to estimate the formation probabilities of fission fragments and to understand many related phenomena occurring in the fission process. (orig.)
The interpolation method based on endpoint coordinate for CT three-dimensional image
International Nuclear Information System (INIS)
Suto, Yasuzo; Ueno, Shigeru.
1997-01-01
Image interpolation is frequently used to improve slice resolution to reach spatial resolution. Improved quality of reconstructed three-dimensional images can be attained with this technique as a result. Linear interpolation is a well-known and widely used method. The distance-image method, which is a non-linear interpolation technique, is also used to convert CT value images to distance images. This paper describes a newly developed method that makes use of end-point coordinates: CT-value images are initially converted to binary images by thresholding them and then sequences of pixels with 1-value are arranged in vertical or horizontal directions. A sequence of pixels with 1-value is defined as a line segment which has starting and end points. For each pair of adjacent line segments, another line segment was composed by spatial interpolation of the start and end points. Binary slice images are constructed from the composed line segments. Three-dimensional images were reconstructed from clinical X-ray CT images, using three different interpolation methods and their quality and processing speed were evaluated and compared. (author)
Roden, Suzanne E; Dutton, Peter H; Morin, Phillip A
2009-01-01
The green sea turtle, Chelonia mydas, was used as a case study for single nucleotide polymorphism (SNP) discovery in a species that has little genetic sequence information available. As green turtles have a complex population structure, additional nuclear markers other than microsatellites could add to our understanding of their complex life history. Amplified fragment length polymorphism technique was used to generate sets of random fragments of genomic DNA, which were then electrophoretically separated with precast gels, stained with SYBR green, excised, and directly sequenced. It was possible to perform this method without the use of polyacrylamide gels, radioactive or fluorescent labeled primers, or hybridization methods, reducing the time, expense, and safety hazards of SNP discovery. Within 13 loci, 2547 base pairs were screened, resulting in the discovery of 35 SNPs. Using this method, it was possible to yield a sufficient number of loci to screen for SNP markers without the availability of prior sequence information.
Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals
Crooks, Kevin R.; Burdett, Christopher L.; Theobald, David M.; King, Sarah R. B.; Rondinini, Carlo; Boitani, Luigi
2017-01-01
Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world’s terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, and most high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world’s terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation. PMID:28673992
International Nuclear Information System (INIS)
Yu, L.; Batlle, F.
2011-01-01
Highlights: → A quasi-three-dimensional slope stability analysis method was proposed. → The proposed method is a good engineering tool for 3D slope stability analysis. → Factor of safety from 3D analysis is higher than from 2D analysis. → 3D analysis results are more sensitive to cohesion than 2D analysis. - Abstract: Limited space for accommodating the ever increasing mounds of municipal solid waste (MSW) demands the capacity of MSW landfill be maximized by building landfills to greater heights with steeper slopes. This situation has raised concerns regarding the stability of high MSW landfills. A hybrid method for quasi-three-dimensional slope stability analysis based on the finite element stress analysis was applied in a case study at a MSW landfill in north-east Spain. Potential slides can be assumed to be located within the waste mass due to the lack of weak foundation soils and geosynthetic membranes at the landfill base. The only triggering factor of deep-seated slope failure is the higher leachate level and the relatively high and steep slope in the front. The valley-shaped geometry and layered construction procedure at the site make three-dimensional slope stability analyses necessary for this landfill. In the finite element stress analysis, variations of leachate level during construction and continuous settlement of the landfill were taken into account. The 'equivalent' three-dimensional factor of safety (FoS) was computed from the individual result of the two-dimensional analysis for a series of evenly spaced cross sections within the potential sliding body. Results indicate that the hybrid method for quasi-three-dimensional slope stability analysis adopted in this paper is capable of locating roughly the spatial position of the potential sliding mass. This easy to manipulate method can serve as an engineering tool in the preliminary estimate of the FoS as well as the approximate position and extent of the potential sliding mass. The result that
Morphologies of fission fragment impacts in diamond and silica
International Nuclear Information System (INIS)
Gammage, R.B.; Espinosa, G.; Vazquez, C.; Moreno, A.
2005-01-01
The morphologies of fission-fragment impact craters in diamond and silica were investigated by atomic force microscopy. The impacts produced micron-sized craters that were especially obvious in diamond; irradiations in air may have allowed the cratering in carbon to be oxidally enhanced. The eject deposit preferentially at ordered sites and have the appearance of hillocks of a few tenths microns in size. On quartz, the hillocks have a parallel-perpendicular, x-y pattern; on diamond, the hillocks form one dimensional, parallel rows. In contrast, the hillocks on amorphous silica fiber show a random pattern. (Author)
Observation of different isoscaling behavior between emitted fragments and residues
Energy Technology Data Exchange (ETDEWEB)
Youngs, M., E-mail: mdyoungs@comp.tamu.edu [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); McIntosh, A.B.; Hagel, K. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Heilborn, L. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Chemistry Department, Texas A& M University, College Station, TX 77843 (United States); Huang, M. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Jedele, A.; Kohley, Z.; May, L.W. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Chemistry Department, Texas A& M University, College Station, TX 77843 (United States); McCleskey, E. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Zarrella, A.; Yennello, S.J. [Cyclotron Institute, Texas A& M University, College Station, TX 77843 (United States); Chemistry Department, Texas A& M University, College Station, TX 77843 (United States)
2017-06-15
The traditional isoscaling technique has been used to analyze all isotopically identified particles from {sup 70}Zn+{sup 70}Zn and {sup 64}Zn+{sup 64}Zn collisions at 35 MeV/u. Two additional techniques, using an energy-averaged ratio and using the data present in the tail of energy spectra, are compared to the traditional method and show similar results. Isoscaling fit parameters α and β are found both globally and for each individual series of constant Z and N. The data are then split up between emitted fragments and projectile-like fragments. Isoscaling values for the two different types of fragments are shown to be different, emphasizing the importance of experimentally distinguishing between projectile-like fragments and emitted fragments in order to achieve accurate isoscaling parameters.
Development of three-dimensional ENRICHED FREE MESH METHOD and its application to crack analysis
International Nuclear Information System (INIS)
Suzuki, Hayato; Matsubara, Hitoshi; Ezawa, Yoshitaka; Yagawa, Genki
2010-01-01
In this paper, we describe a method for three-dimensional high accurate analysis of a crack included in a large-scale structure. The Enriched Free Mesh Method (EFMM) is a method for improving the accuracy of the Free Mesh Method (FMM), which is a kind of meshless method. First, we developed an algorithm of the three-dimensional EFMM. The elastic problem was analyzed using the EFMM and we find that its accuracy compares advantageously with the FMM, and the number of CG iterations is smaller. Next, we developed a method for calculating the stress intensity factor by employing the EFMM. The structure with a crack was analyzed using the EFMM, and the stress intensity factor was calculated by the developed method. The analysis results were very well in agreement with reference solution. It was shown that the proposed method is very effective in the analysis of the crack included in a large-scale structure. (author)
On the nuclear fragmentation mechanisms in nuclear collisions at intermediate and high energies
International Nuclear Information System (INIS)
Jipa, Al; Besliu, C.; Felea, D.
2004-01-01
The nuclear fragmentation mechanisms can be discussed by taking into account different scales related to the fragment sizes. Considering two fragmentation mechanisms of the nuclei at the same incident energy an analysis of the experimental results obtained was done. Goldhaber formula was improved by analyzing the discrepancies between data and theories concerning the projectile fragmentation. We implied that the projectile fragmentation process would be governed by the distribution of nucleon momenta in the projectile after the collision occurred. We used in our analysis protons from the 4 He + 7 Li at 4.5 GeV/c per nucleon incident momentum, as well as from 40 Ar + 12 C at 213 AMeV bombarding energy. We proved that in order to proceed in analyzing the projectile fragmentation process at intermediate and high energies one has to consider the dependence σ 0 on the apparent temperature of projectile nucleus after the collision took place. The generalized Bertsch correction for light projectile nuclei and fragments was used and the number of spatial correlations between identical nucleons having anticorrelated momenta was found. Thus we found apparent temperature values close to the separation energies of the considered fragments per number of fragments. The temperatures associated to kinetic energy spectra of the projectile fragments were calculated following two methods. The results from Bauer's method were compared with those obtained by fitting the kinetic energy distributions of the projectile fragments in the rest frame of the projectile with a Maxwellian curve. We also accomplished the comparison of the experimental results with similar events simulated with RQMD 2.4. All the results obtained suggested two nuclear fragmentation mechanisms: a sudden fragmentation by explosive mechanisms, like shock waves and a slow fragmentation by the 'fission' of the spectator regions, mainly because of the interactions with the particles or fragments emitted from the
Gouge, Michael F.
2011-01-01
Hypervelocity impact tests on test satellites are performed by members of the orbital debris scientific community in order to understand and typify the on-orbit collision breakup process. By analysis of these test satellite fragments, the fragment size and mass distributions are derived and incorporated into various orbital debris models. These same fragments are currently being put to new use using emerging technologies. Digital models of these fragments are created using a laser scanner. A group of computer programs referred to as the Fragment Rotation Analysis and Lightcurve code uses these digital representations in a multitude of ways that describe, measure, and model on-orbit fragments and fragment behavior. The Dynamic Rotation subroutine generates all of the possible reflected intensities from a scanned fragment as if it were observed to rotate dynamically while in orbit about the Earth. This calls an additional subroutine that graphically displays the intensities and the resulting frequency of those intensities as a range of solar phase angles in a Probability Density Function plot. This document reports the additions and modifications to the subset of the Fragment Rotation Analysis and Lightcurve concerned with the Dynamic Rotation and Probability Density Function plotting subroutines.
Energy Technology Data Exchange (ETDEWEB)
Yoon, Hyun Jin; Kim, Dong Il [Korea Maritime University, Busan (Korea, Republic of)
2004-10-15
The purpose of this simulation study is to design and fabricate an electromagnetic (EM) wave absorber in order to develop a wide-band absorber. We have proposed and modeled a bird-eye-type and cutting-cone-type EM wave absorber by using the equivalent material constants method (EMCM), and we simulated them by using a finite-difference time-domain (FDTD) method. A two or a three-dimensional simulation would be desirable to analyze the EM wave absorber characteristics and to develop new structures. The two-dimensional FDTD simulation requires less computer resources than a three-dimensional simulation to consider the structural effects of the EM wave absorbers. The numerical simulation by using the FDTD method shows propagating EM waves in various types of periodic structure EM wave absorbers. Simultaneously, a Fourier analysis is used to characterize the input pulse and the reflected EM waves for ferrite absorbers with various structures. The results have a wide-band reflection-reducing characteristic. The validity of the proposed model was confirmed by comparing the two-dimensional simulation with the experimental results. The simulations were carried out in the frequency band from 30 MHz to 10 GHz.
International Nuclear Information System (INIS)
Yoon, Hyun Jin; Kim, Dong Il
2004-01-01
The purpose of this simulation study is to design and fabricate an electromagnetic (EM) wave absorber in order to develop a wide-band absorber. We have proposed and modeled a bird-eye-type and cutting-cone-type EM wave absorber by using the equivalent material constants method (EMCM), and we simulated them by using a finite-difference time-domain (FDTD) method. A two or a three-dimensional simulation would be desirable to analyze the EM wave absorber characteristics and to develop new structures. The two-dimensional FDTD simulation requires less computer resources than a three-dimensional simulation to consider the structural effects of the EM wave absorbers. The numerical simulation by using the FDTD method shows propagating EM waves in various types of periodic structure EM wave absorbers. Simultaneously, a Fourier analysis is used to characterize the input pulse and the reflected EM waves for ferrite absorbers with various structures. The results have a wide-band reflection-reducing characteristic. The validity of the proposed model was confirmed by comparing the two-dimensional simulation with the experimental results. The simulations were carried out in the frequency band from 30 MHz to 10 GHz.
Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge
Kumar, Ashutosh; Zhang, Kam Y. J.
2012-05-01
SAMPL3 fragment based virtual screening challenge provides a valuable opportunity for researchers to test their programs, methods and screening protocols in a blind testing environment. We participated in SAMPL3 challenge and evaluated our virtual fragment screening protocol, which involves RosettaLigand as the core component by screening a 500 fragments Maybridge library against bovine pancreatic trypsin. Our study reaffirmed that the real test for any virtual screening approach would be in a blind testing environment. The analyses presented in this paper also showed that virtual screening performance can be improved, if a set of known active compounds is available and parameters and methods that yield better enrichment are selected. Our study also highlighted that to achieve accurate orientation and conformation of ligands within a binding site, selecting an appropriate method to calculate partial charges is important. Another finding is that using multiple receptor ensembles in docking does not always yield better enrichment than individual receptors. On the basis of our results and retrospective analyses from SAMPL3 fragment screening challenge we anticipate that chances of success in a fragment screening process could be increased significantly with careful selection of receptor structures, protein flexibility, sufficient conformational sampling within binding pocket and accurate assignment of ligand and protein partial charges.
Directory of Open Access Journals (Sweden)
Ross S Williamson
2015-04-01
Full Text Available Stimulus dimensionality-reduction methods in neuroscience seek to identify a low-dimensional space of stimulus features that affect a neuron's probability of spiking. One popular method, known as maximally informative dimensions (MID, uses an information-theoretic quantity known as "single-spike information" to identify this space. Here we examine MID from a model-based perspective. We show that MID is a maximum-likelihood estimator for the parameters of a linear-nonlinear-Poisson (LNP model, and that the empirical single-spike information corresponds to the normalized log-likelihood under a Poisson model. This equivalence implies that MID does not necessarily find maximally informative stimulus dimensions when spiking is not well described as Poisson. We provide several examples to illustrate this shortcoming, and derive a lower bound on the information lost when spiking is Bernoulli in discrete time bins. To overcome this limitation, we introduce model-based dimensionality reduction methods for neurons with non-Poisson firing statistics, and show that they can be framed equivalently in likelihood-based or information-theoretic terms. Finally, we show how to overcome practical limitations on the number of stimulus dimensions that MID can estimate by constraining the form of the non-parametric nonlinearity in an LNP model. We illustrate these methods with simulations and data from primate visual cortex.
Correlation based method for comparing and reconstructing quasi-identical two-dimensional structures
International Nuclear Information System (INIS)
Mejia-Barbosa, Y.
2000-03-01
We show a method for comparing and reconstructing two similar amplitude-only structures, which are composed by the same number of identical apertures. The structures are two-dimensional and differ only in the location of one of the apertures. The method is based on a subtraction algorithm, which involves the auto-correlations and cross-correlation functions of the compared structures. Experimental results illustrate the feasibility of the method. (author)
A Feature Subset Selection Method Based On High-Dimensional Mutual Information
Directory of Open Access Journals (Sweden)
Chee Keong Kwoh
2011-04-01
Full Text Available Feature selection is an important step in building accurate classifiers and provides better understanding of the data sets. In this paper, we propose a feature subset selection method based on high-dimensional mutual information. We also propose to use the entropy of the class attribute as a criterion to determine the appropriate subset of features when building classifiers. We prove that if the mutual information between a feature set X and the class attribute Y equals to the entropy of Y , then X is a Markov Blanket of Y . We show that in some cases, it is infeasible to approximate the high-dimensional mutual information with algebraic combinations of pairwise mutual information in any forms. In addition, the exhaustive searches of all combinations of features are prerequisite for finding the optimal feature subsets for classifying these kinds of data sets. We show that our approach outperforms existing filter feature subset selection methods for most of the 24 selected benchmark data sets.
Payne, Lloyd R.; Cole, David L.
2010-03-30
A fragment capture device for use in explosive containment. The device comprises an assembly of at least two rows of bars positioned to eliminate line-of-sight trajectories between the generation point of fragments and a surrounding containment vessel or asset. The device comprises an array of at least two rows of bars, wherein each row is staggered with respect to the adjacent row, and wherein a lateral dimension of each bar and a relative position of each bar in combination provides blockage of a straight-line passage of a solid fragment through the adjacent rows of bars, wherein a generation point of the solid fragment is located within a cavity at least partially enclosed by the array of bars.
A new analytical method to solve the heat equation for a multi-dimensional composite slab
International Nuclear Information System (INIS)
Lu, X; Tervola, P; Viljanen, M
2005-01-01
A novel analytical approach has been developed for heat conduction in a multi-dimensional composite slab subject to time-dependent boundary changes of the first kind. Boundary temperatures are represented as Fourier series. Taking advantage of the periodic properties of boundary changes, the analytical solution is obtained and expressed explicitly. Nearly all the published works necessitate searching for associated eigenvalues in solving such a problem even for a one-dimensional composite slab. In this paper, the proposed method involves no iterative computation such as numerically searching for eigenvalues and no residue evaluation. The adopted method is simple which represents an extension of the novel analytical approach derived for the one-dimensional composite slab. Moreover, the method of 'separation of variables' employed in this paper is new. The mathematical formula for solutions is concise and straightforward. The physical parameters are clearly shown in the formula. Further comparison with numerical calculations is presented
Modified Splitting FDTD Methods for Two-Dimensional Maxwell’s Equations
Directory of Open Access Journals (Sweden)
Liping Gao
2017-01-01
Full Text Available In this paper, we develop a new method to reduce the error in the splitting finite-difference method of Maxwell’s equations. By this method two modified splitting FDTD methods (MS-FDTDI, MS-FDTDII for the two-dimensional Maxwell equations are proposed. It is shown that the two methods are second-order accurate in time and space and unconditionally stable by Fourier methods. By energy method, it is proved that MS-FDTDI is second-order convergent. By deriving the numerical dispersion (ND relations, we prove rigorously that MS-FDTDI has less ND errors than the ADI-FDTD method and the ND errors of ADI-FDTD are less than those of MS-FDTDII. Numerical experiments for computing ND errors and simulating a wave guide problem and a scattering problem are carried out and the efficiency of the MS-FDTDI and MS-FDTDII methods is confirmed.
Modeling of three-dimensional diffusible resistors with the one-dimensional tube multiplexing method
International Nuclear Information System (INIS)
Gillet, Jean-Numa; Degorce, Jean-Yves; Meunier, Michel
2009-01-01
Electronic-behavior modeling of three-dimensional (3D) p + -π-p + and n + -ν-n + semiconducting diffusible devices with highly accurate resistances for the design of analog resistors, which are compatible with the CMOS (complementary-metal-oxide-semiconductor) technologies, is performed in three dimensions with the fast tube multiplexing method (TMM). The current–voltage (I–V) curve of a silicon device is usually computed with traditional device simulators of technology computer-aided design (TCAD) based on the finite-element method (FEM). However, for the design of 3D p + -π-p + and n + -ν-n + diffusible resistors, they show a high computational cost and convergence that may fail with fully non-separable 3D dopant concentration profiles as observed in many diffusible resistors resulting from laser trimming. These problems are avoided with the proposed TMM, which divides the 3D resistor into one-dimensional (1D) thin tubes with longitudinal axes following the main orientation of the average electrical field in the tubes. The I–V curve is rapidly obtained for a device with a realistic 3D dopant profile, since a system of three first-order ordinary differential equations has to be solved for each 1D multiplexed tube with the TMM instead of three second-order partial differential equations in the traditional TCADs. Simulations with the TMM are successfully compared to experimental results from silicon-based 3D resistors fabricated by laser-induced dopant diffusion in the gaps of MOSFETs (metal-oxide-semiconductor field-effect transistors) without initial gate. Using thin tubes with other shapes than parallelepipeds as ring segments with toroidal lateral surfaces, the TMM can be generalized to electronic devices with other types of 3D diffusible microstructures
Energy Technology Data Exchange (ETDEWEB)
Blaise, Philippe [Universite Joseph Fourier, Grenoble 1, 74 Annecy (France)
1998-09-29
The aim of this thesis is to study metallic sodium clusters by numerical simulation. We have developed two ab initio molecular dynamics programs within the formalism of density functional theory. The first is based on the semi-classical extended Thomas-Fermi approach. We use a real-space grid and a Car-Parrinello-like scheme. The computational cost is O(N), and we have built a pseudopotential that speeds up the calculations. By neglecting quantum shell effects, we are able to study a very large set of clusters. We show that sodium cluster energies fit well a liquid drop formula, by adjusting a few parameters. We have investigated breathing modes, surface oscillations and the net charge density. We have shown that the surface energy varies strongly with temperature, and that clusters have a lower melting point than bulk material. We have calculated fission barriers by a constraint method. The second program is based on the quantum Kohn-Sham approach. We use a real-space grid, and combine a generalized Broyden scheme for assuring self-consistency with an iterative Davidson-Lanczos algorithm for solving the Eigen-problem. The cost of the method is much higher. First of all, we have calculated some stable structures for small clusters and their energetics. We obtained very good agreement with previous works. Then, we have investigated highly charged cluster dynamics. We have identified a chaotic fission process. For high fissility systems, we observe a multi-fragmentation dynamics and we find preferential emission of monomers on a characteristic time scale less than a pico-second. This has been simulated for the first time, with the help of our adaptive grid method which follows each fragment as they move apart during the fragmentation. (author) 87 refs., 57 figs., 4 tabs.
Mutant DNA quantification by digital PCR can be confounded by heating during DNA fragmentation.
Kang, Qing; Parkin, Brian; Giraldez, Maria D; Tewari, Muneesh
2016-04-01
Digital PCR (dPCR) is gaining popularity as a DNA mutation quantification method for clinical specimens. Fragmentation prior to dPCR is required for non-fragmented genomic DNA samples; however, the effect of fragmentation on DNA analysis has not been well-studied. Here we evaluated three fragmentation methods for their effects on dPCR point mutation assay performance. Wild-type (WT) human genomic DNA was fragmented by heating, restriction digestion, or acoustic shearing using a Covaris focused-ultrasonicator. dPCR was then used to determine the limit of blank (LoB) by quantifying observed WT and mutant allele counts of the proto-oncogenes KRAS and BRAF in the WT DNA sample. DNA fragmentation by heating to 95°C, while the simplest and least expensive method, produced a high background mutation frequency for certain KRAS mutations relative to the other methods. This was due to heat-induced mutations, specifically affecting dPCR assays designed to interrogate guanine to adenine (G>A) mutations. Moreover, heat-induced fragmentation overestimated gene copy number, potentially due to denaturation and partition of single-stranded DNA into different droplets. Covaris acoustic shearing and restriction enzyme digestion showed similar LoBs and gene copy number estimates to one another. It should be noted that moderate heating, commonly used in genomic DNA extraction protocols, did not significantly increase observed KRAS mutation counts.
Directory of Open Access Journals (Sweden)
Hasibun Naher
2012-01-01
Full Text Available We construct new analytical solutions of the (3+1-dimensional modified KdV-Zakharov-Kuznetsev equation by the Exp-function method. Plentiful exact traveling wave solutions with arbitrary parameters are effectively obtained by the method. The obtained results show that the Exp-function method is effective and straightforward mathematical tool for searching analytical solutions with arbitrary parameters of higher-dimensional nonlinear partial differential equation.
Intravitreal Phacoemulsification Using Torsional Handpiece for Retained Lens Fragments
Kumar, Vinod; Takkar, Brijesh
2016-01-01
Purpose: To evaluate the results of intravitreal phacoemulsification with torsional hand piece in eyes with posteriorly dislocated lens fragments. Methods: In this prospective, interventional case series, 15 eyes with retained lens fragments following phacoemulsification were included. All patients underwent standard three-port pars plana vitrectomy and intravitreal phacoemulsification using sleeveless, torsional hand piece (OZiL™, Alcon's Infiniti Vision System). Patients were followed up...
The Y4-RNA fragment, a potential diagnostic marker, exists in saliva
Directory of Open Access Journals (Sweden)
Tatsuya Ishikawa
2017-06-01
Full Text Available The 94-nt full-length Y4-RNA is thought to have roles in the initiation of DNA replication and RNA quality control. Although its 31/32-nt fragment also exists abundantly in plasma, little is known about its physiological role. Since the 31/32-nt Y4-RNA fragment in sera is reported to be more abundant in patients with coronary artery disease than healthy persons, the fragment may have a potential for a diagnostic and/or prognostic biomarker for some diseases regardless of its functionality. As a step toward further investigation of its potential utility, we examined if the 31/32-nt Y4-RNA fragment also exists in saliva that can be obtained noninvasively, and showed that, in addition to the 31/32-nt fragment, 14- and 11-nt Y4-RNA fragments are present in all saliva RNA samples from four healthy persons. We established a PCR method to accurately quantitate the amount of the 31/32-nt Y4-RNA fragment, and estimated its amount in saliva of healthy persons to be 0.06 ± 0.04 fmol per nanogram of saliva RNA. We also tried to develop an easier quantitation method using a DNA molecular beacon. Keywords: Y4-RNA fragment, Saliva RNA, Diagnostic/prognostic marker, Next-generation sequencing, RT-PCR, Molecular beacon
Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJun
2018-06-01
The folding and three-dimensional (3D) organization of chromatin in the nucleus critically impacts genome function. The past decade has witnessed rapid advances in genomic tools for delineating 3D genome architecture. Among them, chromosome conformation capture (3C)-based methods such as Hi-C are the most widely used techniques for mapping chromatin interactions. However, traditional Hi-C protocols rely on restriction enzymes (REs) to fragment chromatin and are therefore limited in resolution. We recently developed DNase Hi-C for mapping 3D genome organization, which uses DNase I for chromatin fragmentation. DNase Hi-C overcomes RE-related limitations associated with traditional Hi-C methods, leading to improved methodological resolution. Furthermore, combining this method with DNA capture technology provides a high-throughput approach (targeted DNase Hi-C) that allows for mapping fine-scale chromatin architecture at exceptionally high resolution. Hence, targeted DNase Hi-C will be valuable for delineating the physical landscapes of cis-regulatory networks that control gene expression and for characterizing phenotype-associated chromatin 3D signatures. Here, we provide a detailed description of method design and step-by-step working protocols for these two methods. Copyright © 2018 Elsevier Inc. All rights reserved.
NMR characterization of weak interactions between RhoGDI2 and fragment screening hits.
Liu, Jiuyang; Gao, Jia; Li, Fudong; Ma, Rongsheng; Wei, Qingtao; Wang, Aidong; Wu, Jihui; Ruan, Ke
2017-01-01
The delineation of intrinsically weak interactions between novel targets and fragment screening hits has long limited the pace of hit-to-lead evolution. Rho guanine-nucleotide dissociation inhibitor 2 (RhoGDI2) is a novel target that lacks any chemical probes for the treatment of tumor metastasis. Protein-observed and ligand-observed NMR spectroscopy was used to characterize the weak interactions between RhoGDI2 and fragment screening hits. We identified three hits of RhoGDI2 using streamlined NMR fragment-based screening. The binding site residues were assigned using non-uniformly sampled C α - and H α -based three dimensional NMR spectra. The molecular docking to the proposed geranylgeranyl binding pocket of RhoGDI2 was guided by NMR restraints of chemical shift perturbations and ligand-observed transferred paramagnetic relaxation enhancement. We further validated the weak RhoGDI2-hit interactions using mutagenesis and structure-affinity analysis. Weak interactions between RhoGDI2 and fragment screening hits were delineated using an integrated NMR approach. Binders to RhoGDI2 as a potential anti-cancer target have been first reported, and their weak interactions were depicted using NMR spectroscopy. Our work highlights the powerfulness and the versatility of the integrative NMR techniques to provide valuable structural insight into the intrinsically weak interactions between RhoGDI2 and the fragment screening hits, which could hardly be conceived using other biochemical techniques. Copyright Â© 2016 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
Jiabing Ji
Full Text Available BACKGROUND: Insertion mutant isolation and characterization are extremely valuable for linking genes to physiological function. Once an insertion mutant phenotype is identified, the challenge is to isolate the responsible gene. Multiple strategies have been employed to isolate unknown genomic DNA that flanks mutagenic insertions, however, all these methods suffer from limitations due to inefficient ligation steps, inclusion of restriction sites within the target DNA, and non-specific product generation. These limitations become close to insurmountable when the goal is to identify insertion sites in a high throughput manner. METHODOLOGY/PRINCIPAL FINDINGS: We designed a novel strategy called Restriction Site Extension PCR (RSE-PCR to efficiently conduct large-scale isolation of unknown genomic DNA fragments linked to DNA insertions. The strategy is a modified adaptor-mediated PCR without ligation. An adapter, with complementarity to the 3' overhang of the endonuclease (KpnI, NsiI, PstI, or SacI restricted DNA fragments, extends the 3' end of the DNA fragments in the first cycle of the primary RSE-PCR. During subsequent PCR cycles and a second semi-nested PCR (secondary RSE-PCR, touchdown and two-step PCR are combined to increase the amplification specificity of target fragments. The efficiency and specificity was demonstrated in our characterization of 37 tex mutants of Arabidopsis. All the steps of RSE-PCR can be executed in a 96 well PCR plate. Finally, RSE-PCR serves as a successful alternative to Genome Walker as demonstrated by gene isolation from maize, a plant with a more complex genome than Arabidopsis. CONCLUSIONS/SIGNIFICANCE: RSE-PCR has high potential application in identifying tagged (T-DNA or transposon sequence or walking from known DNA toward unknown regions in large-genome plants, with likely application in other organisms as well.
DEFF Research Database (Denmark)
Jendresen, Christian Bille; Kilstrup, Mogens; Martinussen, Jan
2011-01-01
-pyrophosphate (PRPP), and inorganic pyrophosphate (PPi) in cell extracts. The method uses one-dimensional thin-layer chromatography (TLC) and radiolabeled biological samples. Nucleotides are resolved at the level of ionic charge in an optimized acidic ammonium formate and chloride solvent, permitting...... quantification of NTPs. The method is significantly simpler and faster than both current two-dimensional methods and high-performance liquid chromatography (HPLC)-based procedures, allowing a higher throughput while common sources of inaccuracies and technical problems are avoided. For determination of PPi...
Land fragmentation and production diversification
Ciaian, Pavel; Guri, Fatmir; Rajcaniova, Miroslava; Drabik, Dusan; Paloma, Sergio Gomez Y.
2018-01-01
We analyze the impact of land fragmentation on production diversification in rural Albania. Albania represents a particularly interesting case for studying land fragmentation as the fragmentation is a direct outcome of land reforms. The results indicate that land fragmentation is an important driver
A Two-Dimensional Solar Tracking Stationary Guidance Method Based on Feature-Based Time Series
Directory of Open Access Journals (Sweden)
Keke Zhang
2018-01-01
Full Text Available The amount of satellite energy acquired has a direct impact on operational capacities of the satellite. As for practical high functional density microsatellites, solar tracking guidance design of solar panels plays an extremely important role. Targeted at stationary tracking problems incurred in a new system that utilizes panels mounted in the two-dimensional turntable to acquire energies to the greatest extent, a two-dimensional solar tracking stationary guidance method based on feature-based time series was proposed under the constraint of limited satellite attitude coupling control capability. By analyzing solar vector variation characteristics within an orbit period and solar vector changes within the whole life cycle, such a method could be adopted to establish a two-dimensional solar tracking guidance model based on the feature-based time series to realize automatic switching of feature-based time series and stationary guidance under the circumstance of different β angles and the maximum angular velocity control, which was applicable to near-earth orbits of all orbital inclination. It was employed to design a two-dimensional solar tracking stationary guidance system, and a mathematical simulation for guidance performance was carried out in diverse conditions under the background of in-orbit application. The simulation results show that the solar tracking accuracy of two-dimensional stationary guidance reaches 10∘ and below under the integrated constraints, which meet engineering application requirements.
The analysis of RPV fast neutron flux calculation for PWR with three-dimensional SN method
International Nuclear Information System (INIS)
Yang Shouhai; Chen Yixue; Wang Weijin; Shi Shengchun; Lu Daogang
2011-01-01
Discrete ordinates (S N ) method is one of the most widely used method for reactor pressure vessel (RPV) design. As the fast development of computer CPU speed and memory capacity and consummation of three-dimensional discrete-ordinates method, it is mature for 3-D S N method to be used to engineering design for nuclear facilities. This work was done specifically for PWR model, with the results of 3-D core neutron transport calculation by 3-D core calculation, 3-D RPV fast neutron flux distribution obtain by 3-D S N method were compared with gained by 1-D and 2-D S N method and the 3-D Monte Carlo (MC) method. In this paper, the application of three-dimensional S N method in calculating RPV fast neutron flux distribution for pressurized water reactor (PWR) is presented and discussed. (authors)
A semiclassical model for quark jet fragmentation
International Nuclear Information System (INIS)
Andersson, B.; Gustafson, G.; Peterson, C.
1979-01-01
A semiclassical model is presented for the way the energy of a fast quark is transformed into observable hadrons. It reproduces the features of 1+1 dimensional QED (the Schwinger model) concerning a flat rapidity distribution in the central region. It also reproduces results from phenomenological considerations, which, based upon scaling, predict that meson formation in the fragmentation region can be described by an iterative scheme, implying a set of coupled integral equations. In particular the model predicts that the probability to find a meson containing the leading quark is independent of the Feynman scaling variable z. The iterative structure corresponds to a Brownian motion with relevance both to the cofinement problems and to the distribution of mass in the quark jet. (orig.) [de
Fragmentation processes in nuclear reactions
International Nuclear Information System (INIS)
Legrain, R.
1984-08-01
Projectile and nuclear fragmentation are defined and processes referred to are recalled. The two different aspects of fragmentation are considered but the emphasis is also put on heavy ion induced reactions. The preliminary results of an experiment performed at GANIL to study peripheral heavy ions induced reactions at intermediate energy are presented. The results of this experiment will illustrate the characteristics of projectile fragmentation and this will also give the opportunity to study projectile fragmentation in the transition region. Then nuclear fragmentation is considered which is associated with more central collisions in the case of heavy ion induced reactions. This aspect of fragmentation is also ilustrated with two heavy ion experiments in which fragments emitted at large angle have been observed
Fragment assignment in the cloud with eXpress-D
2013-01-01
Background Probabilistic assignment of ambiguously mapped fragments produced by high-throughput sequencing experiments has been demonstrated to greatly improve accuracy in the analysis of RNA-Seq and ChIP-Seq, and is an essential step in many other sequence census experiments. A maximum likelihood method using the expectation-maximization (EM) algorithm for optimization is commonly used to solve this problem. However, batch EM-based approaches do not scale well with the size of sequencing datasets, which have been increasing dramatically over the past few years. Thus, current approaches to fragment assignment rely on heuristics or approximations for tractability. Results We present an implementation of a distributed EM solution to the fragment assignment problem using Spark, a data analytics framework that can scale by leveraging compute clusters within datacenters–“the cloud”. We demonstrate that our implementation easily scales to billions of sequenced fragments, while providing the exact maximum likelihood assignment of ambiguous fragments. The accuracy of the method is shown to be an improvement over the most widely used tools available and can be run in a constant amount of time when cluster resources are scaled linearly with the amount of input data. Conclusions The cloud offers one solution for the difficulties faced in the analysis of massive high-thoughput sequencing data, which continue to grow rapidly. Researchers in bioinformatics must follow developments in distributed systems–such as new frameworks like Spark–for ways to port existing methods to the cloud and help them scale to the datasets of the future. Our software, eXpress-D, is freely available at: http://github.com/adarob/express-d. PMID:24314033
Three-dimensional static and dynamic reactor calculations by the nodal expansion method
International Nuclear Information System (INIS)
Christensen, B.
1985-05-01
This report reviews various method for the calculation of the neutron-flux- and power distribution in an nuclear reactor. The nodal expansion method (NEM) is especially described in much detail. The nodal expansion method solves the diffusion equation. In this method the reactor core is divided into nodes, typically 10 to 20 cm in each direction, and the average flux in each node is calculated. To obtain the coupling between the nodes the local flux inside each node is expressed by use of a polynomial expansion. The expansion is one-dimensional, so inside each node such three expansions occur. To calculate the expansion coefficients it is necessary that the polynomial expansion is a solution to the one-dimensional diffusion equation. When the one-dimensional diffusion equation is established a term with the transversal leakage occur, and this term is expanded after the same polynomials. The resulting equation system with the expansion coefficients as the unknowns is solved with weigthed residual technique. The nodal expansion method is built into a computer program (also called NEM), which is divided into two parts, one part for steady-state calculations and one part for dynamic calculations. It is possible to take advantage of symmetry properties of the reactor core. The program is very flexible with regard to the number of energy groups, the node size, the flux expansion order and the transverse leakage expansion order. The boundary of the core is described by albedos. The program and input to it are described. The program is tested on a number of examples extending from small theoretical one up to realistic reactor cores. Many calculations are done on the wellknown IAEA benchmark case. The calculations have tested the accuracy and the computing time for various node sizes and polynomial expansions. In the dynamic examples various strategies for variation of the time step-length have been tested. (author)
Amplification of deoxyribonucleic acid (DNA) fragment using two ...
African Journals Online (AJOL)
user
2011-04-11
Apr 11, 2011 ... polymerases on this method, whether different lengths of. DNA fragments could be amplified by two-step PCR and the difference of DNA product quality produced by the two methods. MATERIALS AND METHODS. PCR template and reagents. Enterobacteria phage lambda DNA (GenBank no: V00636) ...
Energy Technology Data Exchange (ETDEWEB)
Ibnouzahir, M
1995-03-01
The study of relativistic heavy ion collisions permit an approach of the properties of dense and not hadronic matter, and an analysis of the reaction mechanisms. Such studies are also interesting on the biological point of view, since there exist now well defined projects concerning the radiotherapy with high LET particles as neutrons, protons, heavy ions. It is thus necessary to have a good understanding of the processes which occur in the propagation of a relativistic heavy ion beam (E{>=} 100 A.MeV) in matter. We have elaborated a three dimensional transport code, using a Monte Carlo method, in order to describe the propagation of Ne and Ar ions in water. Violent nuclear collisions giving fragmentation process have been taken into account by use of the FREESCO program. We have tested the validity of our transport model and we show an important change of the energy deposition at the vicinity of the Bragg peak; such a distortion, due mainly to fragmentation reactions, is of a great interest for biological applications. (author).
Univalents and fragments in the meiosis of mammals
International Nuclear Information System (INIS)
Vyglenov, A.
1987-01-01
The manifestation of univalents and fragments in spermatocytes in diakinese-metaphase was studied on mice, rats, Syrian hamsters and rabbits irradiated with various dose rates. It was established that the incidence of the univalents resulting from the separation of the XY and autosomic bivalents and of the fragments did not depend on the dose rate and there were no differences between the control and the irradiated animals. A species specificity was found in the manifestation of the gonosomic and to some extent of the autosomic univalents. To a certain extent the differences in the incidence of the autosomic univalents and particularly of the fragments most probably were a consequence of the various measuring methods. In comparative aspect, the investigated mammals rank as follows: with the lowest incidence of univalents and fragments was the macaque-rhesus, with higher was the rat, followed by the Syrian hamster and with very high - the mouse and rabbit
A method for three-dimensional quantitative observation of the microstructure of biological samples
Wang, Pengfei; Chen, Dieyan; Ma, Wanyun; Wu, Hongxin; Ji, Liang; Sun, Jialin; Lv, Danyu; Zhang, Lu; Li, Ying; Tian, Ning; Zheng, Jinggao; Zhao, Fengying
2009-07-01
Contemporary biology has developed into the era of cell biology and molecular biology, and people try to study the mechanism of all kinds of biological phenomena at the microcosmic level now. Accurate description of the microstructure of biological samples is exigent need from many biomedical experiments. This paper introduces a method for 3-dimensional quantitative observation on the microstructure of vital biological samples based on two photon laser scanning microscopy (TPLSM). TPLSM is a novel kind of fluorescence microscopy, which has excellence in its low optical damage, high resolution, deep penetration depth and suitability for 3-dimensional (3D) imaging. Fluorescent stained samples were observed by TPLSM, and afterward the original shapes of them were obtained through 3D image reconstruction. The spatial distribution of all objects in samples as well as their volumes could be derived by image segmentation and mathematic calculation. Thus the 3-dimensionally and quantitatively depicted microstructure of the samples was finally derived. We applied this method to quantitative analysis of the spatial distribution of chromosomes in meiotic mouse oocytes at metaphase, and wonderful results came out last.
Cloning and expression of cell wall acid invertase gene fragment ...
African Journals Online (AJOL)
A fragment of invertase gene containing catalytic sites of cysteine was cloned from poinsettia (Euphorbia pulcherrima wild.) by using the polymerase chain reaction (PCR) method. The length of the fragment was 521 bp, encoding 173 amino acids and containing a part of open reading frames, but no intron. It had a high ...
International Nuclear Information System (INIS)
Pogosbekyan, L.R.; Lysov, D.A.; Bronitskii, L.L.
1993-01-01
Numerical simulators and information systems that support nuclear reactor operators must have fast models to estimate how fuel reloads and control rod displacement affect neutron and power distributions in the core. The consequences of reloads and control rod displacement cannot be evaluated correctly without considering local automatic control-rod operations in maintaining the radial power distribution. Fast three-dimensional models to estimate the effects of reloads and displacement of the control and safety rods have already been examined. I.V. Zonov et al. used the following assumptions in their calculational model: (1) the full-scale problem could be reduced a three-dimensional fragment of a locally perturbed core, and (2) the boundary conditions of the fragment and its total power were constant. The last assumption considers approximately how local automatic control rods stabilize the radial power distribution, but three dimensional calculations with these rods are not considered. These assumptions were introduced to obtain high computational speed. I.L. Bronitskii et al. considered in more detail how moving the local automatic control rods affect the power dimensional in the three-dimensional fragment, because, with on-line monitoring of the reload process, information on control rod positions is periodically renewed, and the calculations are done in real time. This model to predict the three-dimensional power distribution to (1) do a preliminary reload analysis, and (2) prepare the core for reloading did not consider the effect of perturbations from the local automatic control rods. Here we examine a model of a stationary neutron distribution. On one hand it gives results in an acceptable computation time; on the other it is a full-scale three-dimensional model and considers how local automatic control rods affect both the radial and axial power distribution
On a novel matrix method for three-dimensional photoelasticity
International Nuclear Information System (INIS)
Theocaris, P.S.; Gdoutos, E.E.
1978-01-01
A non-destructive method for the photoelastic determination of three-dimensional stress distributions, based on the Mueller and Jones calculi, is developed. The differential equations satisfied by the Stokes and Jones vectors, when a polarized light beam passes through a photoelastic model, presenting rotation of the secondary principal stress directions, are established in matrix form. The Peano-Baker method is used for the solution of these differential equations in a matrix series form, establishing the elements of the Mueller and Jones matrices of the photoelastic model. These matrices are experimentally determined by using different wavelengths in conjunction with Jones' 'equivalence theorem'. The Neumann equations are immediately deduced from the above-mentioned differential equations. (orig.) [de
Directory of Open Access Journals (Sweden)
Muhammad Aslam Noor
2008-01-01
Full Text Available We suggest and analyze a technique by combining the variational iteration method and the homotopy perturbation method. This method is called the variational homotopy perturbation method (VHPM. We use this method for solving higher dimensional initial boundary value problems with variable coefficients. The developed algorithm is quite efficient and is practically well suited for use in these problems. The proposed scheme finds the solution without any discritization, transformation, or restrictive assumptions and avoids the round-off errors. Several examples are given to check the reliability and efficiency of the proposed technique.
Charge distribution in the ternary fragmentation of {sup 252}Cf
Energy Technology Data Exchange (ETDEWEB)
Senthil Kannan, M.T.; Balasubramaniam, M. [Bharathiar University, Department of Physics, Coimbatore (India)
2017-08-15
We present here, for the first time, a study on ternary fragmentation charge distribution of {sup 252}Cf using the convolution integral method and the statistical theory. The charge distribution for all possible charge combinations of a ternary breakup are grouped as a bin containing different mass partitions. Different bins corresponding to various third fragments with mass numbers from A{sub 3} = 16 to 84 are identified with the available experimental masses. The corresponding potential energy surfaces are calculated using the three cluster model for the two arrangements A{sub 1} + A{sub 2} + A{sub 3} and A{sub 1} + A{sub 3} + A{sub 2}. The ternary fragmentation yield values are calculated for the ternary combination from each bin possessing minimum potential energy. The yields of the resulting ternary combinations as a function of the charge numbers of the three fragments are analyzed for both the arrangements. The calculations are carried out at different excitation energies of the parent nucleus. For each excitation energy the temperature of the three fragments are iteratively computed conserving the total energy. The distribution of fragment temperatures corresponding to different excitation energies for some fixed third fragments are discussed. The presence of the closed shell nucleus Sn in the favourable ternary fragmentation is highlighted. (orig.)
International Nuclear Information System (INIS)
Cauvin, B.; Jared, R.C.; Russo, P.; Schmitt, R.P.; Babinet, R.; Moretto, L.G.
1978-01-01
Deep inelastic fragments from the reaction sup(nat)Ag+340MeV 40 Ar have been studied in coincidence. Charged particles (10<=Z<=32) were detected and indentified in Z by means of a ΔE-E telescope, while the complementary fragments were detected in a one-dimensional solid-state position-sensitive detector. Both in-plane and out-of-plane correlations were measured. The results confirm the binary nature of the deep inelastic process for this reaction. From the measured energies and angles of the fragments and the atomic number of one of the fragments, it was possible to determine the total mass loss due to the de-excitation of the fragments as well as the total evaporated charge at symmetry. An iterative procedure is discussed which enables one to determine the masses and kinetic energies of the fragments before evaporation, as well as the total number of particles evaporated by each fragment. The widths of the in-plane and out-of-plane correlations agree with the results of the iterative calculations, as do evaporation calculations which are based on the charge equilibrium model. The experimental results support the charge equilibrium model and indicate that thermal equilibrium is achieved between the fragments at fixed mass asymmetry. (Auth.)
Dimensional analysis and qualitative methods in problem solving: II
International Nuclear Information System (INIS)
Pescetti, D
2009-01-01
We show that the underlying mathematical structure of dimensional analysis (DA), in the qualitative methods in problem-solving context, is the algebra of the affine spaces. In particular, we show that the qualitative problem-solving procedure based on the parallel decomposition of a problem into simple special cases yields the new original mathematical concepts of special points and special representations of affine spaces. A qualitative problem-solving algorithm piloted by the mathematics of DA is illustrated by a set of examples.
Image-Based Compression Method of Three-Dimensional Range Data with Texture
Chen, Xia; Bell, Tyler; Zhang, Song
2017-01-01
Recently, high speed and high accuracy three-dimensional (3D) scanning techniques and commercially available 3D scanning devices have made real-time 3D shape measurement and reconstruction possible. The conventional mesh representation of 3D geometry, however, results in large file sizes, causing difficulties for its storage and transmission. Methods for compressing scanned 3D data therefore become desired. This paper proposes a novel compression method which stores 3D range data within the c...
Deng, Yongbo; Korvink, Jan G
2016-05-01
This paper develops a topology optimization procedure for three-dimensional electromagnetic waves with an edge element-based finite-element method. In contrast to the two-dimensional case, three-dimensional electromagnetic waves must include an additional divergence-free condition for the field variables. The edge element-based finite-element method is used to both discretize the wave equations and enforce the divergence-free condition. For wave propagation described in terms of the magnetic field in the widely used class of non-magnetic materials, the divergence-free condition is imposed on the magnetic field. This naturally leads to a nodal topology optimization method. When wave propagation is described using the electric field, the divergence-free condition must be imposed on the electric displacement. In this case, the material in the design domain is assumed to be piecewise homogeneous to impose the divergence-free condition on the electric field. This results in an element-wise topology optimization algorithm. The topology optimization problems are regularized using a Helmholtz filter and a threshold projection method and are analysed using a continuous adjoint method. In order to ensure the applicability of the filter in the element-wise topology optimization version, a regularization method is presented to project the nodal into an element-wise physical density variable.
Multisymplectic Structure-Preserving in Simple Finite Element Method in High Dimensional Case
Institute of Scientific and Technical Information of China (English)
BAI Yong-Qiang; LIU Zhen; PEI Ming; ZHENG Zhu-Jun
2003-01-01
In this paper, we study a finite element scheme of some semi-linear elliptic boundary value problems inhigh-dimensional space. With uniform mesh, we find that, the numerical scheme derived from finite element method cankeep a preserved multisymplectic structure.
Kernel based methods for accelerated failure time model with ultra-high dimensional data
Directory of Open Access Journals (Sweden)
Jiang Feng
2010-12-01
Full Text Available Abstract Background Most genomic data have ultra-high dimensions with more than 10,000 genes (probes. Regularization methods with L1 and Lp penalty have been extensively studied in survival analysis with high-dimensional genomic data. However, when the sample size n ≪ m (the number of genes, directly identifying a small subset of genes from ultra-high (m > 10, 000 dimensional data is time-consuming and not computationally efficient. In current microarray analysis, what people really do is select a couple of thousands (or hundreds of genes using univariate analysis or statistical tests, and then apply the LASSO-type penalty to further reduce the number of disease associated genes. This two-step procedure may introduce bias and inaccuracy and lead us to miss biologically important genes. Results The accelerated failure time (AFT model is a linear regression model and a useful alternative to the Cox model for survival analysis. In this paper, we propose a nonlinear kernel based AFT model and an efficient variable selection method with adaptive kernel ridge regression. Our proposed variable selection method is based on the kernel matrix and dual problem with a much smaller n × n matrix. It is very efficient when the number of unknown variables (genes is much larger than the number of samples. Moreover, the primal variables are explicitly updated and the sparsity in the solution is exploited. Conclusions Our proposed methods can simultaneously identify survival associated prognostic factors and predict survival outcomes with ultra-high dimensional genomic data. We have demonstrated the performance of our methods with both simulation and real data. The proposed method performs superbly with limited computational studies.
International Nuclear Information System (INIS)
Krebs, W.; Erbel, R.; Schweizer, P.; Richter, H.A.; Massberg, I.; Meyer, J.; Effert, S.; Henn, G.
1982-01-01
The irregularity and complexity of the right ventricle is the reason why no accurate method for right ventricular volume determination exists. A new method for right ventricular volume determination particularly for two-dimensional echocardiography was developed - it is called subtraction method - and was compared with the pyramid and Simpson's methods. The partial volume of the left ventricle and septum was subtracted from total volume of right and left ventricle including interventricular septum. Thus right ventricular volume resulted. Total and partial volume were computer-assisted calculated by use of biplane methods, preferably Simpson's rule. The method was proved with thinwall silicon-rubber model hearts of the left and right ventricle. Two orthogonal planes in the long-axis were filmed by radiography or scanned in a water bath by two-dimensional echocardiography equivalent to RAO and LAO-projections of cineangiocardiograms or to four- and two-chamber views of apical two-dimensional echocardiograms. For calculation of the major axes of the elliptical sections, summed up by Simpson's rule, they were derived from the LAO-projection and the four-chamber view, respectively, the minor axis approximated from the RAO-projection and the two-chamber view. For comparison of direct-measured volume and two-dimensional echocardiographically determined volume, regression equation was given by y = 1.01 x - 3.2, correlation-coefficient, r = 0.977, and standard error of estimate (SEE) +-10.5 ml. For radiography, regression equation was y = 0.909 x + 13.3, r = 0.983, SEE = +-8.0 ml. For pyramid method and Simpson's rule, higher standard errors and lower correlation coefficients were found. Between radiography and two-dimensional echocardiography a mean difference of 4.3 +- 13.2 ml, using subtraction method, and -10.2 +- 22.9 ml, using pyramid method, as well as -0.6 +- 18.5 ml, using Simpson's rule, were calculated for right ventricular volume measurements. (orig./APR) [de
Kutchukian, Peter S; Wassermann, Anne Mai; Lindvall, Mika K; Wright, S Kirk; Ottl, Johannes; Jacob, Jaison; Scheufler, Clemens; Marzinzik, Andreas; Brooijmans, Natasja; Glick, Meir
2015-06-01
A first step in fragment-based drug discovery (FBDD) often entails a fragment-based screen (FBS) to identify fragment "hits." However, the integration of conflicting results from orthogonal screens remains a challenge. Here we present a meta-analysis of 35 fragment-based campaigns at Novartis, which employed a generic 1400-fragment library against diverse target families using various biophysical and biochemical techniques. By statistically interrogating the multidimensional FBS data, we sought to investigate three questions: (1) What makes a fragment amenable for FBS? (2) How do hits from different fragment screening technologies and target classes compare with each other? (3) What is the best way to pair FBS assay technologies? In doing so, we identified substructures that were privileged for specific target classes, as well as fragments that were privileged for authentic activity against many targets. We also revealed some of the discrepancies between technologies. Finally, we uncovered a simple rule of thumb in screening strategy: when choosing two technologies for a campaign, pairing a biochemical and biophysical screen tends to yield the greatest coverage of authentic hits. © 2014 Society for Laboratory Automation and Screening.
Exact rebinning methods for three-dimensional PET.
Liu, X; Defrise, M; Michel, C; Sibomana, M; Comtat, C; Kinahan, P; Townsend, D
1999-08-01
The high computational cost of data processing in volume PET imaging is still hindering the routine application of this successful technique, especially in the case of dynamic studies. This paper describes two new algorithms based on an exact rebinning equation, which can be applied to accelerate the processing of three-dimensional (3-D) PET data. The first algorithm, FOREPROJ, is a fast-forward projection algorithm that allows calculation of the 3-D attenuation correction factors (ACF's) directly from a two-dimensional (2-D) transmission scan, without first reconstructing the attenuation map and then performing a 3-D forward projection. The use of FOREPROJ speeds up the estimation of the 3-D ACF's by more than a factor five. The second algorithm, FOREX, is a rebinning algorithm that is also more than five times faster, compared to the standard reprojection algorithm (3DRP) and does not suffer from the image distortions generated by the even faster approximate Fourier rebinning (FORE) method at large axial apertures. However, FOREX is probably not required by most existing scanners, as the axial apertures are not large enough to show improvements over FORE with clinical data. Both algorithms have been implemented and applied to data simulated for a scanner with a large axial aperture (30 degrees), and also to data acquired with the ECAT HR and the ECAT HR+ scanners. Results demonstrate the excellent accuracy achieved by these algorithms and the important speedup when the sinogram sizes are powers of two.
In silico fragment-based drug design.
Konteatis, Zenon D
2010-11-01
In silico fragment-based drug design (FBDD) is a relatively new approach inspired by the success of the biophysical fragment-based drug discovery field. Here, we review the progress made by this approach in the last decade and showcase how it complements and expands the capabilities of biophysical FBDD and structure-based drug design to generate diverse, efficient drug candidates. Advancements in several areas of research that have enabled the development of in silico FBDD and some applications in drug discovery projects are reviewed. The reader is introduced to various computational methods that are used for in silico FBDD, the fragment library composition for this technique, special applications used to identify binding sites on the surface of proteins and how to assess the druggability of these sites. In addition, the reader will gain insight into the proper application of this approach from examples of successful programs. In silico FBDD captures a much larger chemical space than high-throughput screening and biophysical FBDD increasing the probability of developing more diverse, patentable and efficient molecules that can become oral drugs. The application of in silico FBDD holds great promise for historically challenging targets such as protein-protein interactions. Future advances in force fields, scoring functions and automated methods for determining synthetic accessibility will all aid in delivering more successes with in silico FBDD.
The ADO-nodal method for solving two-dimensional discrete ordinates transport problems
International Nuclear Information System (INIS)
Barichello, L.B.; Picoloto, C.B.; Cunha, R.D. da
2017-01-01
Highlights: • Two-dimensional discrete ordinates neutron transport. • Analytical Discrete Ordinates (ADO) nodal method. • Heterogeneous media fixed source problems. • Local solutions. - Abstract: In this work, recent results on the solution of fixed-source two-dimensional transport problems, in Cartesian geometry, are reported. Homogeneous and heterogeneous media problems are considered in order to incorporate the idea of arbitrary number of domain division into regions (nodes) when applying the ADO method, which is a method of analytical features, to those problems. The ADO-nodal formulation is developed, for each node, following previous work devoted to heterogeneous media problem. Here, however, the numerical procedure is extended to higher number of domain divisions. Such extension leads, in some cases, to the use of an iterative method for solving the general linear system which defines the arbitrary constants of the general solution. In addition to solve alternative heterogeneous media configurations than reported in previous works, the present approach allows comparisons with results provided by other metodologies generated with refined meshes. Numerical results indicate the ADO solution may achieve a prescribed accuracy using coarser meshes than other schemes.
Experimental study on two-dimensional film flow with local measurement methods
Energy Technology Data Exchange (ETDEWEB)
Yang, Jin-Hwa, E-mail: evo03@snu.ac.kr [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Korea Atomic Energy Research Institute, 989-111, Daedeok-daero, Yuseong-gu, Daejeon 305-600 (Korea, Republic of); Cho, Hyoung-Kyu [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Kim, Seok [Korea Atomic Energy Research Institute, 989-111, Daedeok-daero, Yuseong-gu, Daejeon 305-600 (Korea, Republic of); Euh, Dong-Jin, E-mail: djeuh@kaeri.re.kr [Korea Atomic Energy Research Institute, 989-111, Daedeok-daero, Yuseong-gu, Daejeon 305-600 (Korea, Republic of); Park, Goon-Cherl [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of)
2015-12-01
Highlights: • An experimental study on the two-dimensional film flow with lateral air injection was performed. • The ultrasonic thickness gauge was used to measure the local liquid film thickness. • The depth-averaged PIV (Particle Image Velocimetry) method was applied to measure the local liquid film velocity. • The uncertainty of the depth-averaged PIV was quantified with a validation experiment. • Characteristics of two-dimensional film flow were classified following the four different flow patterns. - Abstract: In an accident condition of a nuclear reactor, multidimensional two-phase flows may occur in the reactor vessel downcomer and reactor core. Therefore, those have been regarded as important issues for an advanced thermal-hydraulic safety analysis. In particular, the multi-dimensional two-phase flow in the upper downcomer during the reflood phase of large break loss of coolant accident appears with an interaction between a downward liquid and a transverse gas flow, which determines the bypass flow rate of the emergency core coolant and subsequently, the reflood coolant flow rate. At present, some thermal-hydraulic analysis codes incorporate multidimensional modules for the nuclear reactor safety analysis. However, their prediction capability for the two-phase cross flow in the upper downcomer has not been validated sufficiently against experimental data based on local measurements. For this reason, an experimental study was carried out for the two-phase cross flow to clarify the hydraulic phenomenon and provide local measurement data for the validation of the computational tools. The experiment was performed in a 1/10 scale unfolded downcomer of Advanced Power Reactor 1400 (APR1400). Pitot tubes, a depth-averaged PIV method and ultrasonic thickness gauge were applied for local measurement of the air velocity, the liquid film velocity and the liquid film thickness, respectively. The uncertainty of the depth-averaged PIV method for the averaged
Experimental study on two-dimensional film flow with local measurement methods
International Nuclear Information System (INIS)
Yang, Jin-Hwa; Cho, Hyoung-Kyu; Kim, Seok; Euh, Dong-Jin; Park, Goon-Cherl
2015-01-01
Highlights: • An experimental study on the two-dimensional film flow with lateral air injection was performed. • The ultrasonic thickness gauge was used to measure the local liquid film thickness. • The depth-averaged PIV (Particle Image Velocimetry) method was applied to measure the local liquid film velocity. • The uncertainty of the depth-averaged PIV was quantified with a validation experiment. • Characteristics of two-dimensional film flow were classified following the four different flow patterns. - Abstract: In an accident condition of a nuclear reactor, multidimensional two-phase flows may occur in the reactor vessel downcomer and reactor core. Therefore, those have been regarded as important issues for an advanced thermal-hydraulic safety analysis. In particular, the multi-dimensional two-phase flow in the upper downcomer during the reflood phase of large break loss of coolant accident appears with an interaction between a downward liquid and a transverse gas flow, which determines the bypass flow rate of the emergency core coolant and subsequently, the reflood coolant flow rate. At present, some thermal-hydraulic analysis codes incorporate multidimensional modules for the nuclear reactor safety analysis. However, their prediction capability for the two-phase cross flow in the upper downcomer has not been validated sufficiently against experimental data based on local measurements. For this reason, an experimental study was carried out for the two-phase cross flow to clarify the hydraulic phenomenon and provide local measurement data for the validation of the computational tools. The experiment was performed in a 1/10 scale unfolded downcomer of Advanced Power Reactor 1400 (APR1400). Pitot tubes, a depth-averaged PIV method and ultrasonic thickness gauge were applied for local measurement of the air velocity, the liquid film velocity and the liquid film thickness, respectively. The uncertainty of the depth-averaged PIV method for the averaged
International Nuclear Information System (INIS)
Ibnouzahir, M.
1995-03-01
The study of relativistic heavy ion collisions permit an approach of the properties of dense and not hadronic matter, and an analysis of the reaction mechanisms. Such studies are also interesting on the biological point of view, since there exist now well defined projects concerning the radiotherapy with high LET particles as neutrons, protons, heavy ions. It is thus necessary to have a good understanding of the processes which occur in the propagation of a relativistic heavy ion beam (E≥ 100 A.MeV) in matter. We have elaborated a three dimensional transport code, using a Monte Carlo method, in order to describe the propagation of Ne and Ar ions in water. Violent nuclear collisions giving fragmentation process have been taken into account by use of the FREESCO program. We have tested the validity of our transport model and we show an important change of the energy deposition at the vicinity of the Bragg peak; such a distortion, due mainly to fragmentation reactions, is of a great interest for biological applications. (author)
When fragments link: a bibliometric perspective on the development of fragment-based drug discovery.
Romasanta, Angelo K S; van der Sijde, Peter; Hellsten, Iina; Hubbard, Roderick E; Keseru, Gyorgy M; van Muijlwijk-Koezen, Jacqueline; de Esch, Iwan J P
2018-05-05
Fragment-based drug discovery (FBDD) is a highly interdisciplinary field, rich in ideas integrated from pharmaceutical sciences, chemistry, biology, and physics, among others. To enrich our understanding of the development of the field, we used bibliometric techniques to analyze 3642 publications in FBDD, complementing accounts by key practitioners. Mapping its core papers, we found the transfer of knowledge from academia to industry. Co-authorship analysis showed that university-industry collaboration has grown over time. Moreover, we show how ideas from other scientific disciplines have been integrated into the FBDD paradigm. Keyword analysis showed that the field is organized into four interconnected practices: library design, fragment screening, computational methods, and optimization. This study highlights the importance of interactions among various individuals and institutions from diverse disciplines in newly emerging scientific fields. Copyright © 2018. Published by Elsevier Ltd.
THE FRAGMENTATION OF MAGNETIZED, MASSIVE STAR-FORMING CORES WITH RADIATIVE FEEDBACK
Energy Technology Data Exchange (ETDEWEB)
Myers, Andrew T.; McKee, Christopher F. [Department of Physics, University of California, Berkeley, Berkeley, CA 94720 (United States); Cunningham, Andrew J. [Lawrence Livermore National Laboratory, P.O. Box 808, L-23, Livermore, CA 94550 (United States); Klein, Richard I. [Department of Astronomy, University of California, Berkeley, Berkeley, CA 94720 (United States); Krumholz, Mark R., E-mail: atmyers@berkeley.edu [Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064 (United States)
2013-04-01
We present a set of three-dimensional, radiation-magnetohydrodynamic calculations of the gravitational collapse of massive (300 M{sub Sun }), star-forming molecular cloud cores. We show that the combined effects of magnetic fields and radiative feedback strongly suppress core fragmentation, leading to the production of single-star systems rather than small clusters. We find that the two processes are efficient at suppressing fragmentation in different regimes, with the feedback most effective in the dense, central region and the magnetic field most effective in more diffuse, outer regions. Thus, the combination of the two is much more effective at suppressing fragmentation than either one considered in isolation. Our work suggests that typical massive cores, which have mass-to-flux ratios of about 2 relative to critical, likely form a single-star system, but that cores with weaker fields may form a small star cluster. This result helps us understand why the observed relationship between the core mass function and the stellar initial mass function holds even for {approx}100 M{sub Sun} cores with many thermal Jeans masses of material. We also demonstrate that a {approx}40 AU Keplerian disk is able to form in our simulations, despite the braking effect caused by the strong magnetic field.
File Type Identification of File Fragments using Longest Common Subsequence (LCS)
Rahmat, R. F.; Nicholas, F.; Purnamawati, S.; Sitompul, O. S.
2017-01-01
Computer forensic analyst is a person in charge of investigation and evidence tracking. In certain cases, the file needed to be presented as digital evidence was deleted. It is difficult to reconstruct the file, because it often lost its header and cannot be identified while being restored. Therefore, a method is required for identifying the file type of file fragments. In this research, we propose Longest Common Subsequences that consists of three steps, namely training, testing and validation, to identify the file type from file fragments. From all testing results we can conlude that our proposed method works well and achieves 92.91% of accuracy to identify the file type of file fragment for three data types.
Feyfant, Eric; Cross, Jason B; Paris, Kevin; Tsao, Désirée H H
2011-01-01
Fragment-based drug design (FBDD), which is comprised of both fragment screening and the use of fragment hits to design leads, began more than 15 years ago and has been steadily gaining in popularity and utility. Its origin lies on the fact that the coverage of chemical space and the binding efficiency of hits are directly related to the size of the compounds screened. Nevertheless, FBDD still faces challenges, among them developing fragment screening libraries that ensure optimal coverage of chemical space, physical properties and chemical tractability. Fragment screening also requires sensitive assays, often biophysical in nature, to detect weak binders. In this chapter we will introduce the technologies used to address these challenges and outline the experimental advantages that make FBDD one of the most popular new hit-to-lead process.
Research of nuclear fragmentation characteristics
International Nuclear Information System (INIS)
Richert, J.
1989-01-01
Motivations for the study of nuclear fragmentation are presented. Different models and methods which were developed in the past are reviewed, critically discussed and confronted in connection with the experimental information gathered over the past years. Specific aspects related to the onset of the process, its characteristics and the mechanism which governs it are discussed [fr
Directory of Open Access Journals (Sweden)
Sang-Wook Kang
2016-03-01
Full Text Available A new formulation for the non-dimensional dynamic influence function method, which was developed by the authors, is proposed to efficiently extract eigenvalues and mode shapes of clamped plates with arbitrary shapes. Compared with the finite element and boundary element methods, the non-dimensional dynamic influence function method yields highly accurate solutions in eigenvalue analysis problems of plates and membranes including acoustic cavities. However, the non-dimensional dynamic influence function method requires the uneconomic procedure of calculating the singularity of a system matrix in the frequency range of interest for extracting eigenvalues because it produces a non-algebraic eigenvalue problem. This article describes a new approach that reduces the problem of free vibrations of clamped plates to an algebraic eigenvalue problem, the solution of which is straightforward. The validity and efficiency of the proposed method are illustrated through several numerical examples.
International Nuclear Information System (INIS)
Zou, Zhengping; Liu, Jingyuan; Zhang, Weihao; Wang, Peng
2016-01-01
Multi-dimensional coupling simulation is an effective approach for evaluating the flow and aero-thermal performance of shrouded turbines, which can balance the simulation accuracy and computing cost effectively. In this paper, 1D leakage models are proposed based on classical jet theories and dynamics equations, which can be used to evaluate most of the main features of shroud leakage flow, including the mass flow rate, radial and circumferential momentum, temperature and the jet width. Then, the 1D models are expanded to 2D distributions on the interface by using a multi-dimensional scaling method. Based on the models and multi-dimensional scaling, a multi-dimensional coupling simulation method for shrouded turbines is developed, in which, some boundary source and sink are set on the interface between the shroud and the main flow passage. To verify the precision, some simulations on the design point and off design points of a 1.5 stage turbine are conducted. It is indicated that the models and methods can give predictions with sufficient accuracy for most of the flow field features and will contribute to pursue deeper understanding and better design methods of shrouded axial turbines, which are the important devices in energy engineering. - Highlights: • Free and wall attached jet theories are used to model the leakage flow in shrouds. • Leakage flow rate is modeled by virtual labyrinth number and residual-energy factor. • A scaling method is applied to 1D model to obtain 2D distributions on interfaces. • A multi-dimensional coupling CFD method for shrouded turbines is proposed. • The proposed coupling method can give accurate predictions with low computing cost.
International Nuclear Information System (INIS)
Bogatin, V.I.; Ganza, E.A.; Lozhkin, O.V.; Murin, Yu.A.; Oplavin, V.S.; Perfilov, N.A.; Yakovlev, Yu.P.
1981-01-01
An experimental investigation of inclusive characteristics of nuclei-target fragmentation is conducted for further development and test of physical value of the earlier suggested nuclear fragmentation model based on the connection of the fragmentation with fluctuations of the quasiparticle density in the two-component quantum liquid, an experimental investigation of the inclusive characteristics of the nuclei-target fragmentation is carried out. The processes of sup(3, 4, 6, 8)He and sup(6, 7, 8, 9, 11)Li fragment formation during the interaction of relativistic protons (Esub(p)=6.7 GeV) and deutrons (Esub(d)=3.1 GeV) with 112 Sn and 124 Sn isotopes are studied by the method of semiconductive ΔE-E detectors. Differential energy spectra of fragments and isotopic ratio of cross sections of their formation as well as data on the dependence of isotopic ratios of fragmentation cross sections on the energy of incident particles and on the fragment energy are obtained. Presented is a phenomenological model of fragmentation within the frames of which the obtained experimental data are analyzed [ru
International Nuclear Information System (INIS)
Park, Jai Hak
2009-01-01
SGBEM(Symmetric Galerkin Boundary Element Method)-FEM alternating method has been proposed by Nikishkov, Park and Atluri. In the proposed method, arbitrarily shaped three-dimensional crack problems can be solved by alternating between the crack solution in an infinite body and the finite element solution without a crack. In the previous study, the SGBEM-FEM alternating method was extended further in order to solve elastic-plastic crack problems and to obtain elastic-plastic stress fields. For the elastic-plastic analysis the algorithm developed by Nikishkov et al. is used after modification. In the algorithm, the initial stress method is used to obtain elastic-plastic stress and strain fields. In this paper, elastic-plastic J integrals for three-dimensional cracks are obtained using the method. For that purpose, accurate values of displacement gradients and stresses are necessary on an integration path. In order to improve the accuracy of stress near crack surfaces, coordinate transformation and partitioning of integration domain are used. The coordinate transformation produces a transformation Jacobian, which cancels the singularity of the integrand. Using the developed program, simple three-dimensional crack problems are solved and elastic and elastic-plastic J integrals are obtained. The obtained J integrals are compared with the values obtained using a handbook solution. It is noted that J integrals obtained from the alternating method are close to the values from the handbook
Effectiveness in detecting fission fragments with ionization chambers
International Nuclear Information System (INIS)
Manrique Garcia, J.; Monne, G.
1991-01-01
Detection of fission fragments is important in nuclear measurements. When a high detection accuracy is required it is necessary to take in account the detection losses due to the absorption of fragments in the fissionable material. The losses corrections might change the final results in 2-3%. The traditional expression used in the calculation of the detection efficiency does not consider neither the density variation of the fissionable substance with its width, because it depends on the target material. That's why actually in many labs it is being searched new methods that allow to find the efficiency for each target. In this work a new method for determination of absorption efficiency is presented. The obtained results are analyzed
Looking for bimodal distributions in multi-fragmentation reactions
International Nuclear Information System (INIS)
Gulminelli, F.
2007-01-01
The presence of a phase transition in a finite system can be deduced, together with its order, from the form of the distribution of the order parameter. This issue has been extensively studied in multifragmentation experiments, with results that do not appear fully consistent. In this paper we discuss the effect of the statistical ensemble or sorting conditions on the form of fragment distributions, and propose a new method, which can be easily implemented experimentally, to discriminate between different fragmentation scenarios. This method, based on a re-weighting of the measured distribution to account for the experimental constraints linked to the energy deposit, is tested on different simple models, and appears to provide a powerful discrimination. (author)
Study of the dynamic fragmentation of laser shock-loaded metallic target
International Nuclear Information System (INIS)
Lescoute, E.
2010-01-01
The irradiation of a metallic target by a high power laser pulse induces a shock wave in the material. Under some conditions, it leads to the production of high velocity ejecta which can damage the optical environment (lenses, mirrors, windows, etc.). With the ongoing development of high energy laser facilities designed to achieve inertial confinement fusion, such as the Laser MegaJoule in France or the National Ignition Facility in the USA, the question of debris ejection from metallic samples subjected to intense laser irradiation has become a key issue. It is necessary to understand fragmentation processes induced by laser shock, and to anticipate and quantify generated fragments, in order to design suitable protections and experiments, and to preserve laser facilities. The main fragmentation processes which can occur in a laser-shock-loaded metallic target and generate high velocity ejecta are: (i) micro-jetting, which occurs upon reflection of the incident compressive front from the free surface, (ii) spallation, which is due to the later interaction of the release wave reflected from that surface with the incident unloading wave and (iii) dynamic punching of thin targets. Experimental campaigns have been performed on high energy laser facilities in the Centre d'Etudes Scientifiques et Techniques d'Aquitaine (CESTA, CEA, Alise facility) and in the Laboratoire pour l'Utilisation des Lasers Intenses (LULI, Ecole Polytechnique, LULI 2000 facility). Gold and aluminium have been mainly studied because they are the two main metallic components of the target which will be used to achieved the inertial confinement fusion. Specific diagnostics have been developed and used during these experiments to study the dynamic fragmentation: transverse shadowgraphy, free surface velocity measurement and recovery of generated fragments. Experimental results have been compared with numerical predictions obtained with a bi-dimensional hydrodynamic code, where a specific numerical
DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P.
2016-12-01
Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues.
A method for three-dimensional structural analysis of reinforced concrete containment
International Nuclear Information System (INIS)
Kulak, R.F.; Fiala, C.
1989-01-01
A finite element method designed to assist reactor safety analysts in the three-dimensional numerical simulation of reinforced concrete containments to normal and off-normal mechanical loadings is presented. The development of a lined reinforced concrete plate element is described in detail, and the implementation of an empirical transverse shear failure criteria is discussed. The method is applied to the analysis of a 1/6th scale reinforced concrete containment model subjected to static internal pressurization. 11 refs., 14 figs., 1 tab
Mustafaoglu, Nur; Alves, Nathan J; Bilgicer, Basar
2015-07-01
The nucleotide binding site (NBS) is a highly conserved region between the variable light and heavy chains at the Fab domains of all antibodies, and a small molecule that we identified, indole-3-butyric acid (IBA), binds specifically to this site. Fab fragment, with its small size and simple production methods compared to intact antibody, is good candidate for use in miniaturized diagnostic devices and targeted therapeutic applications. However, commonly used modification techniques are not well suited for Fab fragments as they are often more delicate than intact antibodies. Fab fragments are of particular interest for sensor surface functionalization but immobilization results in damage to the antigen binding site and greatly reduced activity due to their truncated size that allows only a small area that can bind to surfaces without impeding antigen binding. In this study, we describe an NBS-UV photocrosslinking functionalization method (UV-NBS(Biotin) in which a Fab fragment is site-specifically biotinylated with an IBA-EG11-Biotin linker via UV energy exposure (1 J/cm(2)) without affecting its antigen binding activity. This study demonstrates successful immobilization of biotinylated Ebola detecting Fab fragment (KZ52 Fab fragment) via the UV-NBS(Biotin) method yielding 1031-fold and 2-fold better antigen detection sensitivity compared to commonly used immobilization methods: direct physical adsorption and NHS-Biotin functionalization, respectively. Utilization of the UV-NBS(Biotin) method for site-specific conjugation to Fab fragment represents a proof of concept use of Fab fragment for various diagnostic and therapeutic applications with numerous fluorescent probes, affinity molecules and peptides. © 2015 Wiley Periodicals, Inc.
Mathematical processing of experimental data on neutron yield from separate fission fragments
International Nuclear Information System (INIS)
Basova, B.G.; Rabinovich, A.D.; Ryazanov, D.K.
1975-01-01
The algorithm is described for processing the multi-dimensional experiments on measurements of prompt emission of neutrons from separate fission fragments. While processing the data the effect of a number of experimental corrections is correctly taken into account; random coincidence background, neutron spectrum, neutron detector efficiency, instrument angular resolution. On the basis of the described algorithm a program for BESM-4 computer is realized and the treatment of experimental data is performed according to the spontaneous fission of 252 Cf
An improved method for computer generation of three-dimensional digital holography
International Nuclear Information System (INIS)
Hu, Yanlei; Chen, Yuhang; Li, Jiawen; Huang, Wenhao; Chu, Jiaru; Ma, Jianqiang
2013-01-01
A novel method is proposed for designing optimized three-dimensional computer-generated holograms (CGHs). A series of spherical wave factors are introduced into the conventional optimal rotation angle (ORA) algorithm to achieve a varying amount of defocus along the optical axis, and the distraction terms are minimized during the iterative process. Both numerical simulation and experimental reconstructions are presented to demonstrate that this method is able to yield excellent multilayer patterns with high uniformity and signal-to-noise ratio (SNR). This method is significant for applications in laser 3D printing and multilayer data recording. (paper)
International Nuclear Information System (INIS)
Sanchez, Richard.
1980-11-01
This work is divided into two part the first part (note CEA-N-2165) deals with the solution of complex two-dimensional transport problems, the second one treats the critically mixed methods of resolution. These methods are applied for one-dimensional geometries with highly anisotropic scattering. In order to simplify the set of integral equation provided by the integral transport equation, the integro-differential equation is used to obtain relations that allow to lower the number of integral equation to solve; a general mathematical and numerical study is presented [fr
Fragment-based drug discovery and its application to challenging drug targets.
Price, Amanda J; Howard, Steven; Cons, Benjamin D
2017-11-08
Fragment-based drug discovery (FBDD) is a technique for identifying low molecular weight chemical starting points for drug discovery. Since its inception 20 years ago, FBDD has grown in popularity to the point where it is now an established technique in industry and academia. The approach involves the biophysical screening of proteins against collections of low molecular weight compounds (fragments). Although fragments bind to proteins with relatively low affinity, they form efficient, high quality binding interactions with the protein architecture as they have to overcome a significant entropy barrier to bind. Of the biophysical methods available for fragment screening, X-ray protein crystallography is one of the most sensitive and least prone to false positives. It also provides detailed structural information of the protein-fragment complex at the atomic level. Fragment-based screening using X-ray crystallography is therefore an efficient method for identifying binding hotspots on proteins, which can then be exploited by chemists and biologists for the discovery of new drugs. The use of FBDD is illustrated here with a recently published case study of a drug discovery programme targeting the challenging protein-protein interaction Kelch-like ECH-associated protein 1:nuclear factor erythroid 2-related factor 2. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.
DEFF Research Database (Denmark)
Nielsen, Kirstine Klitgaard; Ahrens, Peter
2002-01-01
By a suppression subtractive hybridization based method, nine novel Mycobacterium avium subsp. para tuberculosis (M. para tuberculosis) fragments of between 318 and 596 bp have been identified and characterized. Database search revealed little or no similarity with other mycobacteria. The uniquen......By a suppression subtractive hybridization based method, nine novel Mycobacterium avium subsp. para tuberculosis (M. para tuberculosis) fragments of between 318 and 596 bp have been identified and characterized. Database search revealed little or no similarity with other mycobacteria....... The uniqueness and diagnostic potential of seven of these fragments in relation to M. paratuberculosis closest relative Mycobacterium avium subsp. avium (M. avium) was confirmed by species-specific PCR and Southern blot. Furthermore, RT-PCR indicated that eight of the nine fragments originate from areas...
Lirman
2000-08-23
Acropora palmata, a branching coral abundant on shallow reef environments throughout the Caribbean, is susceptible to physical disturbance caused by storms. Accordingly, the survivorship and propagation of this species are tied to its capability to recover after fragmentation. Fragments of A. palmata comprised 40% of ramets within populations that had experienced recent storms. While the survivorship of A. palmata fragments was not directly related to the size of fragments, removal of fragments from areas where they settled was influenced by size. Survivorship of fragments was also affected by type of substratum; the greatest mortality (58% loss within the first month) was observed on sand, whereas fragments placed on top of live colonies of A. palmata fused to the underlying tissue and did not experience any losses. Fragments created by Hurricane Andrew on a Florida reef in August 1992 began developing new growth (proto-branches) 7 months after the storm. The number of proto-branches on fragments was dependent on size, but growth was not affected by the size of fragments. Growth-rates of proto-branches increased exponentially with time (1.7 cm year(-1) for 1993-1994, 2.7 cm year(-1) for 1994-1995, 4.2 cm year(-1) for 1995-1996, and 6.5 cm year(-1) for 1996-1997), taking over 4 years for proto-branches to achieve rates comparable to those of adult colonies on the same reef (6.9 cm year(-1)). In addition to the initial mortality and reduced growth-rates, fragmentation resulted in a loss of reproductive potential. Neither colonies that experienced severe fragmentation nor fragments contained gametes until 4 years after the initial damage. Although A. palmata may survive periodic fragmentation, the long-term effects of this process will depend ultimately on the balance between the benefits and costs of this process.
Plasminogen fragments K 1-3 and K 5 bind to different sites in fibrin fragment DD.
Grinenko, T V; Kapustianenko, L G; Yatsenko, T A; Yusova, O I; Rybachuk, V N
2016-01-01
Specific plasminogen-binding sites of fibrin molecule are located in Аα148-160 regions of C-terminal domains. Plasminogen interaction with these sites initiates the activation process of proenzyme and subsequent fibrin lysis. In this study we investigated the binding of plasminogen fragments K 1-3 and K 5 with fibrin fragment DD and their effect on Glu-plasminogen interaction with DD. It was shown that the level of Glu-plasminogen binding to fibrin fragment DD is decreased by 50-60% in the presence of K 1-3 and K 5. Fragments K 1-3 and K 5 have high affinity to fibrin fragment DD (Kd is 0.02 for K 1-3 and 0.054 μМ for K 5). K 5 interaction is independent and K 1-3 is partly dependent on C-terminal lysine residues. K 1-3 interacts with complex of fragment DD-immobilized K 5 as well as K 5 with complex of fragment DD-immobilized K 1-3. The plasminogen fragments do not displace each other from binding sites located in fibrin fragment DD, but can compete for the interaction. The results indicate that fibrin fragment DD contains different binding sites for plasminogen kringle fragments K 1-3 and K 5, which can be located close to each other. The role of amino acid residues of fibrin molecule Аα148-160 region in interaction with fragments K 1-3 and K 5 is discussed.
A study on three dimensional layout design by the simulated annealing method
International Nuclear Information System (INIS)
Jang, Seung Ho
2008-01-01
Modern engineered products are becoming increasingly complicated and most consumers prefer compact designs. Layout design plays an important role in many engineered products. The objective of this study is to suggest a method to apply the simulated annealing method to the arbitrarily shaped three-dimensional component layout design problem. The suggested method not only optimizes the packing density but also satisfies constraint conditions among the components. The algorithm and its implementation as suggested in this paper are extendable to other research objectives
About dynamic model of limiting fragmentation of heavy nuclei
International Nuclear Information System (INIS)
Kuchin, I.A.
2001-01-01
Full text: As is known, during last years defined progress in understanding of static aspect of a dynamic structure organization of massive nuclei was reached. The offered model of a 'crystalline' structure of the nucleus generalizes drop, shell and cluster models in a natural way. Now increased interest induces the phenomenon of limiting fragmentation of heavy nuclei. There is a hope, that clearing up the general regularities of a soft disintegration of the massive nuclei on nucleons, component it, in a broad range of high energies can give a valuable information about dynamics of origin of nuclear structures and nature of their qualitative difference from a quark system structure, i.e. from nucleons. The key for understanding the indicated phenomenon can be it's study in connection with other aspects of disintegration of the nuclei - Coulomb and diffraction dissociation, fission etc. The sequential analysis of all these a processes from a single point of view is possible only within the framework of results and methods of the dynamic system theory. The purpose of the present research is clearing up a possibility to understand the nature of limiting fragmentation as a consequence of development of dynamic instability in a system of the nuclei as a result of ions interaction at high energy. In the analysis we based on data of the phenomenological analysis of heavy ion interactions at ultra-relativistic energies obtained by many authors for a number of years. As a result we came to a conclusion about general stochastic nature of an investigated phenomenon. In it development the fragmentation passes three different stages. On the first there is a process of preparation of chaos at a quantum level in an outcome of a Coulomb dissociation of the approaching nuclei and isotopic recharge of their nucleons, carrying a random character. A dominant here - viscous dissociation of nuclei under an operation of Coulomb forces. (A two body initial state). Then the multiparticle
Fractal statistics of brittle fragmentation
Directory of Open Access Journals (Sweden)
M. Davydova
2013-04-01
Full Text Available The study of fragmentation statistics of brittle materials that includes four types of experiments is presented. Data processing of the fragmentation of glass plates under quasi-static loading and the fragmentation of quartz cylindrical rods under dynamic loading shows that the size distribution of fragments (spatial quantity is fractal and can be described by a power law. The original experimental technique allows us to measure, apart from the spatial quantity, the temporal quantity - the size of time interval between the impulses of the light reflected from the newly created surfaces. The analysis of distributions of spatial (fragment size and temporal (time interval quantities provides evidence of obeying scaling laws, which suggests the possibility of self-organized criticality in fragmentation.
Three-dimensional dynamics of protostellar evolution
International Nuclear Information System (INIS)
Cook, T.L.; Harlow, F.H.
1978-01-01
A three-dimensional finite difference numerical methodology has been developed for self-gravitating, rotating gaseous systems. The fully nonlinear equations for time-varying fluid dynamics are solved by high-speed computer in a cylindrical coordinate system rotating with an instantaneous angular velocity. The time-dependent adiabatic collapse of gravitationally bound, rotating, protostellar clouds is studied for specified uniform and nonuniform initial conditions. Uniform clouds can form axisymmetric, rotating toroidal configurations. If the thermal pressure is high, nonuniform clouds can also collapse to axisymmetric ellipsoids. For low thermal pressures, however, the collapsing cloud is unstable to perturbations. The resulting fragmentation of unstable protostellar clouds is investigated by studying the response of rotating, self-gravitating, equilibrium toroids to nonaxisymmetric perturbations. The detailed evolution of the fragmentation toroid depends upon a nondimensional function of the initial entropy, the total mass in the toroid, the angular velocity of rotation, and the number of perturbation wave-lengths around the circumference of the toroid. For low and intermediate entropies, the configuration develops into corotating components with spiral streamers. In the spiral regions retrograde vortices are observed in some examples. For high levels of entropy, barred spirals can exist as intermediate states of the fragmentation
Rühmann, Eggert; Betz, Michael; Fricke, Marie; Heine, Andreas; Schäfer, Martina; Klebe, Gerhard
2015-04-01
Detailed characterization of the thermodynamic signature of weak binding fragments to proteins is essential to support the decision making process which fragments to take further for the hit-to-lead optimization. Isothermal titration calorimetry (ITC) is the method of choice to record thermodynamic data, however, weak binding ligands such as fragments require the development of meaningful and reliable measuring protocols as usually sigmoidal titration curves are hardly possible to record due to limited solubility. Fragments can be titrated either directly under low c-value conditions (no sigmoidal curve) or indirectly by use of a strong binding ligand displacing the pre-incubated weak fragment from the protein. The determination of Gibbs free energy is reliable and rather independent of the applied titration protocol. Even though the displacement method achieves higher accuracy, the obtained enthalpy-entropy profile depends on the properties of the used displacement ligand. The relative enthalpy differences across different displacement experiments reveal a constant signature and can serve as a thermodynamic fingerprint for fragments. Low c-value titrations are only reliable if the final concentration of the fragment in the sample cell exceeds 2-10 fold its K(D) value. Limited solubility often prevents this strategy. The present study suggests an applicable protocol to characterize the thermodynamic signature of protein-fragment binding. It shows however, that such measurements are limited by protein and fragment solubility. Deviating profiles obtained by use of different displacement ligands indicate that changes in the solvation pattern and protein dynamics most likely take influence on the resulting overall binding signature. Copyright © 2014 Elsevier B.V. All rights reserved.
Current perspectives in fragment-based lead discovery (FBLD)
Lamoree, Bas; Hubbard, Roderick E.
2017-01-01
It is over 20 years since the first fragment-based discovery projects were disclosed. The methods are now mature for most ‘conventional’ targets in drug discovery such as enzymes (kinases and proteases) but there has also been growing success on more challenging targets, such as disruption of protein–protein interactions. The main application is to identify tractable chemical startpoints that non-covalently modulate the activity of a biological molecule. In this essay, we overview current practice in the methods and discuss how they have had an impact in lead discovery – generating a large number of fragment-derived compounds that are in clinical trials and two medicines treating patients. In addition, we discuss some of the more recent applications of the methods in chemical biology – providing chemical tools to investigate biological molecules, mechanisms and systems. PMID:29118093
Native Frames: Disentangling Sequential from Concerted Three-Body Fragmentation
Rajput, Jyoti; Severt, T.; Berry, Ben; Jochim, Bethany; Feizollah, Peyman; Kaderiya, Balram; Zohrabi, M.; Ablikim, U.; Ziaee, Farzaneh; Raju P., Kanaka; Rolles, D.; Rudenko, A.; Carnes, K. D.; Esry, B. D.; Ben-Itzhak, I.
2018-03-01
A key question concerning the three-body fragmentation of polyatomic molecules is the distinction of sequential and concerted mechanisms, i.e., the stepwise or simultaneous cleavage of bonds. Using laser-driven fragmentation of OCS into O++C++S+ and employing coincidence momentum imaging, we demonstrate a novel method that enables the clear separation of sequential and concerted breakup. The separation is accomplished by analyzing the three-body fragmentation in the native frame associated with each step and taking advantage of the rotation of the intermediate molecular fragment, CO2 + or CS2 + , before its unimolecular dissociation. This native-frame method works for any projectile (electrons, ions, or photons), provides details on each step of the sequential breakup, and enables the retrieval of the relevant spectra for sequential and concerted breakup separately. Specifically, this allows the determination of the branching ratio of all these processes in OCS3 + breakup. Moreover, we find that the first step of sequential breakup is tightly aligned along the laser polarization and identify the likely electronic states of the intermediate dication that undergo unimolecular dissociation in the second step. Finally, the separated concerted breakup spectra show clearly that the central carbon atom is preferentially ejected perpendicular to the laser field.
International Nuclear Information System (INIS)
Zhao, Weizhao; Ginsberg, M.; Young, T.Y.
1993-01-01
Quantitative autoradiography is a powerful radio-isotopic-imaging method for neuroscientists to study local cerebral blood flow and glucose-metabolic rate at rest, in response to physiologic activation of the visual, auditory, somatosensory, and motor systems, and in pathologic conditions. Most autoradiographic studies analyze glucose utilization and blood flow in two-dimensional (2-D) coronal sections. With modern digital computer and image-processing techniques, a large number of closely spaced coronal sections can be stacked appropriately to form a three-dimensional (3-d) image. 3-D autoradiography allows investigators to observe cerebral sections and surfaces from any viewing angle. A fundamental problem in 3-D reconstruction is the alignment (registration) of the coronal sections. A new alignment method based on disparity analysis is presented which can overcome many of the difficulties encountered by previous methods. The disparity analysis method can deal with asymmetric, damaged, or tilted coronal sections under the same general framework, and it can be used to match coronal sections of different sizes and shapes. Experimental results on alignment and 3-D reconstruction are presented
High-speed fan-beam reconstruction using direct two-dimensional Fourier transform method
International Nuclear Information System (INIS)
Niki, Noboru; Mizutani, Toshio; Takahashi, Yoshizo; Inouye, Tamon.
1984-01-01
Since the first development of X-ray computer tomography (CT), various efforts have been made to obtain high quality of high-speed image. However, the development of high resolution CT and the ultra-high speed CT to be applied to hearts is still desired. The X-ray beam scanning method was already changed from the parallel beam system to the fan-beam system in order to greatly shorten the scanning time. Also, the filtered back projection (DFBP) method has been employed to directly processing fan-beam projection data as reconstruction method. Although the two-dimensional Fourier transform (TFT) method significantly faster than FBP method was proposed, it has not been sufficiently examined for fan-beam projection data. Thus, the ITFT method was investigated, which first executes rebinning algorithm to convert the fan-beam projection data to the parallel beam projection data, thereafter, uses two-dimensional Fourier transform. By this method, although high speed is expected, the reconstructed images might be degraded due to the adoption of rebinning algorithm. Therefore, the effect of the interpolation error of rebinning algorithm on the reconstructed images has been analyzed theoretically, and finally, the result of the employment of spline interpolation which allows the acquisition of high quality images with less errors has been shown by the numerical and visual evaluation based on simulation and actual data. Computation time was reduced to 1/15 for the image matrix of 512 and to 1/30 for doubled matrix. (Wakatsuki, Y.)
Chen, Hui; Deng, Ju-Zhi; Yin, Min; Yin, Chang-Chun; Tang, Wen-Wu
2017-03-01
To speed up three-dimensional (3D) DC resistivity modeling, we present a new multigrid method, the aggregation-based algebraic multigrid method (AGMG). We first discretize the differential equation of the secondary potential field with mixed boundary conditions by using a seven-point finite-difference method to obtain a large sparse system of linear equations. Then, we introduce the theory behind the pairwise aggregation algorithms for AGMG and use the conjugate-gradient method with the V-cycle AGMG preconditioner (AGMG-CG) to solve the linear equations. We use typical geoelectrical models to test the proposed AGMG-CG method and compare the results with analytical solutions and the 3DDCXH algorithm for 3D DC modeling (3DDCXH). In addition, we apply the AGMG-CG method to different grid sizes and geoelectrical models and compare it to different iterative methods, such as ILU-BICGSTAB, ILU-GCR, and SSOR-CG. The AGMG-CG method yields nearly linearly decreasing errors, whereas the number of iterations increases slowly with increasing grid size. The AGMG-CG method is precise and converges fast, and thus can improve the computational efficiency in forward modeling of three-dimensional DC resistivity.
Directory of Open Access Journals (Sweden)
Valentin L. Popov
2014-04-01
Full Text Available The Method of Dimensionality Reduction (MDR is a method of calculation and simulation of contacts of elastic and viscoelastic bodies. It consists essentially of two simple steps: (a substitution of the three-dimensional continuum by a uniquely defined one-dimensional linearly elastic or viscoelastic foundation (Winkler foundation and (b transformation of the three-dimensional profile of the contacting bodies by means of the MDR-transformation. As soon as these two steps are completed, the contact problem can be considered to be solved. For axial symmetric contacts, only a small calculation by hand is required which does not exceed elementary calculus and will not be a barrier for any practically-oriented engineer. Alternatively, the MDR can be implemented numerically, which is almost trivial due to the independence of the foundation elements. In spite of their simplicity, all the results are exact. The present paper is a short practical guide to the MDR.
Fracture resistance of reattached incisor fragments with mini fibre-reinforced composite anchors.
Fennis, W.M.M.; Kreulen, C.M.; Wolke, J.G.C.; Fokkinga, W.A.; Machado, C.; Creugers, N.H.J.
2009-01-01
OBJECTIVES: Fractured coronal fragments of incisors can be adhered to the remaining tooth with resin composite, but are prone to failure. This study explores whether mini fibre-reinforced composite (FRC) anchors increase fracture resistance of reattached fragments. METHODS: Forty-five extracted
Energy Technology Data Exchange (ETDEWEB)
Kamp, Florian [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut (United States); Department of Radiation Oncology, Technische Universität München, Klinikum Rechts der Isar, München (Germany); Physik-Department, Technische Universität München, Garching (Germany); Cabal, Gonzalo [Experimental Physics–Medical Physics, Ludwig Maximilians University Munich, Garching (Germany); Mairani, Andrea [Medical Physics Unit, Centro Nazionale Adroterapia Oncologica (CNAO), Pavia (Italy); Heidelberg Ion-Beam Therapy Center, Heidelberg (Germany); Parodi, Katia [Experimental Physics–Medical Physics, Ludwig Maximilians University Munich, Garching (Germany); Wilkens, Jan J. [Department of Radiation Oncology, Technische Universität München, Klinikum Rechts der Isar, München (Germany); Physik-Department, Technische Universität München, Garching (Germany); Carlson, David J., E-mail: david.j.carlson@yale.edu [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut (United States)
2015-11-01
Purpose: The physical and biological differences between heavy ions and photons have not been fully exploited and could improve treatment outcomes. In carbon ion therapy, treatment planning must account for physical properties, such as the absorbed dose and nuclear fragmentation, and for differences in the relative biological effectiveness (RBE) of ions compared with photons. We combined the mechanistic repair-misrepair-fixation (RMF) model with Monte Carlo-generated fragmentation spectra for biological optimization of carbon ion treatment plans. Methods and Materials: Relative changes in double-strand break yields and radiosensitivity parameters with particle type and energy were determined using the independently benchmarked Monte Carlo damage simulation and the RMF model to estimate the RBE values for primary carbon ions and secondary fragments. Depth-dependent energy spectra were generated with the Monte Carlo code FLUKA for clinically relevant initial carbon ion energies. The predicted trends in RBE were compared with the published experimental data. Biological optimization for carbon ions was implemented in a 3-dimensional research treatment planning tool. Results: We compared the RBE and RBE-weighted dose (RWD) distributions of different carbon ion treatment scenarios with and without nuclear fragments. The inclusion of fragments in the simulations led to smaller RBE predictions. A validation of RMF against measured cell survival data reported in published studies showed reasonable agreement. We calculated and optimized the RWD distributions on patient data and compared the RMF predictions with those from other biological models. The RBE values in an astrocytoma tumor ranged from 2.2 to 4.9 (mean 2.8) for a RWD of 3 Gy(RBE) assuming (α/β){sub X} = 2 Gy. Conclusions: These studies provide new information to quantify and assess uncertainties in the clinically relevant RBE values for carbon ion therapy based on biophysical mechanisms. We present results from
Directory of Open Access Journals (Sweden)
Zhang Jing
2016-01-01
Full Text Available To assist physicians to quickly find the required 3D model from the mass medical model, we propose a novel retrieval method, called DRFVT, which combines the characteristics of dimensionality reduction (DR and feature vector transformation (FVT method. The DR method reduces the dimensionality of feature vector; only the top M low frequency Discrete Fourier Transform coefficients are retained. The FVT method does the transformation of the original feature vector and generates a new feature vector to solve the problem of noise sensitivity. The experiment results demonstrate that the DRFVT method achieves more effective and efficient retrieval results than other proposed methods.
International Nuclear Information System (INIS)
Rubin, Joshua George
2009-11-01
The motivation for this work was to improve upon prior analyses that extracted the quark helicity distributions, Δ(x), of the proton. Chapter 4 contains several new double-spin asymmetries which are results in their own right. The ph? dependence is plotted for the first time with HERMES data which is uniquely hadron separated. The hadron charge difference asymmetry is presented which, in combination with the quark helicity densities can put limits on fragmentation symmetry breaking in semi-inclusive DIS. Additionally, a novel method of unfolding yields (reducing smearing effects from detector resolution limitations and QED radiation) was developed and presented here for the first time which potentially allows new kinds of asymmetries to be constructed which were unavailable before. Also, this chapter describes the method by which the first ever three dimensionally binned SIDIS double-spin asymmetries were produced. These asymmetries, which will be used as the data inputs for the Δ(x) extraction, are valuable inputs to world fits being performed by theorists. Chapter 5 further explores this idea of fragmentation symmetry breaking with Monte Carlo studies of fragmentation functions. These studies test assumptions which are frequently made in the interpretation of asymmetries like the hadron charge difference of the prior chapter and suggest that these assumptions should be approached with some caution. Also, a technique for tuning and more importantly propagating systematic uncertainty through non-analytic Monte Carlo models, like the Lund-String model which provides an essential input to the Δ(x) extraction, is developed (orig.)
Energy Technology Data Exchange (ETDEWEB)
Rubin, Joshua George
2009-11-15
The motivation for this work was to improve upon prior analyses that extracted the quark helicity distributions, {delta}(x), of the proton. Chapter 4 contains several new double-spin asymmetries which are results in their own right. The ph? dependence is plotted for the first time with HERMES data which is uniquely hadron separated. The hadron charge difference asymmetry is presented which, in combination with the quark helicity densities can put limits on fragmentation symmetry breaking in semi-inclusive DIS. Additionally, a novel method of unfolding yields (reducing smearing effects from detector resolution limitations and QED radiation) was developed and presented here for the first time which potentially allows new kinds of asymmetries to be constructed which were unavailable before. Also, this chapter describes the method by which the first ever three dimensionally binned SIDIS double-spin asymmetries were produced. These asymmetries, which will be used as the data inputs for the {delta}(x) extraction, are valuable inputs to world fits being performed by theorists. Chapter 5 further explores this idea of fragmentation symmetry breaking with Monte Carlo studies of fragmentation functions. These studies test assumptions which are frequently made in the interpretation of asymmetries like the hadron charge difference of the prior chapter and suggest that these assumptions should be approached with some caution. Also, a technique for tuning and more importantly propagating systematic uncertainty through non-analytic Monte Carlo models, like the Lund-String model which provides an essential input to the {delta}(x) extraction, is developed (orig.)
Determination of size distribution of small DNA fragments by polyacrylamide gel electrophoresis
International Nuclear Information System (INIS)
Lau How Mooi
1998-01-01
Size distribution determination of DNA fragments can be normally determined by the agarose gel electrophoresis, including the normal DNA banding pattern analysis. However this method is only good for large DNA, such as the DNA of the size of kilo base pairs to mega base pairs range. DNA of size less than kilo base pairs is difficult to be quantified by the agarose gel method. Polyacrylamide gel electrophoresis however can be used to measure the quantity of DNA fragments of size less than kilo base pairs in length, down to less than ten base pairs. This method is good for determining the quantity of the smaller size DNA, single stranded polymers or even some proteins, if the known standards are available. In this report detail description of the method of preparing the polyacrylamide gel, and the experimental set up is discussed. Possible uses of this method, and the comparison with the standard sizes of DNA is also shown. This method is used to determine the distribution of the amount of the fragmented DNA after the Calf-thymus DNA has been exposed to various types of radiation and of different doses. The standards were used to determine the sizes of the fragmented Calf-thymus DNA. The higher the dose the higher is the amount of the smaller size DNA measured
International Nuclear Information System (INIS)
Naymik, T.G.
1978-01-01
To evaluate the inability of a one-dimensional ground-water model to interact continuously with surrounding hydraulic head gradients, simulations using one-dimensional and two-dimensional ground-water flow models were compared. This approach used two types of models: flow-conserving one-and-two dimensional models, and one-dimensional and two-dimensional models designed to yield two-dimensional solutions. The hydraulic conductivities of controlling features were varied and model comparison was based on the travel times of marker particles. The solutions within each of the two model types compare reasonably well, but a three-dimensional solution is required to quantify the comparison
International Nuclear Information System (INIS)
Chen, G.S.
1997-01-01
We apply and compare the preconditioned generalized conjugate gradient methods to solve the linear system equation that arises in the two-dimensional neutron and photon transport equation in this paper. Several subroutines are developed on the basis of preconditioned generalized conjugate gradient methods for time-independent, two-dimensional neutron and photon transport equation in the transport theory. These generalized conjugate gradient methods are used. TFQMR (transpose free quasi-minimal residual algorithm), CGS (conjuage gradient square algorithm), Bi-CGSTAB (bi-conjugate gradient stabilized algorithm) and QMRCGSTAB (quasi-minimal residual variant of bi-conjugate gradient stabilized algorithm). These sub-routines are connected to computer program DORT. Several problems are tested on a personal computer with Intel Pentium CPU. (author)
Chen, Tao; Clauser, Christoph; Marquart, Gabriele; Willbrand, Karen; Hiller, Thomas
2018-02-01
Upscaling permeability of grid blocks is crucial for groundwater models. A novel upscaling method for three-dimensional fractured porous rocks is presented. The objective of the study was to compare this method with the commonly used Oda upscaling method and the volume averaging method. First, the multiple boundary method and its computational framework were defined for three-dimensional stochastic fracture networks. Then, the different upscaling methods were compared for a set of rotated fractures, for tortuous fractures, and for two discrete fracture networks. The results computed by the multiple boundary method are comparable with those of the other two methods and fit best the analytical solution for a set of rotated fractures. The errors in flow rate of the equivalent fracture model decrease when using the multiple boundary method. Furthermore, the errors of the equivalent fracture models increase from well-connected fracture networks to poorly connected ones. Finally, the diagonal components of the equivalent permeability tensors tend to follow a normal or log-normal distribution for the well-connected fracture network model with infinite fracture size. By contrast, they exhibit a power-law distribution for the poorly connected fracture network with multiple scale fractures. The study demonstrates the accuracy and the flexibility of the multiple boundary upscaling concept. This makes it attractive for being incorporated into any existing flow-based upscaling procedures, which helps in reducing the uncertainty of groundwater models.
Nakajima, Kazuhiro; Yamamoto, Yuji; Arima, Yutaka
2018-04-01
To easily assemble a three-dimensional binocular range sensor, we devised an alignment method for two image sensors using a silicon interposer with trenches. The trenches were formed using deep reactive ion etching (RIE) equipment. We produced a three-dimensional (3D) range sensor using the method and experimentally confirmed that sufficient alignment accuracy was realized. It was confirmed that the alignment accuracy of the two image sensors when using the proposed method is more than twice that of the alignment assembly method on a conventional board. In addition, as a result of evaluating the deterioration of the detection performance caused by the alignment accuracy, it was confirmed that the vertical deviation between the corresponding pixels in the two image sensors is substantially proportional to the decrease in detection performance. Therefore, we confirmed that the proposed method can realize more than twice the detection performance of the conventional method. Through these evaluations, the effectiveness of the 3D binocular range sensor aligned by the silicon interposer with the trenches was confirmed.
Uranium in the rock fragments from Lunar soil
International Nuclear Information System (INIS)
Komarov, A.N.; Sergeev, S.A.
1983-01-01
Uranium content and distribution in Lunar rock fragments 0.4-0.9 mm in size from ''Lunar-16+ -20, -24'' stations were studied by the method of autoradiography. Uranium is almost absent in rock-forming minerals and is concentrated in some accessory mineral. Uranium content in microgabro fragments from ''Lunar-20 and -24'' equals (0.0n - n.0)16 -6 g/g. Variations are not related to fragment representation. Radiogra-- phies of fragments from Lunar soil showed the uranium distribution from uniform (in glasses) to extremely nonuniform in some holocrystalline rocks. It was pointed out, that uranium micro distributions in Lunar and Earth (effusive and magmatic) rocks have common features. In both cases rock-forming minerals don't contain appreciable uranium amount in the form of isomorphic admixture; uranium is highly concentrated in some accessory minerais. The difference lies in tne absence of hydroxyl -containing secondary minerals, which are enriched with uranium on Earth, in Lunar rocks. ''Film'' uranium micromineralization, which occurs in rocks of the Earth along the boundaries of mineral grains is absent in Lunar rocks as well
Energy Technology Data Exchange (ETDEWEB)
Brax, Philippe [Institut de Physique Théorique, CEA, IPhT, CNRS, URA 2306, F-91191Gif/Yvette Cedex (France); Upadhye, Amol, E-mail: philippe.brax@cea.fr, E-mail: aupadhye@anl.gov [Institute for the Early Universe, Ewha University, International Education, Building #601, 11-1, Daehyun-Dong Seodaemun-Gu, Seoul 120-750 (Korea, Republic of)
2014-02-01
A scalar field dark energy candidate could couple to ordinary matter and photons, enabling its detection in laboratory experiments. Here we study the quantum properties of the chameleon field, one such dark energy candidate, in an ''afterglow'' experiment designed to produce, trap, and detect chameleon particles. In particular, we investigate the possible fragmentation of a beam of chameleon particles into multiple particle states due to the highly non-linear interaction terms in the chameleon Lagrangian. Fragmentation could weaken the constraints of an afterglow experiment by reducing the energy of the regenerated photons, but this energy reduction also provides a unique signature which could be detected by a properly-designed experiment. We show that constraints from the CHASE experiment are essentially unaffected by fragmentation for φ{sup 4} and 1/φ potentials, but are weakened for steeper potentials, and we discuss possible future afterglow experiments.
International Nuclear Information System (INIS)
Brax, Philippe; Upadhye, Amol
2014-01-01
A scalar field dark energy candidate could couple to ordinary matter and photons, enabling its detection in laboratory experiments. Here we study the quantum properties of the chameleon field, one such dark energy candidate, in an ''afterglow'' experiment designed to produce, trap, and detect chameleon particles. In particular, we investigate the possible fragmentation of a beam of chameleon particles into multiple particle states due to the highly non-linear interaction terms in the chameleon Lagrangian. Fragmentation could weaken the constraints of an afterglow experiment by reducing the energy of the regenerated photons, but this energy reduction also provides a unique signature which could be detected by a properly-designed experiment. We show that constraints from the CHASE experiment are essentially unaffected by fragmentation for φ 4 and 1/φ potentials, but are weakened for steeper potentials, and we discuss possible future afterglow experiments
International Nuclear Information System (INIS)
Shestakov, A.I.; Mirin, A.A.
1984-01-01
A numerical method based on Fourier expansions and finite differences is presented. The method is demonstrated by solving a scalar, three-dimensional elliptic equation arising in MFE research, but has applicability to a wider class of problems. The scheme solves equations whose solutions are expected to be periodic in one or more of the independent variables
Yin, Zhifu; Sun, Lei; Zou, Helin; Cheng, E.
2015-05-01
A method for obtaining a low-cost and high-replication precision two-dimensional (2D) nanofluidic device with a polymethyl methacrylate (PMMA) sheet is proposed. To improve the replication precision of the 2D PMMA nanochannels during the hot embossing process, the deformation of the PMMA sheet was analyzed by a numerical simulation method. The constants of the generalized Maxwell model used in the numerical simulation were calculated by experimental compressive creep curves based on previously established fitting formula. With optimized process parameters, 176 nm-wide and 180 nm-deep nanochannels were successfully replicated into the PMMA sheet with a replication precision of 98.2%. To thermal bond the 2D PMMA nanochannels with high bonding strength and low dimensional loss, the parameters of the oxygen plasma treatment and thermal bonding process were optimized. In order to measure the dimensional loss of 2D nanochannels after thermal bonding, a dimension loss evaluating method based on the nanoindentation experiments was proposed. According to the dimension loss evaluating method, the total dimensional loss of 2D nanochannels was 6 nm and 21 nm in width and depth, respectively. The tensile bonding strength of the 2D PMMA nanofluidic device was 0.57 MPa. The fluorescence images demonstrate that there was no blocking or leakage over the entire microchannels and nanochannels.
Asiri, Sharefa M.; Laleg-Kirati, Taous-Meriem
2016-01-01
In this paper, modulating functions-based method is proposed for estimating space–time-dependent unknowns in one-dimensional partial differential equations. The proposed method simplifies the problem into a system of algebraic equations linear
Wang, Wei; Shen, Jianqi
2018-06-01
The use of a shaped beam for applications relying on light scattering depends much on the ability to evaluate the beam shape coefficients (BSC) effectively. Numerical techniques for evaluating the BSCs of a shaped beam, such as the quadrature, the localized approximation (LA), the integral localized approximation (ILA) methods, have been developed within the framework of generalized Lorenz-Mie theory (GLMT). The quadrature methods usually employ the 2-/3-dimensional integrations. In this work, the expressions of the BSCs for an elliptical Gaussian beam (EGB) are simplified into the 1-dimensional integral so as to speed up the numerical computation. Numerical results of BSCs are used to reconstruct the beam field and the fidelity of the reconstructed field to the given beam field is estimated. It is demonstrated that the proposed method is much faster than the 2-dimensional integrations and it can acquire more accurate results than the LA method. Limitations of the quadrature method and also the LA method in the numerical calculation are analyzed in detail.
Degradation of a field index by introduction of weakly ferromagnetic material fragment
International Nuclear Information System (INIS)
Pillet, E.
1957-06-01
After having recalled a problem met on chamber doors made of dural (eddy currents resulted in a too important index degradation) which lead to the replacement of dural by a magnetic stainless steel, this technical note report a study which aimed at determining whether the corresponding low magnetism would create a new degradation, but opposite to the previous one. The author first outlines why conventional methods are insufficient for this kind of assessment, and proposes a differential method to apply the superposition principle. This method results in the determination of the reduced magnetisation within the fragment, and in the study of the field created by this magnetisation. The author reports an approximate calculation, and then proposes another approximate method which is based on the determination of the rate between degradation due to fragment magnetisation and that due to eddy current induced in the same fragment
Two-Dimensional Space-Time Dependent Multi-group Diffusion Equation with SLOR Method
International Nuclear Information System (INIS)
Yulianti, Y.; Su'ud, Z.; Waris, A.; Khotimah, S. N.
2010-01-01
The research of two-dimensional space-time diffusion equations with SLOR (Successive-Line Over Relaxation) has been done. SLOR method is chosen because this method is one of iterative methods that does not required to defined whole element matrix. The research is divided in two cases, homogeneous case and heterogeneous case. Homogeneous case has been inserted by step reactivity. Heterogeneous case has been inserted by step reactivity and ramp reactivity. In general, the results of simulations are agreement, even in some points there are differences.
International Nuclear Information System (INIS)
Vardaci, Emanuele; Kaplan, Morton; Parker, Winifred E.; Moses, David J.; Boger, J.T.; Gilfoyle, G.T.; McMahan, M.A.; Montoya, M.
2000-05-01
A new technique has been applied to coincidence measurements between fission fragments (FF) and intermediate mass fragments (IMF) emitted from the composite system 149 65 Tb at an excitation energy of 224 MeV. The method permits simultaneous observation of IMF emissions along and normal to the FF separation axes. For the integrated total of 0.10 +-0.02 IMF emitted per fission, we find no significant correlation with FF direction, suggesting that IMFs associated with fission reactions are predominantly emitted from the system prior to fission
Three-dimensional ICT reconstruction
International Nuclear Information System (INIS)
Zhang Aidong; Li Ju; Chen Fa; Sun Lingxia
2005-01-01
The three-dimensional ICT reconstruction method is the hot topic of recent ICT technology research. In the context, qualified visual three-dimensional ICT pictures are achieved through multi-piece two-dimensional images accumulation by, combining with thresholding method and linear interpolation. Different direction and different position images of the reconstructed pictures are got by rotation and interception respectively. The convenient and quick method is significantly instructive to more complicated three-dimensional reconstruction of ICT images. (authors)
Three-dimensional ICT reconstruction
International Nuclear Information System (INIS)
Zhang Aidong; Li Ju; Chen Fa; Sun Lingxia
2004-01-01
The three-dimensional ICT reconstruction method is the hot topic of recent ICT technology research. In the context qualified visual three-dimensional ICT pictures are achieved through multi-piece two-dimensional images accumulation by order, combining with thresholding method and linear interpolation. Different direction and different position images of the reconstructed pictures are got by rotation and interception respectively. The convenient and quick method is significantly instructive to more complicated three-dimensional reconstruction of ICT images. (authors)
Szemiako, Kasjan; Śledzińska, Anna; Krawczyk, Beata
2017-08-01
Candida sp. have been responsible for an increasing number of infections, especially in patients with immunodeficiency. Species-specific differentiation of Candida sp. is difficult in routine diagnosis. This identification can have a highly significant association in therapy and prophylaxis. This work has shown a new application of the terminal restriction fragment length polymorphism (t-RFLP) method in the molecular identification of six species of Candida, which are the most common causes of fungal infections. Specific for fungi homocitrate synthase gene was chosen as a molecular target for amplification. The use of three restriction enzymes, DraI, RsaI, and BglII, for amplicon digestion can generate species-specific fluorescence labeled DNA fragment profiles, which can be used to determine the diagnostic algorithm. The designed method can be a cost-efficient high-throughput molecular technique for the identification of six clinically important Candida species.
Universality of projectile fragmentation model
International Nuclear Information System (INIS)
Chaudhuri, G.; Mallik, S.; Das Gupta, S.
2012-01-01
Presently projectile fragmentation reaction is an important area of research as it is used for the production of radioactive ion beams. In this work, the recently developed projectile fragmentation model with an universal temperature profile is used for studying the charge distributions of different projectile fragmentation reactions with different projectile target combinations at different incident energies. The model for projectile fragmentation consists of three stages: (i) abrasion, (ii) multifragmentation and (iii) evaporation
Influence of joint direction and position of explosive charge on fragmentation
International Nuclear Information System (INIS)
Hafsaoui, Abdellah; Talhi, Korichi
2009-01-01
Although researchers have realized varying degrees of success in small-scale physical in situ testing, most will agree that the greatest uncertainty stems from the uncontrollable field variables. Given the diverse nature of field conditions encountered, there exists no reliable and proven method of predicting fragmentation. Due to the lack of adequate field controls, it is unlikely that a universal physical model will ever be developed for all blasting. This paper presents the results of a test conducted at the Hadjar Essoud quarry to investigate the problems associated with the discontinuities in the rock, which are among the factors causing the reduction of the resistance of the rocks to the explosive. Nevertheless, the distance between the joints, their dip and strike, and the position of the detonator play a significant role in the final fragmentation of the rock. In this work, we studied the role of the abovementioned factors on models of limestone rock of 150 X 375 X 450 mm. Accurate measurement of blast, fragmentation is important in mining and quarrying operations, in monitoring blasts, and optimizing their design. We shall use the Kuznetsov-Rammler method to measure fragmentation. It shows great potential as a practical aid to predict and control the quality of the fragmented material in the Hadjar Essoud quarry. (author)
Linkage map of the fragments of herpesvirus papio DNA.
Lee, Y S; Tanaka, A; Lau, R Y; Nonoyama, M; Rabin, H
1981-01-01
Herpesvirus papio (HVP), an Epstein-Barr-like virus, causes lymphoblastoid disease in baboons. The physical map of HVP DNA was constructed for the fragments produced by cleavage of HVP DNA with restriction endonucleases EcoRI, HindIII, SalI, and PvuI, which produced 12, 12, 10, and 4 fragments, respectively. The total molecular size of HVP DNA was calculated as close to 110 megadaltons. The following methods were used for construction of the map; (i) fragments near the ends of HVP DNA were identified by treating viral DNA with lambda exonuclease before restriction enzyme digestion; (ii) fragments containing nucleotide sequences in common with fragments from the second enzyme digest of HVP DNA were examined by Southern blot hybridization; and (iii) the location of some fragments was determined by isolating individual fragments from agarose gels and redigesting the isolated fragments with a second restriction enzyme. Terminal heterogeneity and internal repeats were found to be unique features of HVP DNA molecule. One to five repeats of 0.8 megadaltons were found at both terminal ends. Although the repeats of both ends shared a certain degree of homology, it was not determined whether they were identical repeats. The internal repeat sequence of HVP DNA was found in the EcoRI-C region, which extended from 8.4 to 23 megadaltons from the left end of the molecule. The average number of the repeats was calculated to be seven, and the molecular size was determined to be 1.8 megadaltons. Similar unique features have been reported in EBV DNA (D. Given and E. Kieff, J. Virol. 28:524-542, 1978). Images PMID:6261015
Primary and secondary fragmentation of crystal-bearing intermediate magma
Jones, Thomas J.; McNamara, Keri; Eychenne, Julia; Rust, Alison C.; Cashman, Katharine V.; Scheu, Bettina; Edwards, Robyn
2016-11-01
Crystal-rich intermediate magmas are subjected to both primary and secondary fragmentation processes, each of which may produce texturally distinct tephra. Of particular interest for volcanic hazards is the extent to which each process contributes ash to volcanic plumes. One way to address this question is by fragmenting pyroclasts under controlled conditions. We fragmented pumice samples from Soufriere Hills Volcano (SHV), Montserrat, by three methods: rapid decompression in a shock tube-like apparatus, impact by a falling piston, and milling in a ball mill. Grain size distributions of the products reveal that all three mechanisms produce fractal breakage patterns, and that the fractal dimension increases from a minimum of 2.1 for decompression fragmentation (primary fragmentation) to a maximum of 2.7 by repeated impact (secondary fragmentation). To assess the details of the fragmentation process, we quantified the shape, texture and components of constituent ash particles. Ash shape analysis shows that the axial ratio increases during milling and that particle convexity increases with repeated impacts. We also quantify the extent to which the matrix is separated from the crystals, which shows that secondary processes efficiently remove adhering matrix from crystals, particularly during milling (abrasion). Furthermore, measurements of crystal size distributions before (using x-ray computed tomography) and after (by componentry of individual grain size classes) decompression-driven fragmentation show not only that crystals influence particular size fractions across the total grain size distribution, but also that free crystals are smaller in the fragmented material than in the original pumice clast. Taken together, our results confirm previous work showing both the control of initial texture on the primary fragmentation process and the contributions of secondary processes to ash formation. Critically, however, our extension of previous analyses to characterisation
Manoharan, Prabu; Ghoshal, Nanda
2018-05-01
Traditional structure-based virtual screening method to identify drug-like small molecules for BACE1 is so far unsuccessful. Location of BACE1, poor Blood Brain Barrier permeability and P-glycoprotein (Pgp) susceptibility of the inhibitors make it even more difficult. Fragment-based drug design method is suitable for efficient optimization of initial hit molecules for target like BACE1. We have developed a fragment-based virtual screening approach to identify/optimize the fragment molecules as a starting point. This method combines the shape, electrostatic, and pharmacophoric features of known fragment molecules, bound to protein conjugate crystal structure, and aims to identify both chemically and energetically feasible small fragment ligands that bind to BACE1 active site. The two top-ranked fragment hits were subjected for a 53 ns MD simulation. Principle component analysis and free energy landscape analysis reveal that the new ligands show the characteristic features of established BACE1 inhibitors. The potent method employed in this study may serve for the development of potential lead molecules for BACE1-directed Alzheimer's disease therapeutics.
Political fragmentation and widening disparities in African-American and white mortality, 1972-1988.
Kim, Yonsu; Bruckner, Tim A
2016-12-01
During the 1970s and 1980s in the U.S., population movement, urban sprawl and urban governance reform led to a proliferation of local, autonomous jurisdictions. Prior literature examines how this creation of local governments, also referred to as political fragmentation, contributes to economic growth and social inequality. We examine the impact of political fragmentation on health equity by testing the hypothesis that the mortality disparity between whites and African-Americans varies positively with political fragmentation. We retrieved mortality data from the multiple cause-of-death file and calculated total number of local governments per 1000 residents in a county to measure the degree of political fragmentation. We focused on 226 U.S. counties with population size greater than 200,000 and restricted the analysis to four distinct periods with overlapping government and mortality data (1972-73, 1977-78, 1982-83, and 1987-88). We applied generalized estimating equation methods that permit analysis of clustered data over time. Methods also controlled for the age structure of the population, reductions in mortality over time, and confounding by county-level sociodemographic variables. Adjusted coefficients of fragmentation are positive and statistically significant for both whites (coef: 2.60, SE: 0.60, p politically fragmented urban counties and/or time periods. From 1972 to 1988, political fragmentation in large urban counties moves positively with the racial/ethnic gap in mortality between whites and African-Americans. We discuss intervening mechanisms through which political fragmentation may disproportionately affect mortality among African-Americans.
Energy Technology Data Exchange (ETDEWEB)
Wang, Le; Pratt, John K.; Soltwedel, Todd; Sheppard, George S.; Fidanze, Steven D.; Liu, Dachun; Hasvold, Lisa A.; Mantei, Robert A.; Holms, James H.; McClellan, William J.; Wendt, Michael D.; Wada, Carol; Frey, Robin; Hansen, T.Matthew; Hubbard, Robert; Park, Chang H.; Li, Leiming; Magoc, Terrance J.; Albert, Daniel H.; Lin, Xiaoyu; Warder, Scott E.; Kovar, Peter; Huang, Xiaoli; Wilcox, Denise; Wang, Rongqi; Rajaraman, Ganesh; Petros, Andrew M.; Hutchins, Charles W.; Panchal, Sanjay C.; Sun, Chaohong; Elmore, Steven W.; Shen, Yu; Kati, Warren M.; McDaniel, Keith F. (AbbVie)
2017-03-24
Members of the BET family of bromodomain containing proteins have been identified as potential targets for blocking proliferation in a variety of cancer cell lines. A two-dimensional NMR fragment screen for binders to the bromodomains of BRD4 identified a phenylpyridazinone fragment with a weak binding affinity (1, Ki = 160 μM). SAR investigation of fragment 1, aided by X-ray structure-based design, enabled the synthesis of potent pyridone and macrocyclic pyridone inhibitors exhibiting single digit nanomolar potency in both biochemical and cell based assays. Advanced analogs in these series exhibited high oral exposures in rodent PK studies and demonstrated significant tumor growth inhibition efficacy in mouse flank xenograft models.
Continuum methods of physical modeling continuum mechanics, dimensional analysis, turbulence
Hutter, Kolumban
2004-01-01
The book unifies classical continuum mechanics and turbulence modeling, i.e. the same fundamental concepts are used to derive model equations for material behaviour and turbulence closure and complements these with methods of dimensional analysis. The intention is to equip the reader with the ability to understand the complex nonlinear modeling in material behaviour and turbulence closure as well as to derive or invent his own models. Examples are mostly taken from environmental physics and geophysics.
International Nuclear Information System (INIS)
Polivanskij, V.P.
1989-01-01
The method to solve two-dimensional equations of neutron transport using 4P 0 -approximation is presented. Previously such approach was efficiently used for the solution of one-dimensional problems. New an attempt is made to apply the approach to solution of two-dimensional problems. Algorithm of the solution is given, as well as results of test neutron-physical calculations. A considerable as compared with diffusion approximation is shown. 11 refs
Fragmentation of water on swift {sup 3}He{sup 2+} ion impact
Energy Technology Data Exchange (ETDEWEB)
Sabin, John R. [Quantum Theory Project, Departments of Chemistry and Physics, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435 (United States); Institut for Fysik og Kemi, Suddansk Universitet, 5230 Odense M (Denmark)], E-mail: sabin@qtp.ufl.edu; Cabrerra-Trujillo, Remigio [Instituto de Ciencias Fisicas, Universidad Nacional Autonoma de Mexico, Apartado Postal 48-3, Cuernavaca, Morelos 62251 (Mexico); Stolterfoht, Nikolaus [Hahn-Meitner Institut, Glienickerstrasse 100, D-14109 Berlin (Germany); Deumens, Erik; Ohrn, Yngve [Quantum Theory Project, Departments of Chemistry and Physics, P.O. Box 118435, University of Florida, Gainesville, FL 32611-8435 (United States)
2009-01-15
Charge exchange and fragmentation are the usual results in ion-molecule collision systems, and the specifics of the fragmentation process determine the chemical destiny of the target system. In this paper, we report recent progress on calculations of the fragmentation patterns for the model system He{sup 2+} + H{sub 2}O for projectile energies of a few keV. The calculations are obtained using the electron-nuclear dynamics (END) method for solution of the time-dependent Schroedinger equation.
PARALLEL ALGORITHM FOR THREE-DIMENSIONAL STOKES FLOW SIMULATION USING BOUNDARY ELEMENT METHOD
Directory of Open Access Journals (Sweden)
D. G. Pribytok
2016-01-01
Full Text Available Parallel computing technique for modeling three-dimensional viscous flow (Stokes flow using direct boundary element method is presented. The problem is solved in three phases: sampling and construction of system of linear algebraic equations (SLAE, its decision and finding the velocity of liquid at predetermined points. For construction of the system and finding the velocity, the parallel algorithms using graphics CUDA cards programming technology have been developed and implemented. To solve the system of linear algebraic equations the implemented software libraries are used. A comparison of time consumption for three main algorithms on the example of calculation of viscous fluid motion in three-dimensional cavity is performed.
Development of the method for the dimensional measurement of the HANARO nuclear fuel
International Nuclear Information System (INIS)
Kim, Tae Yeon; Lee, K. S.; Park, D. G.; Choo, Y. S.; Ahn, S. B.
1998-06-01
Dimension of the nuclear fuel is altered in nuclear reactor because of the neutron exposure with high pressure water. If the deformation is overlarge, the severe problem in safety of the nuclear fuel and the reactor come about. Therefore the accurate dimensional data of the nuclear fuel in diameter and length is very important for the design of the nuclear fuel and the estimation of the nuclear safety. Measurement of diameter for the dummy HANARO fuel rod which has not filled with real fuel material was carried out in hot cell. And also the length of the HANARO fuel assembly and the rod are measured. Dimensional measuring method for the HANARO fuel was developed. The test result show our method is good enough to distinguish change in volume with statistical uncertainty of 0.6 %. (author). 2 refs., 7 tabs., 20 figs
Desvillettes, Laurent
2010-01-01
We study a continuous coagulation-fragmentation model with constant kernels for reacting polymers (see [M. Aizenman and T. Bak, Comm. Math. Phys., 65 (1979), pp. 203-230]). The polymers are set to diffuse within a smooth bounded one-dimensional domain with no-flux boundary conditions. In particular, we consider size-dependent diffusion coefficients, which may degenerate for small and large cluster-sizes. We prove that the entropy-entropy dissipation method applies directly in this inhomogeneous setting. We first show the necessary basic a priori estimates in dimension one, and second we show faster-than-polynomial convergence toward global equilibria for diffusion coefficients which vanish not faster than linearly for large sizes. This extends the previous results of [J.A. Carrillo, L. Desvillettes, and K. Fellner, Comm. Math. Phys., 278 (2008), pp. 433-451], which assumes that the diffusion coefficients are bounded below. © 2009 Society for Industrial and Applied Mathematics.
International Nuclear Information System (INIS)
Fink, B.K.; Fink, U.; Pentenrieder, M.; Kohz, P.; Englmeier, H.K.; Schmeller, N.
1994-01-01
5 patients with staghorn calculi in the renal pelvis were examined by spiral CT. From the raw data three dimensional reconstructions of the stones were obtained. In all patients it was possible to compare the three dimensional model with the stone following performance of percutaneous lithopaxy and endoscopic removal of the fragments. In all cases the three dimensional reconstruction provided a realistic image of the stones and was of practical value for the urologist for preoperative diagnosis and intraoperative control. (orig.) [de
Self-organized criticality in fragmenting
DEFF Research Database (Denmark)
Oddershede, L.; Dimon, P.; Bohr, J.
1993-01-01
The measured mass distributions of fragments from 26 fractured objects of gypsum, soap, stearic paraffin, and potato show evidence of obeying scaling laws; this suggests the possibility of self-organized criticality in fragmenting. The probability of finding a fragment scales inversely to a power...
A molecular fragment cheminformatics roadmap for mesoscopic simulation.
Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias
2014-12-01
Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and
Energy production using fission fragment rockets
International Nuclear Information System (INIS)
Chapline, G.; Matsuda, Y.
1991-08-01
Fission fragment rockets are nuclear reactors with a core consisting of thin fibers in a vacuum, and which use magnetic fields to extract the fission fragments from the reactor core. As an alternative to ordinary nuclear reactors, fission fragment rockets would have the following advantages: Approximately twice as efficient if one can directly convert the fission fragment energy into electricity; by reducing the buildup of a fission fragment inventory in the reactor one could avoid a Chernobyl type disaster; and collecting the fission fragments outside the reactor could simplify the waste disposal problem. 6 refs., 4 figs., 2 tabs
Fast multiview three-dimensional reconstruction method using cost volume filtering
Lee, Seung Joo; Park, Min Ki; Jang, In Yeop; Lee, Kwan H.
2014-03-01
As the number of customers who want to record three-dimensional (3-D) information using a mobile electronic device increases, it becomes more and more important to develop a method which quickly reconstructs a 3-D model from multiview images. A fast multiview-based 3-D reconstruction method is presented, which is suitable for the mobile environment by constructing a cost volume of the 3-D height field. This method consists of two steps: the construction of a reliable base surface and the recovery of shape details. In each step, the cost volume is constructed using photoconsistency and then it is filtered according to the multiscale. The multiscale-based cost volume filtering allows the 3-D reconstruction to maintain the overall shape and to preserve the shape details. We demonstrate the strength of the proposed method in terms of computation time, accuracy, and unconstrained acquisition environment.
Real-time Tracking of DNA Fragment Separation by Smartphone.
Tao, Chunxian; Yang, Bo; Li, Zhenqing; Zhang, Dawei; Yamaguchi, Yoshinori
2017-06-01
Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and others. However, the traditional SGE protocol is quite tedious, and the experiment takes a long time. Moreover, the chemical consumption in SGE experiments is very high. This work proposes a simple method for the separation of DNA fragments based on an SGE chip. The chip is made by an engraving machine. Two plastic sheets are used for the excitation and emission wavelengths of the optical signal. The fluorescence signal of the DNA bands is collected by smartphone. To validate this method, 50, 100, and 1,000 bp DNA ladders were separated. The results demonstrate that a DNA ladder smaller than 5,000 bp can be resolved within 12 min and with high resolution when using this method, indicating that it is an ideal substitute for the traditional SGE method.
Can We Train Machine Learning Methods to Outperform the High-dimensional Propensity Score Algorithm?
Karim, Mohammad Ehsanul; Pang, Menglan; Platt, Robert W
2018-03-01
The use of retrospective health care claims datasets is frequently criticized for the lack of complete information on potential confounders. Utilizing patient's health status-related information from claims datasets as surrogates or proxies for mismeasured and unobserved confounders, the high-dimensional propensity score algorithm enables us to reduce bias. Using a previously published cohort study of postmyocardial infarction statin use (1998-2012), we compare the performance of the algorithm with a number of popular machine learning approaches for confounder selection in high-dimensional covariate spaces: random forest, least absolute shrinkage and selection operator, and elastic net. Our results suggest that, when the data analysis is done with epidemiologic principles in mind, machine learning methods perform as well as the high-dimensional propensity score algorithm. Using a plasmode framework that mimicked the empirical data, we also showed that a hybrid of machine learning and high-dimensional propensity score algorithms generally perform slightly better than both in terms of mean squared error, when a bias-based analysis is used.
International Nuclear Information System (INIS)
Chen Yong; Yan Zhenya
2005-01-01
In this paper (2 + 1)-dimensional Gardner equation is investigated using a sine-Gordon equation expansion method, which was presented via a generalized sine-Gordon reduction equation and a new transformation. As a consequence, it is shown that the method is more powerful to obtain many types of new doubly periodic solutions of (2 + 1)-dimensional Gardner equation. In particular, solitary wave solutions are also given as simple limits of doubly periodic solutions
Yu, L; Batlle, F
2011-12-01
Limited space for accommodating the ever increasing mounds of municipal solid waste (MSW) demands the capacity of MSW landfill be maximized by building landfills to greater heights with steeper slopes. This situation has raised concerns regarding the stability of high MSW landfills. A hybrid method for quasi-three-dimensional slope stability analysis based on the finite element stress analysis was applied in a case study at a MSW landfill in north-east Spain. Potential slides can be assumed to be located within the waste mass due to the lack of weak foundation soils and geosynthetic membranes at the landfill base. The only triggering factor of deep-seated slope failure is the higher leachate level and the relatively high and steep slope in the front. The valley-shaped geometry and layered construction procedure at the site make three-dimensional slope stability analyses necessary for this landfill. In the finite element stress analysis, variations of leachate level during construction and continuous settlement of the landfill were taken into account. The "equivalent" three-dimensional factor of safety (FoS) was computed from the individual result of the two-dimensional analysis for a series of evenly spaced cross sections within the potential sliding body. Results indicate that the hybrid method for quasi-three-dimensional slope stability analysis adopted in this paper is capable of locating roughly the spatial position of the potential sliding mass. This easy to manipulate method can serve as an engineering tool in the preliminary estimate of the FoS as well as the approximate position and extent of the potential sliding mass. The result that FoS obtained from three-dimensional analysis increases as much as 50% compared to that from two-dimensional analysis implies the significance of the three-dimensional effect for this study-case. Influences of shear parameters, time elapse after landfill closure, leachate level as well as unit weight of waste on FoS were also
International Nuclear Information System (INIS)
Ka-Lin, Su; Yuan-Xi, Xie
2010-01-01
By introducing a more general auxiliary ordinary differential equation (ODE), a modified variable separated ordinary differential equation method is presented for solving the (2 + 1)-dimensional sine-Poisson equation. As a result, many explicit and exact solutions of the (2 + 1)-dimensional sine-Poisson equation are derived in a simple manner by this technique. (general)
Yin, Kedong; Yang, Benshuo; Li, Xuemei
2018-01-24
In this paper, we investigate multiple attribute group decision making (MAGDM) problems where decision makers represent their evaluation of alternatives by trapezoidal fuzzy two-dimensional uncertain linguistic variable. To begin with, we introduce the definition, properties, expectation, operational laws of trapezoidal fuzzy two-dimensional linguistic information. Then, to improve the accuracy of decision making in some case where there are a sort of interrelationship among the attributes, we analyze partition Bonferroni mean (PBM) operator in trapezoidal fuzzy two-dimensional variable environment and develop two operators: trapezoidal fuzzy two-dimensional linguistic partitioned Bonferroni mean (TF2DLPBM) aggregation operator and trapezoidal fuzzy two-dimensional linguistic weighted partitioned Bonferroni mean (TF2DLWPBM) aggregation operator. Furthermore, we develop a novel method to solve MAGDM problems based on TF2DLWPBM aggregation operator. Finally, a practical example is presented to illustrate the effectiveness of this method and analyses the impact of different parameters on the results of decision-making.
Fragmentation of relativistic nuclei
International Nuclear Information System (INIS)
Cork, B.
1975-06-01
Nuclei with energies of several GeV/n interact with hadrons and produce fragments that encompass the fields of nuclear physics, meson physics, and particle physics. Experimental results are now available to explore problems in nuclear physics such as the validity of the shell model to explain the momentum distribution of fragments, the contribution of giant dipole resonances to fragment production cross sections, the effective Coulomb barrier, and nuclear temperatures. A new approach to meson physics is possible by exploring the nucleon charge-exchange process. Particle physics problems are explored by measuring the energy and target dependence of isotope production cross sections, thus determining if limiting fragmentation and target factorization are valid, and measuring total cross sections to determine if the factorization relation, sigma/sub AB/ 2 = sigma/sub AA/ . sigma/sub BB/, is violated. Also, new experiments have been done to measure the angular distribution of fragments that could be explained as nuclear shock waves, and to explore for ultradense matter produced by very heavy ions incident on heavy atoms. (12 figures, 2 tables)
Energy Technology Data Exchange (ETDEWEB)
Audias, A [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires
1965-07-01
This fission fragment detecting apparatus is based on the principle that fragments traversing a thin foil will cause emission of secondary electrons. These electrons are then accelerated (10 kV) and directly detected by means of a plastic scintillator and associated photomultiplier. Some of the advantages of such a detector are, its rapidity, its discriminating power between alpha particles and fission fragments, its small energy loss in detecting the fragments and the relatively great amount of fissionable material which it can contain. This paper is subdivided as follows: a) theoretical considerations b) constructional details of apparatus and some experimental details and c) a study of the secondary emission effect itself. (author) [French] Le detecteur de fragments de fission que nous avons realise est base sur le principe de l'emission secondaire produite par les fragments de fission traversant une feuille mince: les electrons secondaires emis sont acceleres a des tensions telles (de l'ordre de 10 kV), qu'ils soient directement detectables par un scintillateur plastique associe a un photomultiplicateur. L'interet d'un tel detecteur reside: dans sa rapidite, sa tres bonne discrimination alpha, fission, la possibilite de detecter les fragments de fission avec une perte d'energie pouvant rester relativement faible, et la possibilite d'introduire des quantites de matiere fissile plus importantes que dans les autres types de detecteurs. Ce travail comporte: -) un apercu bibliographique de la theorie du phenomene, -) realisation et mise au point du detecteur avec etude experimentale de quelques parametres intervenant dans l'emission secondaire, -) etude de l'emission secondaire (sur la face d'emergence des fragments de fission) en fonction de l'energie du fragment et en fonction de l'epaisseur de matiere traversee avant emission secondaire, et -) une etude comparative de l'emission secondaire sur la face d'incidence et sur la face d'emergence des fragments de
Göth, Melanie; Badock, Volker; Weiske, Jörg; Pagel, Kevin; Kuropka, Benno
2017-08-08
Fragment-based screening presents a promising alternative to high-throughput screening and has gained great attention in recent years. So far, only a few studies have discussed mass spectrometry as a screening technology for fragments. Herein, we report the application of native electrospray ionization mass spectrometry (MS) for screening defined sets of fragments against four different target proteins. Fragments were selected from a primary screening conducted with a thermal shift assay (TSA) and represented different binding categories. Our data indicated that, beside specific complex formation, many fragments show extensive multiple binding and also charge-state shifts. Both of these factors complicate automated data analysis and decrease the attractiveness of native MS as a primary screening tool for fragments. A comparison of the hits identified by native MS and TSA showed good agreement for two of the proteins. Furthermore, we discuss general challenges, including the determination of an optimal fragment concentration and the question of how to rank fragment hits according to their affinity. In conclusion, we consider native MS to be a highly valuable tool for the validation and deeper investigation of promising fragment hits rather than a method for primary screening. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
International Nuclear Information System (INIS)
Ravi Kanth, A.S.V.; Aruna, K.
2009-01-01
In this paper, we propose a reliable algorithm to develop exact and approximate solutions for the linear and nonlinear Schroedinger equations. The approach rest mainly on two-dimensional differential transform method which is one of the approximate methods. The method can easily be applied to many linear and nonlinear problems and is capable of reducing the size of computational work. Exact solutions can also be achieved by the known forms of the series solutions. Several illustrative examples are given to demonstrate the effectiveness of the present method.
Sellers, Benjamin D; James, Natalie C; Gobbi, Alberto
2017-06-26
Reducing internal strain energy in small molecules is critical for designing potent drugs. Quantum mechanical (QM) and molecular mechanical (MM) methods are often used to estimate these energies. In an effort to determine which methods offer an optimal balance in accuracy and performance, we have carried out torsion scan analyses on 62 fragments. We compared nine QM and four MM methods to reference energies calculated at a higher level of theory: CCSD(T)/CBS single point energies (coupled cluster with single, double, and perturbative triple excitations at the complete basis set limit) calculated on optimized geometries using MP2/6-311+G**. The results show that both the more recent MP2.X perturbation method as well as MP2/CBS perform quite well. In addition, combining a Hartree-Fock geometry optimization with a MP2/CBS single point energy calculation offers a fast and accurate compromise when dispersion is not a key energy component. Among MM methods, the OPLS3 force field accurately reproduces CCSD(T)/CBS torsion energies on more test cases than the MMFF94s or Amber12:EHT force fields, which struggle with aryl-amide and aryl-aryl torsions. Using experimental conformations from the Cambridge Structural Database, we highlight three example structures for which OPLS3 significantly overestimates the strain. The energies and conformations presented should enable scientists to estimate the expected error for the methods described and we hope will spur further research into QM and MM methods.
Thermodynamics of the fuel fragmentation gas
International Nuclear Information System (INIS)
Perez, R.B.; Alsmiller, R.G. Jr.
1977-01-01
In the context of nuclear reactor safety studies, a program is in progress at ORNL whereby fuel-fragmentation situations are mocked up by the application of high-current capacitor discharges through solid UO 2 samples. The goal of the present work is to predict such quantities as the number of gas and liquid fragments and their energy distributions. The point of view adopted is that upon fragmentation, a cloud of UO 2 vapor is formed containing ''primeval'' liquid fragments which act as condensation centers. In the evolution of time, fragment growth is controlled by nucleation, coagulation and evaporation processes. Eventually, the vapor-droplet system will reach a situation in which clusters (fragments) of various sizes and UO 2 vapor will coexist in an ''association-disassociation'' equilibrium. Thus, the physical model considered here consists of the identification of the fragmentation gas with an ''imperfect'' vapor, made up of interacting UO 2 vapor and liquid fragments. The results of the study are presented
James, Andrew J A; Konik, Robert M; Lecheminant, Philippe; Robinson, Neil J; Tsvelik, Alexei M
2018-02-26
We review two important non-perturbative approaches for extracting the physics of low-dimensional strongly correlated quantum systems. Firstly, we start by providing a comprehensive review of non-Abelian bosonization. This includes an introduction to the basic elements of conformal field theory as applied to systems with a current algebra, and we orient the reader by presenting a number of applications of non-Abelian bosonization to models with large symmetries. We then tie this technique into recent advances in the ability of cold atomic systems to realize complex symmetries. Secondly, we discuss truncated spectrum methods for the numerical study of systems in one and two dimensions. For one-dimensional systems we provide the reader with considerable insight into the methodology by reviewing canonical applications of the technique to the Ising model (and its variants) and the sine-Gordon model. Following this we review recent work on the development of renormalization groups, both numerical and analytical, that alleviate the effects of truncating the spectrum. Using these technologies, we consider a number of applications to one-dimensional systems: properties of carbon nanotubes, quenches in the Lieb-Liniger model, 1 + 1D quantum chromodynamics, as well as Landau-Ginzburg theories. In the final part we move our attention to consider truncated spectrum methods applied to two-dimensional systems. This involves combining truncated spectrum methods with matrix product state algorithms. We describe applications of this method to two-dimensional systems of free fermions and the quantum Ising model, including their non-equilibrium dynamics.
James, Andrew J. A.; Konik, Robert M.; Lecheminant, Philippe; Robinson, Neil J.; Tsvelik, Alexei M.
2018-04-01
We review two important non-perturbative approaches for extracting the physics of low-dimensional strongly correlated quantum systems. Firstly, we start by providing a comprehensive review of non-Abelian bosonization. This includes an introduction to the basic elements of conformal field theory as applied to systems with a current algebra, and we orient the reader by presenting a number of applications of non-Abelian bosonization to models with large symmetries. We then tie this technique into recent advances in the ability of cold atomic systems to realize complex symmetries. Secondly, we discuss truncated spectrum methods for the numerical study of systems in one and two dimensions. For one-dimensional systems we provide the reader with considerable insight into the methodology by reviewing canonical applications of the technique to the Ising model (and its variants) and the sine-Gordon model. Following this we review recent work on the development of renormalization groups, both numerical and analytical, that alleviate the effects of truncating the spectrum. Using these technologies, we consider a number of applications to one-dimensional systems: properties of carbon nanotubes, quenches in the Lieb–Liniger model, 1 + 1D quantum chromodynamics, as well as Landau–Ginzburg theories. In the final part we move our attention to consider truncated spectrum methods applied to two-dimensional systems. This involves combining truncated spectrum methods with matrix product state algorithms. We describe applications of this method to two-dimensional systems of free fermions and the quantum Ising model, including their non-equilibrium dynamics.
Amplified-fragment length polymorphism fingerprinting of Mycoplasma species
DEFF Research Database (Denmark)
Kokotovic, Branko; Friis, N.F.; Jensen, J.S.
1999-01-01
Amplified-fragment length polymorphism (AFLP) is a whole-genome fingerprinting method based on selective amplification of restriction fragments. The potential of the method for the characterization of mycoplasmas was investigated in a total of 50 strains of human and animal origin, including...... Mycoplasma genitalium (n = 11), Mycoplasma pneumoniae (n = 5), Mycoplasma hominis (n = 5), Mycoplasma hyopneunmoniae (n = 9), Myco plasma flocculare (n = 5), Mycoplasma hyosynoviae (n = 10), and Mycoplasma dispar (n = 5), AFLP templates were prepared by the digestion of mycoplasmal DNA with BglII and Mfe...... to discriminate the analyzed strains at species and intraspecies levels as well, Each of the tested Mycoplasma species developed a banding pattern entirely different from those obtained from other species under analysis, Subtle intraspecies genomic differences were detected among strains of all of the Mycoplasma...
Sperm DNA fragmentation affects epigenetic feature in human male pronucleus.
Rajabi, H; Mohseni-Kouchesfehani, H; Eslami-Arshaghi, T; Salehi, M
2018-02-01
To evaluate whether the sperm DNA fragmentation affects male pronucleus epigenetic factors, semen analysis was performed and DNA fragmentation was assessed by the method of sperm chromatin structure assay (SCSA). Human-mouse interspecies fertilisation was used to create human male pronucleus. Male pronucleus DNA methylation and H4K12 acetylation were evaluated by immunostaining. Results showed a significant positive correlation between the level of sperm DNA fragmentation and DNA methylation in male pronuclei. In other words, an increase in DNA damage caused an upsurge in DNA methylation. In the case of H4K12 acetylation, no correlation was detected between DNA damage and the level of histone acetylation in the normal group, but results for the group in which male pronuclei were derived from sperm cells with DNA fragmentation, increased DNA damage led to a decreased acetylation level. Sperm DNA fragmentation interferes with the active demethylation process and disrupts the insertion of histones into the male chromatin in the male pronucleus, following fertilisation. © 2017 Blackwell Verlag GmbH.
A Shell Multi-dimensional Hierarchical Cubing Approach for High-Dimensional Cube
Zou, Shuzhi; Zhao, Li; Hu, Kongfa
The pre-computation of data cubes is critical for improving the response time of OLAP systems and accelerating data mining tasks in large data warehouses. However, as the sizes of data warehouses grow, the time it takes to perform this pre-computation becomes a significant performance bottleneck. In a high dimensional data warehouse, it might not be practical to build all these cuboids and their indices. In this paper, we propose a shell multi-dimensional hierarchical cubing algorithm, based on an extension of the previous minimal cubing approach. This method partitions the high dimensional data cube into low multi-dimensional hierarchical cube. Experimental results show that the proposed method is significantly more efficient than other existing cubing methods.
International Nuclear Information System (INIS)
Shtromberger, N.L.
1989-01-01
To design a cyclotron magnetic system the legitimacy of two-dimensional approximations application is discussed. In all the calculations the finite difference method is used, and the linearization method with further use of the gradient conjugation method is used to solve the set of finite-difference equations. 3 refs.; 5 figs
Models of fragmentation with composite power laws
Tavassoli, Z.; Rodgers, G. J.
1999-06-01
Some models for binary fragmentation are introduced in which a time dependent transition size produces two regions of fragment sizes above and below the transition size. In the first model we assume a fixed rate of fragmentation for the largest fragment and two different rates of fragmentation in the two regions of sizes above and below the transition size. The model is solved exactly in the long time limit to reveal stable time-invariant solutions for the fragment size and mass distributions. These solutions exhibit composite power law behaviours; power laws with two different exponents for fragments in smaller and larger regions. A special case of the model with no fragmentation in the smaller size region is also examined. Another model is also introduced which have three regions of fragment sizes with different rates of fragmentation. The similarities between the stable distributions in our models and composite power law distributions from experimental work on shock fragmentation of long thin glass rods and thick clay plates are discussed.
Kinetics of fragmentation-annihilation processes
Filipe, JAN; Rodgers, GJ
1996-01-01
We investigate the kinetics of systems in which particles of one species undergo binary fragmentation and pair annihilation. In the latter, nonlinear process, fragments react at collision to produce an inert species, causing loss of mass. We analyze these systems in the reaction-limited regime by solving a continuous model within the mean-field approximation. The rate of fragmentation for a particle of mass x to break into fragments of masses y and x-y has the form x(lambda-1) (lambda > 0), a...
Fission fragment spins and spectroscopy
International Nuclear Information System (INIS)
Durell, J.L.
1988-01-01
Prompt γ-ray coincidence experiments have been carried out on γ-rays emitted from post-neutron emission fission fragments produced by the aup 19F + 197 Au and 18 O + 232 Th reactions. Decay schemes have been established for even-even nuclei ranging from 78 Se to 148 Nd. Many new states with spin up to ∼ 12h have been observed. Apart from providing a wealth of new information on the spectroscopy of neutron-rich nuclei, the data have been analyzed to determine the average spin of primary fission fragments as a function of fragment mass. The results suggest that the fragment spins are determined by the temperature and shape of the primary fragments at or near to scission
Langevin description of fission fragment charge distribution from excited nuclei
Karpov, A V
2002-01-01
A stochastic approach to fission dynamics based on a set of three-dimensional Langevin equations was applied to calculate fission-fragment charge distribution of compound nucleus sup 2 sup 3 sup 6 U. The following collective coordinates have been chosen - elongation coordinate, neck-thickness coordinate, and charge-asymmetry coordinate. The friction coefficient of charge mode has been calculated in the framework of one-body and two-body dissipation mechanisms. Analysis of the results has shown that Langevin approach is appropriate for investigation of isobaric distribution. Moreover, the dependences of the variance of the charge distribution on excitation energy and on the two-body viscosity coefficient has been studied
Parton jet fragmentation at small momentum fraction (x)
International Nuclear Information System (INIS)
Kirschner, R.
1984-05-01
The parton fragmentation function is calculated at small x and the angular ordering condition is rederived by extending the method of separation of the softest particle, which is based on unitarity and gauge invariance. (author)
Development of a particle method of characteristics (PMOC) for one-dimensional shock waves
Hwang, Y.-H.
2018-03-01
In the present study, a particle method of characteristics is put forward to simulate the evolution of one-dimensional shock waves in barotropic gaseous, closed-conduit, open-channel, and two-phase flows. All these flow phenomena can be described with the same set of governing equations. The proposed scheme is established based on the characteristic equations and formulated by assigning the computational particles to move along the characteristic curves. Both the right- and left-running characteristics are traced and represented by their associated computational particles. It inherits the computational merits from the conventional method of characteristics (MOC) and moving particle method, but without their individual deficiencies. In addition, special particles with dual states deduced to the enforcement of the Rankine-Hugoniot relation are deliberately imposed to emulate the shock structure. Numerical tests are carried out by solving some benchmark problems, and the computational results are compared with available analytical solutions. From the derivation procedure and obtained computational results, it is concluded that the proposed PMOC will be a useful tool to replicate one-dimensional shock waves.
Fragmentation of atomic clusters: A theoretical study
International Nuclear Information System (INIS)
Lopez, M.J.; Jellinek, J.
1994-01-01
Collisionless fragmentation of nonrotating model n-atom metal clusters (n=12, 13, and 14) is studied using isoergic molecular-dynamics simulations. Minimum-energy paths for fragmentation are mapped out as functions of the distance between the centers of mass of the fragments. These paths provide information on the fragmentation energies for the different fragmentation channels. Fragmentation patterns (distributions of the fragmentation channel probabilities) and global and channel-specific fragmentation rate constants are computed and analyzed as functions of the internal energy and of the size of the clusters. The trends derived from the dynamics are compared with those obtained using the RRK and TST statistical approaches. The dynamics of the fragmentation process is analyzed in terms of characteristic quantities such as the distance between the centers of mass of the fragments, their relative translational energy, and their interaction energy, all considered as functions of time
Numerical method for solving the three-dimensional time-dependent neutron diffusion equation
International Nuclear Information System (INIS)
Khaled, S.M.; Szatmary, Z.
2005-01-01
A numerical time-implicit method has been developed for solving the coupled three-dimensional time-dependent multi-group neutron diffusion and delayed neutron precursor equations. The numerical stability of the implicit computation scheme and the convergence of the iterative associated processes have been evaluated. The computational scheme requires the solution of large linear systems at each time step. For this purpose, the point over-relaxation Gauss-Seidel method was chosen. A new scheme was introduced instead of the usual source iteration scheme. (author)
Observing Femtosecond Fragmentation Using Ultrafast X-ray-Induced Auger Spectra
Directory of Open Access Journals (Sweden)
Thomas J. A. Wolf
2017-07-01
Full Text Available Molecules often fragment after photoionization in the gas phase. Usually, this process can only be investigated spectroscopically as long as there exists electron correlation between the photofragments. Important parameters, like their kinetic energy after separation, cannot be investigated. We are reporting on a femtosecond time-resolved Auger electron spectroscopy study concerning the photofragmentation dynamics of thymine. We observe the appearance of clearly distinguishable signatures from thymine′s neutral photofragment isocyanic acid. Furthermore, we observe a time-dependent shift of its spectrum, which we can attribute to the influence of the charged fragment on the Auger electron. This allows us to map our time-dependent dataset onto the fragmentation coordinate. The time dependence of the shift supports efficient transformation of the excess energy gained from photoionization into kinetic energy of the fragments. Our method is broadly applicable to the investigation of photofragmentation processes.
Multi-dimensional Fuzzy Euler Approximation
Directory of Open Access Journals (Sweden)
Yangyang Hao
2017-05-01
Full Text Available Multi-dimensional Fuzzy differential equations driven by multi-dimen-sional Liu process, have been intensively applied in many fields. However, we can not obtain the analytic solution of every multi-dimensional fuzzy differential equation. Then, it is necessary for us to discuss the numerical results in most situations. This paper focuses on the numerical method of multi-dimensional fuzzy differential equations. The multi-dimensional fuzzy Taylor expansion is given, based on this expansion, a numerical method which is designed for giving the solution of multi-dimensional fuzzy differential equation via multi-dimensional Euler method will be presented, and its local convergence also will be discussed.
Posterior extradural migration of extruded thoracic and lumbar disc fragments: role of MRI
International Nuclear Information System (INIS)
Neugroschl, C.; Dietemann, J.L.; Kehrli, P.; Ragragui, O.; Maitrot, D.; Gigaud, M.; Manelfe, C.
1999-01-01
We report three patients with a sequestrated disc fragment posterior to the thecal sac. The affected disc was lumbar in two cases and thoracic in the third. Disc fragment migration is usually limited to the anterior extra dural space. Migration of a disc fragment behind the dural sac is seldom encountered. MRI appears to be the method of choice to make this diagnosis. The disc fragments gave low signal on T1- and slightly high signal on T2-weighted images and showed rim contrast enhancement. The differential diagnosis includes abscess, metastatic tumour and haematoma. (orig.)
Simulation of Thermal Stratification in BWR Suppression Pools with One Dimensional Modeling Method
Energy Technology Data Exchange (ETDEWEB)
Haihua Zhao; Ling Zou; Hongbin Zhang
2014-01-01
The suppression pool in a boiling water reactor (BWR) plant not only is the major heat sink within the containment system, but also provides the major emergency cooling water for the reactor core. In several accident scenarios, such as a loss-of-coolant accident and extended station blackout, thermal stratification tends to form in the pool after the initial rapid venting stage. Accurately predicting the pool stratification phenomenon is important because it affects the peak containment pressure; the pool temperature distribution also affects the NPSHa (available net positive suction head) and therefore the performance of the Emergency Core Cooling System and Reactor Core Isolation Cooling System pumps that draw cooling water back to the core. Current safety analysis codes use zero dimensional (0-D) lumped parameter models to calculate the energy and mass balance in the pool; therefore, they have large uncertainties in the prediction of scenarios in which stratification and mixing are important. While three-dimensional (3-D) computational fluid dynamics (CFD) methods can be used to analyze realistic 3-D configurations, these methods normally require very fine grid resolution to resolve thin substructures such as jets and wall boundaries, resulting in a long simulation time. For mixing in stably stratified large enclosures, the BMIX++ code (Berkeley mechanistic MIXing code in C++) has been developed to implement a highly efficient analysis method for stratification where the ambient fluid volume is represented by one-dimensional (1-D) transient partial differential equations and substructures (such as free or wall jets) are modeled with 1-D integral models. This allows very large reductions in computational effort compared to multi-dimensional CFD modeling. One heat-up experiment performed at the Finland POOLEX facility, which was designed to study phenomena relevant to Nordic design BWR suppression pool including thermal stratification and mixing, is used for
International Nuclear Information System (INIS)
Thackray, M.
1976-01-01
A method is described for producing a photographic image on a normally non-photo-receptive surface comprising the steps of 1) toning the photograph with substances which combine with or replace the silver grains so that the photograph emits either spontaneously or indirectly fission fragments or alpha particles in amounts related to the distribution of the silver grains in the photograph, 2) placing the toned photograph contiguous with the surface on which the image is to be reproduced, for sufficient time for the emissions from the photograph to reproduce the image as a radiation-damage image on the surface, the damage areas having a close positional relationship to the silver grains in the original photograph. (author)
Sperm DNA fragmentation, recurrent implantation failure and recurrent miscarriage
Directory of Open Access Journals (Sweden)
Carol Coughlan
2015-01-01
Full Text Available Evidence is increasing that the integrity of sperm DNA may also be related to implantation failure and recurrent miscarriage (RM. To investigate this, the sperm DNA fragmentation in partners of 35 women with recurrent implantation failure (RIF following in vitro fertilization, 16 women diagnosed with RM and seven recent fathers (control were examined. Sperm were examined pre- and post-density centrifugation by the sperm chromatin dispersion (SCD test and the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL assay. There were no significant differences in the age of either partner or sperm concentration, motility or morphology between three groups. Moreover, there were no obvious differences in sperm DNA fragmentation measured by either test. However, whilst on average sperm DNA fragmentation in all groups was statistically lower in prepared sperm when measured by the SCD test, this was not seen with the results from the TUNEL assay. These results do not support the hypothesis that sperm DNA fragmentation is an important cause of RIF or RM, or that sperm DNA integrity testing has value in such patients. It also highlights significant differences between test methodologies and sperm preparation methods in interpreting the data from sperm DNA fragmentation tests.
FRAGMENTATION ISSUE IN MALAYSIAN INDUSTRIALISED BUILDING SYSTEM (IBS PROJECTS
Directory of Open Access Journals (Sweden)
MOHD NASRUN MOHD NAWI
2014-02-01
Full Text Available As a developing country, Malaysian is currently driving for implementing a new or modern construction method, the Industrialised Building System (IBS, as an alternative towards enhancing construction performance. Currently, most of the IBS project developments in Malaysia are still conducted by using the traditional construction process approach. This traditional construction process has been widely criticised for its fragmented approach to project delivery and its failure to form effective teams thus created a number of issues such as reworks, time delay, rising costs, lack of communication and coordination, and wastages. This paper through literature review aims to highlight this fragmentation issue and clarify how far it affects the process of IBS implementation. Suggestions on how an integrated approach in design and construction in order to minimise the fragmentation gaps will be concluded.
International Nuclear Information System (INIS)
Luevano, Jose-Ruben
2011-01-01
Analytical expressions for the invariant densities for a class of discrete two dimensional chaotic systems are given. The method of separation of variables for the associated Frobenius-Perron equation is introduced. These systems are related to nonlinear difference equations which are of the type x k+2 = T(x k ). The function T is a chaotic map of an interval whose chaotic behaviour is inherited to the two dimensional one. We work out in detail some examples, with T an expansive or intermittent map, in order to expose the method. Finally, we discuss how to generalize the method to higher dimensional maps.
DNA fragmentation in spermatozoa
DEFF Research Database (Denmark)
Rex, A S; Aagaard, J.; Fedder, J
2017-01-01
Sperm DNA Fragmentation has been extensively studied for more than a decade. In the 1940s the uniqueness of the spermatozoa protein complex which stabilizes the DNA was discovered. In the fifties and sixties, the association between unstable chromatin structure and subfertility was investigated....... In the seventies, the impact of induced DNA damage was investigated. In the 1980s the concept of sperm DNA fragmentation as related to infertility was introduced as well as the first DNA fragmentation test: the Sperm Chromatin Structure Assay (SCSA). The terminal deoxynucleotidyl transferase nick end labelling...... (TUNEL) test followed by others was introduced in the nineties. The association between DNA fragmentation in spermatozoa and pregnancy loss has been extensively investigated spurring the need for a therapeutic tool for these patients. This gave rise to an increased interest in the aetiology of DNA damage...
Calculation of parton fragmentation functions from jet calculus: gluon applications
International Nuclear Information System (INIS)
Lassila, K.E.; Ng, A.
1985-01-01
A method is presented for calculation of general parton fragmentation functions based on jet calculus plus meson and baryon wave functions. Results for gluon fragmentation into mesons and baryons are discussed and related to recent information on upsilon decay into gluons. The expressions derived can be used directly in e + e - cross section predictions and will need to be folded in with baryon parton distribution functions when used in p-barp collisions. (author)