bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic insights into the uncultured genus ‘Candidatus Magnetobacterium’ in the phylum Nitrospirae
Authors: Lin Wei , Deng Aihua , Wang Zhang , Li Ying , Wen Tingyi , Wu Long-Fei , Wu Martin , Pan Yongxin
Published: June 2014

Magnetotactic bacteria (MTB) of the genus ‘Candidatus Magnetobacterium’ in phylum Nitrospirae are of great interest because of the formation of hundreds of bullet-shaped magnetite magnetosomes in multiple bundles of chains per cell. These bacteria are worldwide distributed in aquatic environments and have important roles in the biogeochemical cycles of iron and sulfur. However, except for a few short genomic fragments, no genome data are available for this ecologically important genus, and little is known about their metabolic capacity owing to the lack of pure cultures. Here we report the first draft genome sequence of 3.42 Mb from an uncultivated strain tentatively named ‘Ca. Magnetobacterium casensis’ isolated from Lake Miyun, China. The genome sequence indicates an autotrophic lifestyle using the Wood–Ljungdahl pathway for CO2 fixation, which has not been described in any previously known MTB or Nitrospirae organisms. Pathways involved in the denitrification, sulfur oxidation and sulfate reduction have been predicted, indicating its considerable capacity for adaptation to variable geochemical conditions and roles in local biogeochemical cycles. Moreover, we have identified a complete magnetosome gene island containing mam, mad and a set of novel genes (named as man genes) putatively responsible for the formation of bullet-shaped magnetite magnetosomes and the arrangement of multiple magnetosome chains. This first comprehensive genomic analysis sheds light on the physiology, ecology and biomineralization of the poorly understood ‘Ca. Magnetobacterium’ genus.
Optical excitation and external photoluminescence quantum efficiency of Eu3+ in GaN
Authors: de Boer W. D. A. M. , McGonigle C. , Gregorkiewicz T. , Fujiwara Y. , Tanabe S. , Stallinga P.
Published: June 2014

We investigate photoluminescence of Eu-related emission in a GaN host consisting of thin layers grown by organometallic vapor-phase epitaxy. By comparing it with a reference sample of Eu-doped Y2O3, we find that the fraction of Eu3+ ions that can emit light upon optical excitation is of the order of 1%. We also measure the quantum yield of the Eu-related photoluminescence and find this to reach (~10%) and (~3%) under continuous wave and pulsed excitation, respectively.
Novel topotactically transformed carbon–CoO–NiO–NiCo2O4 nanosheet hybrid hetero-structured arrays as ultrahigh performance supercapacitors
Authors: Wang Hai , Guo Junling , Qing Chen , Sun Daming , Wang Bixiao , Tang Yiwen
Published: June 2014

A novel carbon–CoO–NiO–NiCo2O4 integrated electrode was designed and synthesized from NiCo2O4 in a topotactical transformation. Such unique nanoarchitectures exhibit excellent electrochemical performance with ultrahigh capacitance.
“Soldier–Sergeant–Soldier” triblock copolymers: revealing the folded structure of single-chain polymeric nanoparticles
Authors: Hosono Nobuhiko , Palmans Anja R. A. , Meijer E. W.
Published: June 2014

“Sergeant-and-Soldiers” experiments were performed on single-chain polymeric nanoparticles (SCPNs) with an ABA-type triblock architecture that gives information about the folding structure of the SCPNs.
Noncovalent interaction-assisted polymeric micelles for controlled drug delivery
Authors: Ding Jianxun , Chen Linghui , Xiao Chunsheng , Chen Li , Zhuang Xiuli , Chen Xuesi
Published: June 2014

Various individual or synergistic noncovalent interactions were employed to mediate polymeric micelles for controlled drug delivery.
C5-Amino acid functionalized LNA: positively poised for antisense applications
Authors: Guenther Dale C. , Kumar Pawan , Anderson Brooke A. , Hrdlicka Patrick J.
Published: June 2014

Oligonucleotides modified with C5-amino acid LNA uridine result in highly thermostable duplexes, with excellent discrimination of single nucleotide mismatches. Additionally, these ONs are inert toward 3′-exonuclease degradation.
Protein mixtures of environmentally friendly zein to understand protein–protein interactions through biomaterials synthesis, hemolysis, and their antimicrobial activities
Authors: Mahal Aabroo , Goshisht Manoj Kumar , Khullar Poonam , Kumar Harsh , Singh Narinder , Kaur Gurinder , Bakshi Mandeep Singh
Published: June 2014

Protein–protein interactions through biomaterials synthesis for biological applications.
Ultrafast excited state dynamics of S2 and S1 states of triphenylmethane dyes
Authors: Singhal Pallavi , Ghosh Hirendra N.
Published: June 2014

Excited state dynamics of S2 and S1 states for a series of TPM dyes, pyrogallol red (PGR), bromopyrogallol red (Br-PGR) and aurin tricarboxylic acid (ATC), have been monitored by using ultrafast transient absorption and fluorescence up-conversion techniques.
A cracked polymer templated metal network as a transparent conducting electrode for ITO-free organic solar cells
Authors: Rao K. D. M. , Hunger Christoph , Gupta Ritu , Kulkarni Giridhar U. , Thelakkat Mukundan
Published: June 2014

We study the incorporation of a highly transparent and highly conducting Ag metallic network obtained using a cracked polymer template, in a thin film organic solar cell for the first time.
Photoinduced water splitting with oxotitanium tetraphenylporphyrin
Authors: Morawski O. , Izdebska K. , Karpiuk E. , Nowacki J. , Suchocki A. , Sobolewski A. L.
Published: June 2014

TiOPP very efficiently catalyses photooxidation of water with visible light.
Electrochemical conversion of CO2 to fuels: tuning of the reaction zone using suitable functional groups in a solid polymer electrolyte
Authors: Aeshala Leela Manohar , Uppaluri Ramagopal , Verma Anil
Published: June 2014

The electrochemical reduction of gaseous CO2 is studied for the first time using sterically hindered bulky quaternary ammonium ions in a solid polymer matrix at room temperature and atmospheric pressure in a developed electrochemical reactor.
Species differences in drug plasma protein binding
Authors: Colclough Nicola , Ruston Linette , Wood J. Matthew , MacFaul Philip A.
Published: June 2014

Comparison of the human plasma protein binding data for a variety of drug discovery compounds indicates that compounds tend to be slightly more bound to human plasma proteins, than compared to plasma proteins from rats, dogs or mice.
Heterometallic complexes combining [MnIII(salpn)]+ and [Fe(CN)6]4− units as the products of reactions between [MnIII(salpn)(H2O)C(CN)3] and [Fe(CN)6]3−/4−
Authors: Kopotkov Vyacheslav A. , Yagubskii Eduard B. , Simonov Sergey V. , Zorina Leokadiya V. , Starichenko Denis V. , Korolyov Alexander V. , Ustinov Vladimir V. , Shvachko Yuri N.
Published: June 2014

The tricyanomethanide ligand reduces Fe(iii) to Fe(ii) yielding the discrete and chain complexes.
Influence of ligand environment on the structure and properties of silver(i) dithiocarbamate cluster-based coordination polymers and dimers
Authors: Kumar Vinod , Singh Vikram , Gupta Ajit N. , Manar Krishna K. , Prasad Lal Bahadur , Drew Michael G. B. , Singh Nanhai
Published: June 2014

Four silver dithiocarbamate complexes have been synthesized and characterized by microanalysis.1and2are tetranuclear cluster-based coordination polymers whereas3and4are dinuclear. All complexes are strongly luminescent in solid phase.
Fibril-shaped aggregates of doxorubicin with poly-l-lysine and its derivative
Authors: Zhu Lijun , Yang Saina , Qu Xiaozhong , Zhu Feiyan , Liang Yongri , Liang Fuxin , Wang Qian , Li Jiaoli , Li Zhibo , Yang Zhenzhong
Published: June 2014

Doxorubicin forms fibril-like aggregates in phosphate buffer and complexes with poly-l-lysine and cholate-grafted poly-l-lysine.
Simulation of conformational properties of end-grafted diblock copolymers
Authors: Li Hong , Gong Bin , Qian Chang-Ji , Li Chao-Yang , Huang Jian-Hua , Luo Meng-Bo
Published: June 2014

The conformational properties of end-grafted diblock copolymers XAnBn and XBnAn are dependent on the position of the grafted end X.
Synthesis of a superparamagnetic MFNs@SiO2@Ag4SiW12O40/Ag composite photocatalyst, its superior photocatalytic performance under visible light illumination, and its easy magnetic separation
Authors: Tang Wenshu , Su Yu , Wang Xiaoxin , Li Qi , Gao Shian , Shang Jian Ku
Published: June 2014

A novel superparamagnetic Ag@silver-based salt photocatalyst was created with highly efficient visible light photocatalytic performance and easy magnetic separation.
Kinetic effects in predicting adsorption using the GCMC method – using CO2 adsorption on ZIFs as an example
Authors: Cao Fenglei , Sun Yingxin , Wang Lin , Sun Huai
Published: June 2014

The calculated PMFs indicate that the small channels of ZIF-68 are blocked by adsorbed CO2 molecules in the HRP cages.
Hydrogen bond donor–acceptor–donor organocatalysis for conjugate addition of benzylidene barbiturates via complementary DAD–ADA hydrogen bonding
Authors: Leung Franco King-Chi , Cui Jian-Fang , Hui Tsz-Wai , Zhou Zhong-Yuan , Wong Man-Kin
Published: June 2014

Organocatalysts featuring a hydrogen bond donor–acceptor–donor structural element catalyze conjugate addition via complementary DAD–ADA hydrogen bonding.
The jamming elasticity of emulsions stabilized by ionic surfactants
Authors: Scheffold Frank , Wilking James N. , Haberko Jakub , Cardinaux Frédéric , Mason Thomas G.
Published: June 2014

A new model predicts the storage modulus and yield stress of ionic emulsions for nanoscale to microscale droplet radii.
Linear and nonlinear microrheology of lysozyme layers forming at the air–water interface
Authors: Allan Daniel B. , Firester Daniel M. , Allard Victor P. , Reich Daniel H. , Stebe Kathleen J. , Leheny Robert L.
Published: June 2014

Microrheology tracks the evolution in the linear and nonlinear mechanical properties of layers of the protein lysozyme adsorbing at the air–water interface as the layers undergo a viscoelastic transition.
Surface effects on the structure and mobility of the ionic liquid C6C1ImTFSI in silica gels
Authors: Nayeri Moheb , Aronson Matthew T. , Bernin Diana , Chmelka Bradley F. , Martinelli Anna
Published: June 2014

We report on how the dynamical and structural properties of the ionic liquid 1-hexyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide (C6C1ImTFSI) change upon different degrees of confinement in silica gels.
Torque density measurements on vortex fluids produced by symmetry-breaking rational magnetic fields
Authors: Solis Kyle J. , Martin James E.
Published: June 2014

A recently-discovered infinite family of symmetry-breaking rational magnetic fields creates “vortex fluids” that produce strong vorticity along any axis in magnetic particle suspensions.
pH-responsive cancer-targeted selenium nanoparticles: a transformable drug carrier with enhanced theranostic effects
Authors: Yu Bo , Li Xiaoling , Zheng Wenjie , Feng Yanxian , Wong Yum-Shing , Chen Tianfeng
Published: June 2014

A cancer-targeted and structure-transformable drug delivery system has been constructed, which displays enhanced anticancer efficacy and exhibits the characteristics of shape transformation and pH-controlled drug release under acidifying cell organelles.
Ordering dynamics in symmetric PS-b-PMMA diblock copolymer thin films during rapid thermal processing
Authors: Perego Michele , Ferrarese Lupi Federico , Ceresoli Monica , Giammaria Tommaso Jacopo , Seguini Gabriele , Enrico Emanuele , Boarino Luca , Antonioli Diego , Gianotti Valentina , Sparnacci Katia , Laus Michele
Published: June 2014

The morphological evolution of self-registered morphologies, with lamellae laying over hexagonally packed cylinders, is investigated in symmetric PS-b-PMMA .
Complex IV-deficient Surf1−/− mice initiate mitochondrial stress responses
Authors: Pulliam Daniel A. , Deepa Sathyaseelan S. , Liu Yuhong , Hill Shauna , Lin Ai-Ling , Bhattacharya Arunabh , Shi Yun , Sloane Lauren , Viscomi Carlo , Zeviani Massimo , Van Remmen Holly
Published: June 2014

Mutations in SURF1 (surfeit locus protein 1) COX (cytochrome c oxidase) assembly protein are associated with Leigh's syndrome, a human mitochondrial disorder that manifests as severe mitochondrial phenotypes and early lethality. In contrast, mice lacking the SURF1 protein (Surf1−/−) are viable and were previously shown to have enhanced longevity and a greater than 50% reduction in COX activity. We measured mitochondrial function in heart and skeletal muscle, and despite the significant reduction in COX activity, we found little or no difference in ROS (reactive oxygen species) generation, membrane potential, ATP production or respiration in isolated mitochondria from Surf1−/− mice compared with wild-type. However, blood lactate levels were elevated and Surf1−/− mice had reduced running endurance, suggesting compromised mitochondrial energy metabolism in vivo. Decreased COX activity in Surf1−/− mice is associated with increased markers of mitochondrial biogenesis [PGC-1α (peroxisome-proliferator-activated receptor γ co-activator 1α) and VDAC (voltage-dependent anion channel)] in both heart and skeletal muscle. Although mitochondrial biogenesis is a common response in the two tissues, skeletal muscle has an up-regulation of the UPRMT (mitochondrial unfolded protein response) and heart exhibits induction of the Nrf2 (nuclear factor-erythroid 2-related factor 2) antioxidant response pathway. These data are the first to show induction of the UPRMT in a mammalian model of decreased COX activity. In addition, the results of the present study suggest that impaired mitochondrial function can lead to induction of mitochondrial stress pathways to confer protective effects on cellular homoeostasis.
Energy‐efficiency region for multiple access channels
Authors: Yu Guanding , Jiang Yuhuan
Published: June 2014

To investigate the trade‐off between energy efficiency (EE) and spectral efficiency (SE) for Gaussian multiple access channels (MACs), a novel concept of the EE region is developed. The EE region for the time division multiple access system is also derived and compared. The SE–EE trade‐off order is introduced to explicitly describe how fast the EE decays with SE in the high SE region. For a symmetric MAC, a constraint on SE–EE trade‐off orders is derived and the Pareto optimum can be achieved by the corner points on the EE region.
Throughput enhancement of slow adaptive orthogonal frequency division multiple access based passive optical network uplink transmission in 20‐km single fibre loopback link employing channel stabilisation
Authors: Jung Sang‐Min , Hong Moon‐Ki , Jung Sun‐Young , Yang Seung‐Min , Han Sang‐Kook
Published: June 2014

The authors have proposed and experimentally demonstrated a novel slow adaptive orthogonal frequency division multiple access (OFDMA)‐based passive optical network (PON) uplink transmission scheme using a 1‐GHz reflective semiconductor optical amplifier operating as an optical network unit (ONU) in combination with Rayleigh backscattering (RB) mitigation in a 20‐km single fibre loopback link. This RB mitigation, which can dramatically stabilise the channel state information and enhance the total throughput so that the OFDMA‐PON transmitters can operate in the slow adaptive concept and provides beyond 15‐Gbit/s uplink transmission, is achieved by employing 10‐MHz low‐frequency dithering of an optical seed carrier cooperating with a gain‐saturated semiconductor optical amplifier at an optical line terminal. In doing so, the proposed scheme could guarantee a 50% total throughput enhancement with a proof‐of‐concept multiple access scenario for two ONUs, compared to its counterpart that does not apply the RB mitigation technique.
Weak global navigation satellite system signal acquisition with bit transition
Authors: Zhu Can , Fan Xiangning
Published: June 2014

This study analyses the bit transition and integration over multiple code periods in weak global navigation satellite system signal acquisition. Bit transition must be considered in weak signal environments as it causes a correlation peak splitting reducing the correlation gain. In this study, a modified time parallel acquisition (MTPA) scheme is designed to solve the bit transition problem, and different accumulation schemes over multiple code periods are proposed to detect weak signals. Especially, a fast Fourier transform‐based symbol combination for bit transition algorithm, which is suitable for the MTPA scheme, is presented in order to accelerate the coherent accumulation. Simulation results, along with the receiver operative characteristic curves, are presented to verify the performance of the MTPA and accumulation algorithms.
Research on dynamic real‐time error correction method using Wiener‐based neural network
Authors: Wu Dehui , You Dehai , Chen Jun , Li Chao
Published: June 2014

A novel structure of Wiener‐based neural network is proposed and applied to correct the dynamic real‐time error for the improvement of the sensor's dynamic performance. First, the compensation filter was established based on the principle of inverse model and was described by a dynamic linear‐static nonlinear cascade (Wiener model). Then, the neural network structure was devised and the network weights were accord with the parameters of the compensation filter. Followed that, some experimental devices were designed for dynamic calibration of the uIRt/c infrared temperature sensor. Finally, the identification of compensation filter was achieved by network iteration and the actual calibration data of the uIRt/c were made use of in the testing experiments. The results show that the stabilising time of the sensor is reduced to less than 7 ms from 27 ms and the dynamic performance is obviously improved after compensation.
Adaptive control of solar tracking system
Authors: Hammad Bashar K. , Fouad Rami H. , Ashhab Moh'd Sami , Nijmeh Salem D. , Mohsen Mousa , Tamimi Asma
Published: June 2014

In this study, an adaptive controller of a solar tracking system is designed and its performance is evaluated through computer simulation. To achieve this goal, two tracker systems based on open‐ and closed‐loop control strategies are studied. The instantaneous and total errors that represent the differences between the tilt and rotation angles of both the open‐ and closed‐loop systems are analysed. An adaptive controller that regulates the electric signals to the motors is designed. Owing to uncertainty in the sun position data, the performance of solar tracker suffers degradation. Towards this end, sun position data are analysed to extract the error sources. The designed control system objective is to keep the tracker perpendicular to sunlight at all times during the day and eliminate modelling errors such as sun position data deviations, friction and environmental changes. System performance is verified through computer simulation where the controller corrected for modelling errors and date changes from the date used for algorithm design. More specifically, in the first case the square error reduces from 15.43 to 12.18 degrees2 for azimuth angle and from 39.05 to 19.09 degrees2 for altitude, whereas in the latter case the square error reduces from 236.92 to 105.90 degrees2 for azimuth angle and from 402.82 to 40.40 degrees2 for altitude.
Self‐matched high‐Q reconfigurable antenna concept for mobile terminals
Authors: Bahramzy Pevand , Jagielski Ole , Svendsen Simon , Pedersen Gert F.
Published: June 2014

This study presents reconfigurable antenna design for a front end (FE) that has separate transmit (Tx) and receive (Rx) path. In such an FE, the Tx and Rx antennas can be content with covering only the transmit and receive channels in a frequency band. Therefore they can be quite narrow‐band. Narrow‐band antennas can exhibit high losses, because of the relative high current density per area and limited tuning/matching component Q. To address this, a self‐matched antenna design is introduced, having the tunable capacitor as the only physical component. The Tx and Rx narrow‐band antennas are designed to cover the frequency range 1710–2170 MHz. Metrics as for example, impedance bandwidth and efficiency are obtained both in simulations and measurements.
AC creeping discharges propagating over solid–gas interfaces
Authors: Sadaoui Fares , Beroual Abderrahmane
Published: June 2014

This study is aimed at the characterisation of surface discharges propagating over different solid materials namely glass, bakelite and epoxy resin immersed in three gases and their mixtures (namely SF6, N2 and CO2, SF6/N2 and SF6/CO2) under AC voltage (50 Hz) in a point‐plane electrode system. It is shown that the stopping length of discharges (Lf) increases linearly with the applied voltage and decreases when the gas pressure is increased. Lf is longer in CO2 and N2 than in SF6 [Lf(N2) > Lf(CO2) > Lf(SF6)]; and the increase of SF6 content in the investigated mixtures leads to a significant decrease of Lf. Also, for a given gas, Lf is slightly longer with glass and bakelite than that with epoxy resin indicating that the higher the dielectric constant, the longer the discharge is. Thus, the density of the discharge branches and Lf reduce when the thickness of insulators increases and/or their dielectric constant decreases. Such observations evidence the implication of capacitive charge effect and electric field in the development of creeping discharges.
Multi‐objective probabilistic reconfiguration considering uncertainty and multi‐level load model
Authors: Kavousi‐Fard Abdollah , Niknam Taher , Taherpoor Hoda , Abbasi Alireza
Published: June 2014

This study aims to investigate the role of the reconfiguration strategy to enhance the reliability of the distribution systems. In this regard, the idea of failure rate reduction approach is employed to assess three significant reliability indices including the System Average Interruption Frequency Index, System Average Interruption Duration Index and Average Energy Not Supplied. In addition, as a result of attractiveness and importance of the power loss objective function in the system, this target is also considered in the problem. The problem is then formulated in a stochastic framework based on 2m + 1 point estimate method to capture the uncertainty of load, failure rate and repair rate forecast error. In order to make the analysis more practical, the idea of yearly multi‐level load modelling is employed. The feasibility and effectiveness of the proposed method are examined on the IEEE 32‐bus test system.
Applicability of 3D Monte Carlo simulations for local values calculations in a PWR core
Authors: Bernard Franck , Cochet Bertrand , Jinaphanh Alexis , Jacquet Olivier
Published: June 2014

As technical support of the French Nuclear Safety Authority, IRSN has been developing the MORET Monte Carlo code for many years in the framework of criticality safety assessment and is now working to extend its application to reactor physics. For that purpose, beside the validation for criticality safety (more than 2000 benchmarks from the ICSBEP Handbook have been modeled and analyzed), a complementary validation phase for reactor physics has been started, with benchmarks from IRPHEP Handbook and others.

In particular, to evaluate the applicability of MORET and other Monte Carlo codes for local flux or power density calculations in large power reactors, it has been decided to contribute to the “Monte Carlo Performance Benchmark” (hosted by OECD/NEA). The aim of this benchmark is to monitor, in forthcoming decades, the performance progress of detailed Monte Carlo full core calculations. More precisely, it measures their advancement towards achieving high statistical accuracy in reasonable computation time for local power at fuel pellet level. A full PWR reactor core is modeled to compute local power densities for more than 6 million fuel regions.

This paper presents results obtained at IRSN for this benchmark with MORET and comparisons with MCNP. The number of fuel elements is so large that source convergence as well as statistical convergence issues could cause large errors in local tallies, especially in peripheral zones. Various sampling or tracking methods have been implemented in MORET, and their operational effects on such a complex case have been studied. Beyond convergence issues, to compute local values in so many fuel regions could cause prohibitive slowing down of neutron tracking. To avoid this, energy grid unification and tallies preparation before tracking have been implemented, tested and proved to be successful. In this particular case, IRSN obtained promising results with MORET compared to MCNP, in terms of local power densities, standard deviations and computing times.
Using SERPENT Monte Carlo and Burnup code to model Traveling Wave Reactors (TWR)
Authors: Gulik Volodymyr , Pavlovych Volodymyr , Henry Tkaczyk Alan
Published: June 2014

This paper is mainly devoted to the proof-of-principle implementation of the SERPENT code for the simulation of traveling wave reactors. The investigation of SERPENT 1.1.19 code for multiprocessor tasks with long burnup steps was performed. The investigation of SERPENT 2 code for multiprocessor tasks with long burnup steps was performed. Methods to remove the influence of the ignition zone were considered, and neutronics simulations with various fragmentations of the burnup zone were performed.
Numerical Analysis on the Calandria Tubes in the Moderator of a Heavy Water Reactor Using OpenFOAM and Other Codes
Authors: Chang Se-Myong , Tae Kim Hyoung
Published: June 2014

CANDU, a prototype of heavy water reactor is modeled for the moderator system with porous media buoyancy-effect heat-transfer turbulence model. OpenFOAM, a set of C++ classes and libraries developed under the object-oriented concept, is selected as the tool of numerical analysis. The result from this computational code is compared with experiments and other commercial code data through ANSYS-CFX and COMSOL Multi-physics. The three-dimensional code concerning buoyancy force, turbulence, and heat transfer is tested and shown to be successful for the analysis of thermo-hydraulic system of heavy water reactors.
Large scale ab initio calculations of extended defects in materials: screw dislocations in bcc metals
Authors: Dézerald Lucile , Ventelon Lisa , Willaime François , Clouet Emmanuel , Rodney David
Published: June 2014

Ab initio methods, based on the Density Functional Theory (DFT), have been extensively used to study point defects and defect clusters in materials. Present HPC resources and DFT codes now allow similar investigations to be performed on dislocations. The study of these extended defects requires not only larger simulation cells but also a higher accuracy because the energy differences, which are involved, are rather small, typically 50-to-100 meV for supercells containing 50-to-500 atoms.

The topology of the Peierls potential of screw dislocations with 1/2 <111>Burgers vector, i.e. the 2D energy landscape seen by these dislocations, is being completely revisited by DFT calculations. From results obtained in all body-centered cubic (bcc) transition metals, except Cr (V, Nb, Ta, Mo, W and Fe), using the PWSCF code, which is part of the Quantum-Espresso package, we concluded that the 2D Peierls potentials have two common features: the single-hump shape of the barrier between two minima of the potential, and the presence of a maximum – and not a minimum as predicted by most empirical potentials – around the split core. In iron, the topology of the Peierls potential is reversed compared to the classical sinusoidal picture: the location of the saddle point and the maximum are indeed inverted with unexpected flat regions.

The first results obtained within the framework of the PRACE project, DIMAIM (DIslocations in Metals using Ab Initio Methods), started at the beginning of 2013, will also be presented. In particular, in order to address the twinning-antitwinning asymmetry often observed in bcc metals and regarded as the major contribution to the breakdown of Schmid's law, we have determined the crystal orientation dependence of the Peierls stress, i.e. the critical stress required for dislocation motion. These computationally most expensive simulations were performed on the PRACE Tier-0 system at Barcelona Supercomputing Center (Marenostrum III). The scalability results using the various parallelization levels of the PWSCF code up to 10 000 cores will be presented.
Molecular dynamics simulation of displacement cascades in UO2
Authors: Martin Guillaume , Garcia Philippe , Sabathier Catherine , Palancher Hervé , Maillard Serge
Published: June 2014

The primary damage induced within a uranium dioxide matrix subjected to a flux of energetic ions was investigated by classical molecular dynamics. UO2 was modeled using the set of empirical potentials based on a rigid ion model. Displacement cascades were initiated by accelerating a uranium primary knock-on atom to a kinetic energy up to 100 keV. It was first shown that the estimated RID a-thermal coefficient is well below those which are deemed relevant for spent nuclear fuels. Cascades were then purposely overlapped within the same simulation box so as to study the response of the material to increasing damage levels. During cascade overlap sequences, the growth of nanometric voids was observed. Obtained results evidenced a radiation damage controlled heterogeneous mechanism for insoluble fission product segregation in UO2.
Atomic kinetic Monte Carlo modeling of multi-component Fe dilute alloys under irradiation
Authors: Domain C. , Becquart C.S.
Published: June 2014

The ageing of pressure vessel steels under radiation has been correlated with the formation of more or less dilute solute clusters which are investigated in this work using a multiscale approach based on ab initio and atomistic kinetic Monte Carlo (AKMC) simulations. The microstructure evolution of Fe alloys is modeled by AKMC on a lattice, using pair interactions adjusted on DFT calculations. Several substitutional elements (Cu, Ni, Mn, Si, P) and foreign interstitials (C, N) are taken into account to describe the alloy. The point defect created by the irradiation, i.e. the vacancies and self interstitials have a tendency to form clusters. The evolution of these clusters is governed by the migration energy of the individual point defects which is very heavy in terms of computing time due to the large number of AKMC steps required. The structure of all the possible objects that can form is complex and some optimized and accelerated methods will be presented.
Improvements to the Pool Critical Assembly Pressure Vessel Benchmark with 3-D Parallel SN PENTRAN
Authors: Edgar Christopher A. , Sjoden Glenn E. , Yi Ce
Published: June 2014

The internationally circulated Pool Critical Assembly (PCA) Pressure Vessel Benchmark was analyzed using the PENTRAN Parallel SN code system for the geometry, material, and source specifications as described in the PCA Benchmark documentation. Improvements to the benchmark are proposed here through the application of more representative flux and volume weighted homogenized cross sections for the PCA reactor core, which were obtained from a rigorous heterogeneous modeling of all fuel assembly types in the core. A new source term definition is also proposed based on calculated relative power in each core fuel assembly with a spectrum based on the Uranium-235 fission spectra. This research focused on utilizing the BUGLE-96 cross section library and accompanying reaction rates, while also examining PENTRAN’s adaptive differencing implemented on a coarse mesh basis, as well as fixed use of Directional Theta-Weighted (DTW) SN differencing scheme in order to compare the calculated PENTRAN results to measured data. The results show good comparison with the measured benchmark data, which suggests PENTRAN is a viable, reliable code system for calculation of light water reactor neutron shielding and pressure vessel dosimetry calculations. Furthermore, the improvements to the benchmark methodology resulting from this work provide a 6 percent increase in accuracy of the calculation (based on the average of all calculation points), when compared with experimentally measured results at the same spatial locations in the PCA pressure vessel simulator.
Monte Carlo PENRADIO software for dose calculation in medical imaging
Authors: Adrien Camille , Lòpez Noriega Mercedes , Bonniaud Guillaume , Bordy Jean-Marc , Le Loirec Cindy , Poumarede Bénédicte
Published: June 2014

The increase on the collective radiation dose due to the large number of medical imaging exams has led the medical physics community to deeply consider the amount of dose delivered and its associated risks in these exams. For this purpose we have developed a Monte Carlo tool, PENRADIO, based on a modiﬁed version of PENELOPE code 2006 release, to obtain an accurate individualized radiation dose in conventional and interventional radiography and in computed tomography (CT). This tool has been validated showing excellent agreement between the measured and simulated organ doses in the case of a hip conventional radiography and a coronography. We expect the same accuracy in further results for other localizations and CT examinations.
COMET-PE as an Alternative to Monte Carlo for Photon and Electron Transport
Authors: Hayward Robert M. , Rahnema Farzad
Published: June 2014

Monte Carlo methods are a central component of radiotherapy treatment planning, shielding design, detector modeling, and other applications. Long calculation times, however, can limit the usefulness of these purely stochastic methods. The coarse mesh method for photon and electron transport (COMET-PE) provides an attractive alternative. By combining stochastic pre-computation with a deterministic solver, COMET-PE achieves accuracy comparable to Monte Carlo methods in only a fraction of the time. The method’s implementation has been extended to 3D, and in this work, it is validated by comparison to DOSXYZnrc using a photon radiotherapy benchmark. The comparison demonstrates excellent agreement; of the voxels that received more than 10% of the maximum dose, over 97.3% pass a 2% / 2mm acceptance test and over 99.7% pass a 3% / 3mm test. Furthermore, the method is over an order of magnitude faster than DOSXYZnrc and is able to take advantage of both distributed-memory and shared-memory parallel architectures for increased performance.
Accelerated equilibrium core composition search using a new MCNP-based simulator
Authors: Seifried Jeffrey E. , Gorman Phillip M. , Vujic Jasmina L. , Greenspan Ehud
Published: June 2014

MocDown is a new Monte Carlo depletion and recycling simulator which couples neutron transport with MCNP and transmutation with ORIGEN. This modular approach to depletion allows for flexible operation by incorporating the accelerated progression of a complex fuel processing scheme towards equilibrium and by allowing for the online coupling of thermo-fluids feedback. MocDown also accounts for the variation of decay heat with fuel isotopics evolution. In typical cases, MocDown requires just over a day to find the equilibrium core composition for a multi-recycling fuel cycle, with a self-consistent thermo-fluids solution–a task that required between one and two weeks using previous Monte Carlo-based approaches.
Attempt to Estimate Reactor Period by Natural Mode Eigenvalue Calculation
Authors: Nauchi Yasushi
Published: June 2014

A calculation technique of the inverse reactor period of a perturbed state is investigated. That is achieved by solving the natural mode equation which expresses the neutron balance where the core power changes exponentially with time. The technique is implemented into the MCNP-5 code and tested for perturbed states. The convergence of the calculated inverse reactor period is observed and the ratio of the converged values to experimental data in literature ranges 0.93~1.28. The error would be mainly attributed to estimations of the neutron balance between production and annihilation.
Parallelisation of MONK with Coupling to Thermal Hydraulics and Gamma Heating Calculations for Reactor Physics Applications
Authors: Richards Simon D. , Davies Nigel , Armishaw Malcolm J. , Dobson Geoff P. , Wright George A.
Published: June 2014

Monte Carlo methods are increasingly being used for whole core reactor physics modelling. We describe a number of recent developments to the MONK nuclear criticality and reactor physics code to implement parallel processing, mesh-dependent burn-up and coupling to both thermal hydraulics and gamma transport codes. Results are presented which demonstrate the e_ects of gamma heating in a MONK calculation coupled to the MCBEND Monte Carlo shielding code. Experimental validation of the mesh-dependent tracking and gamma coupling methods is provided by comparison with the results of the NESSUS experiment. The gamma heating calculated by coupled MONK-MCBEND, and the neutron heating calculated by MONK, both compare well against measurement. Finally results are presented from a parallel MONK calculation of a highly detailed PWR benchmark model, which show encouraging speed-up factors on a small development cluster.
Conjugate heat transfer study of a wire spacer SFR fuel assembly thanks to the thermal code SYRTHES and the CFD code Code_Saturne
Authors: Péniguel C. , Rupp I. , Rolfo S. , Hermouet D.
Published: June 2014

The paper presents a HPC calculation of a conjugate heat transfer simulation in fuel assembly as those found in liquid metal coolant fast reactors. The wire spacers, helically wound along each pin axis, generate a strong secondary flow pattern in opposition to smooth pins. Assemblies with a range of pins going from 7 to 271 have been simulated, 271 pins corresponding to the industrial case. Both the fluid domain, as well as the solid part, are detailed leading to large meshes. The fluid is handled by the CFD code Code_Saturne using 98 million cells, while the solid domain is taken care of thanks to the thermal code SYRTHES on meshes up to 240 million cells. Both codes are fully parallel and run on cluster with hundreds of processors. Simulations allow access to the temperature field in nominal conditions and degraded situations.
Reconstruction of Human Monte Carlo Geometry from Segmented Images
Authors: Zhao Kai , Cheng Mengyun , Fan Yanchang , Wang Wen , Long Pengcheng , Wu Yican ,   FDS Team
Published: June 2014

Human computational phantoms have been used extensively for scientific experimental analysis and experimental simulation. This article presented a method for human geometry reconstruction from a series of segmented images of a Chinese visible human dataset. The phantom geometry could actually describe detailed structure of an organ and could be converted into the input file of the Monte Carlo codes for dose calculation.

A whole-body computational phantom of Chinese adult female has been established by FDS Team which is named Rad-HUMAN with about 28.8 billion voxel number. For being processed conveniently, different organs on images were segmented with different RGB colors and the voxels were assigned with positions of the dataset. For refinement, the positions were first sampled. Secondly, the large sums of voxels inside the organ were three-dimensional adjacent, however, there were not thoroughly mergence methods to reduce the cell amounts for the description of the organ. In this study, the voxels on the organ surface were taken into consideration of the mergence which could produce fewer cells for the organs. At the same time, an indexed based sorting algorithm was put forward for enhancing the mergence speed. Finally, the Rad-HUMAN which included a total of 46 organs and tissues was described by the cuboids into the Monte Carlo Monte Carlo Geometry for the simulation.

The Monte Carlo geometry was constructed directly from the segmented images and the voxels was merged exhaustively. Each organ geometry model was constructed without ambiguity and self-crossing, its geometry information could represent the accuracy appearance and precise interior structure of the organs. The constructed geometry largely retaining the original shape of organs could easily be described into different Monte Carlo codes input file such as MCNP. Its universal property was testified and high-performance was experimentally verified
On-The-Fly Neutron Doppler Broadening in MCNP
Authors: Martin William R. , Brown Forrest B. , Wilderman Scott , Yesilyurt Gokhan
Published: June 2014

Multi-physics calculations may involve coupling continuous-energy Monte Carlo neutronics codes to CFD codes that provide many thousands or even millions of region temperatures. The traditional Monte Carlo approach – using precalculated Doppler broadened nuclear cross-sections – is not feasible for these large multiphysics problems. Instead, an On-the-Fly (OTF) Doppler broadening methodology is required, whereby neutron cross-sections are broadened during the Monte Carlo transport. To this end, we have developed a methodology for MCNP to provide OTF broadening based on cell temperatures during neutron tracking. The method enables the use of many thousands or more temperatures in MCNP Monte Carlo calculations for multiphysics applications, significantly advancing the state-of-the-art by permitting the solution of problems that were not previously possible with continuous-energy Monte Carlo codes. A production library with an extended set of isotopes has been developed for use with MCNP6. Calculations of test problems with MCNP6 and the new library demonstrate the accuracy and effectiveness of the OTF approach.
Importance Sampling Implemented in the Code PRIZMA for Deep Penetration and Detection Problems in Reactor Physics
Authors: Kandiev Y.Z. , Zatsepin O.V.
Published: June 2014

At RFNC-VNIITF a code PRIZMA which has been developed for more than 30 years is used to model radiation transport by the Monte Carlo method. The code implements individual and coupled tracking of neutrons, photons, electrons, positrons and ions in 1D, 2D or 3D geometry. Attendance estimators are used for tallying, i.e., the estimators whose scores are only nonzero from particles which cross a region or surface of interest. Importance sampling is used to make deep penetration and detection calculations more effective. However, its application to reactor analysis appeared peculiar and required further development.

The paper reviews methods used for deep penetration and detection calculations by PRIZMA. It describes in what these calculations differ when applied to reactor analysis and how we compute approximated importance functions and parameters for biased distributions. Methods to control the statistical weight of particles are also discussed.

A number of test and applied calculations which were done for the purpose of verification are provided. They are shown to agree either with asymptotic solutions if exist, or with results of analog calculations or predictions by other codes. The applied calculations include the estimation of ex-core detector response from neutron sources arranged in the core, and the estimation of in-core detector response.
The Specific Bias in Dynamic Monte Carlo Simulations of Nuclear Reactor
Authors: Yamamoto Toshihisa , Endo Hiroshi , Ishizu Tomoko , Tatewaki Isao
Published: June 2014

During the development of Monte-Carlo-based dynamic code system, we have encountered two major Monte-Carlo-specific problems. One is the break down due to “false super-criticality” which is caused by an accidentally large eigenvalue due to statistical error in spite of the fact that the reactor is actually not. The other problem, which is the main topic in this paper, is that the statistical error in power level using the reactivity calculated with Monte Carlo code is not symmetric about its mean but always positively biased. This signifies that the bias is accumulated as the calculation proceeds and consequently results in over-estimation of the final power level. It should be noted that the bias will not eliminated by refining time step as long as the variance is not zero. A preliminary investigation on this matter using the one-group-precursor point kinetic equations was made and it was concluded that the bias in power level is approximately proportional to the product of variance in Monte Carlo calculation and elapsed time. This conclusion was verified with some numerical experiments. This outcome is important in quantifying the required precision of the Monte-Carlo-based reactivity calculations.
Performance of the Adaptive Collision Source (ACS) Method for Discrete Ordinates in Parallel Environments
Authors: Walters William J. , Haghighat Alireza
Published: June 2014

A new collision source method has been developed to solve the Linear Boltzmann Equation (LBE) more efficiently by adaptation of the angular quadrature order. The angular adaptation method is unique in that the flux from each scattering source iteration is obtained separately, with potentially a different quadrature order. This allows for an optimal use of processing power, by using a high order quadrature for the first few iterations that need it, before shifting to lower order quadratures for the remaining iterations. This is essentially an extension of the first collision source method, and we call it the adaptive collision source method (ACS). The ACS methodolog y has been implemented in the TITAN discrete ordinates code, and has shown a speedup of 2-3 on a test problem, with very little loss of accuracy (within a provided adaptive tolerance). Further, the code has been extended to work in parallel environments by angular decomposition. Although the method requires increased parallel communication, tests have shown excellent scalability, with parallel fractions of up to 99%.
Implementation of Domain Decomposition and Data Decomposition Algorithms in RMC code
Authors: Liang Jin’gang , Cai Yun , Wang Kan , She Ding
Published: June 2014

The applications of Monte Carlo method in reactor physics analysis is somewhat restricted due to excessive memory demand in solving large-scale problems. Domain decomposition and data decomposition are two remedies. Memory demand in MC simulation is analyzed firstly. Domain decomposition and tally data decomposition algorithms separately are designed and implemented based on reactor Monte Carlo code RMC. Numerical tests are executed to evaluate performance of new algorithms respectively. Domain decomposition algorithm shows potentials to speed up MC simulation as a space parallel method. As for tally data decomposition algorithms, memory size is reduced obviously.
Optimization of Monte Carlo Algorithms and Ray Tracing on GPUs
Authors: Bergmann Ryan M. , Vujić Jasmina L.
Published: June 2014

To take advantage of the computational power of GPUs, algorithms that work well on CPUs must be modified to conform to the GPU execution model. In this study, typical task-parallel Monte Carlo algorithms have been reformulated in a data-parallel way, and the benefits of doing so are examined. In-progress 3D ray tracing work is also touched upon as a milestone in developing a full-featured neutron transport code. Possible solutions to problems are examined.