A numerical formulation and algorithm for limit and shakedown analysis of large-scale elastoplastic structures

NASA Astrophysics Data System (ADS)

Peng, Heng; Liu, Yinghua; Chen, Haofeng

2018-05-01

In this paper, a novel direct method called the stress compensation method (SCM) is proposed for limit and shakedown analysis of large-scale elastoplastic structures. Without needing to solve the specific mathematical programming problem, the SCM is a two-level iterative procedure based on a sequence of linear elastic finite element solutions where the global stiffness matrix is decomposed only once. In the inner loop, the static admissible residual stress field for shakedown analysis is constructed. In the outer loop, a series of decreasing load multipliers are updated to approach to the shakedown limit multiplier by using an efficient and robust iteration control technique, where the static shakedown theorem is adopted. Three numerical examples up to about 140,000 finite element nodes confirm the applicability and efficiency of this method for two-dimensional and three-dimensional elastoplastic structures, with detailed discussions on the convergence and the accuracy of the proposed algorithm.

Has the pelvic renal stone position inside the upper loop of JJ stent any influence on the extracorporeal shock wave lithotripsy results?

PubMed

Pricop, Catalin; Serban, Dragomir N; Serban, Ionela Lacramioara; Cumpanas, Alin-Adrian; Gingu, Constantin-Virgil

2016-01-01

JJ stents are often encountered in patients with pelvic renal stones referred for shock wave lithotripsy, most of them being placed either for obstructive renal pelvic stones or for ureteric stones mobilized retrograde during the JJ stent insertion. The aim of the study was to determine whether the relative stone position in the upper loop of the JJ stent during extracorporeal shock wave lithotripsy (SWL) influences the efficiency of the procedure. The study was designed as a prospective cohort study on 162 patients addressing the same urological department, with single renal pelvic stone (primary or mobilized to the renal pelvis during the insertion of JJ stent), smaller than 15 mm, with JJ stent, treated by SWL using a second generation spark gap lithotripter, 18 kV, 3000 waves/session. Patients were divided in three groups according to the relative position of the stone to the upper loop of the JJ stent as appears on plain X-ray: stone-inside-loop, loop-crossing-stone and stone-outside the loop. The SWL success rate was the primary outcome of the study. p Value, Chi square and Kruskal-Wallis tests were used for statistical analysis. For stone-inside-loop cases, SWL efficiency was 22.7 versus 42 % for all the other cases (p = 0.002). Other factors for decreased SWL success rate were: higher stone radio-opacity, larger JJ of stent and obese patients. Study limitation is represented by the relative small study group and by the evaluation of stone density using plain X-ray instead of computer tomography. For pelvic renal stones having the same density characteristics studied by plain X-ray, the SWL efficiency is lower in stone-inside-loop cases comparing with the other positions. The overall stone free rate for renal pelvic stones could be explained by the second generation lithotripter used for all procedures.

RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability.

PubMed

Chang, Emily Yun-Chia; Novoa, Carolina A; Aristizabal, Maria J; Coulombe, Yan; Segovia, Romulo; Chaturvedi, Richa; Shen, Yaoqing; Keong, Christelle; Tam, Annie S; Jones, Steven J M; Masson, Jean-Yves; Kobor, Michael S; Stirling, Peter C

2017-12-04

Sgs1, the orthologue of human Bloom's syndrome helicase BLM, is a yeast DNA helicase functioning in DNA replication and repair. We show that SGS1 loss increases R-loop accumulation and sensitizes cells to transcription-replication collisions. Yeast lacking SGS1 accumulate R-loops and γ-H2A at sites of Sgs1 binding, replication pausing regions, and long genes. The mutation signature of sgs1 Δ reveals copy number changes flanked by repetitive regions with high R-loop-forming potential. Analysis of BLM in Bloom's syndrome fibroblasts or by depletion of BLM from human cancer cells confirms a role for Sgs1/BLM in suppressing R-loop-associated genome instability across species. In support of a potential direct effect, BLM is found physically proximal to DNA:RNA hybrids in human cells, and can efficiently unwind R-loops in vitro. Together, our data describe a conserved role for Sgs1/BLM in R-loop suppression and support an increasingly broad view of DNA repair and replication fork stabilizing proteins as modulators of R-loop-mediated genome instability. © 2017 Chang et al.

Influence of minor displacements in loops of the porcine parvovirus VP2 capsid on virus-like particles assembly and the induction of antibody responses.

PubMed

Pan, Qunxing; He, Kongwang; Wang, Yongshan; Wang, Xiaoli; Ouyang, Wei

2013-06-01

An antigen-delivery system based on hybrid virus-like particles (VLPs) formed by the self-assembly of the capsid VP2 protein of porcine parvovirus (PPV) and expressing foreign peptides offers an alternative method for vaccination. In this study, the three-dimensional structure of the PPV capsid protein and surface loops deletion mutants were analyzed to define essential domains in PPV VP2 for the assembly of VLPs. Electron microscopic analysis and SDS-PAGE analysis confirmed the presence of abundant VLPs in a loop2 deletion mutant of expected size and appropriate morphology. Loop4 and loop2-loop4 deletion mutants, however, resulted in a lower number of particles and the morphology of the particles was not well preserved. Furthermore, the green fluorescent protein (gfp) gene was used as a model. GFP was observed at the same level in displacements mutants. However, GFP displacement mutants in loop2 construct allowed better adaptation for the fusion GFP to be further displayed on the surface of the capsid-like structure. Immunogenicity study showed that there is no obvious difference in mice inoculated with rAd-VP2(Δloop2), rAd-VP2(Δloop4), rAd-VP2(Δloop2-Δloop4), and PPV inactivated vaccine. The results suggested the possibility of inserting simultaneously B and T cell epitopes in the surface loop2 and the N-terminus. The combination of different types of epitopes (B, CD4+, and CD8+) in different positions of the PPV particles opens the way to the development of highly efficient vaccines, able to stimulate at the same time the different branches of the immune system.

The theory, design, and operation of the suppressed carrier data-aided tracking receiver

NASA Technical Reports Server (NTRS)

Simon, M. K.; Springett, J. C.

1973-01-01

A viable, efficient, and easily mechanized carrier regenerating receiver for use in suppressed carrier-tracking system is described. The receiver referred to as a data-aided receiver (DAR) incorporates a data-aided loop (DAL) which provides the required carrier reference signal. The DAL employs the principle of decision feedback and as such is more efficient than other forms of suppressed carrier-tracking loops. The analysis, design, and implementation of the DAR are covered in detail. Performance comparisons and mechanization tradeoffs are made, wherever possible, with discrete carrier systems and other suppressed carrier systems presently in use. Experimental performance verification is given throughout in support of the theory presented.

Carbon-free hydrogen production from low rank coal

NASA Astrophysics Data System (ADS)

Aziz, Muhammad; Oda, Takuya; Kashiwagi, Takao

2018-02-01

Novel carbon-free integrated system of hydrogen production and storage from low rank coal is proposed and evaluated. To measure the optimum energy efficiency, two different systems employing different chemical looping technologies are modeled. The first integrated system consists of coal drying, gasification, syngas chemical looping, and hydrogenation. On the other hand, the second system combines coal drying, coal direct chemical looping, and hydrogenation. In addition, in order to cover the consumed electricity and recover the energy, combined cycle is adopted as addition module for power generation. The objective of the study is to find the best system having the highest performance in terms of total energy efficiency, including hydrogen production efficiency and power generation efficiency. To achieve a thorough energy/heat circulation throughout each module and the whole integrated system, enhanced process integration technology is employed. It basically incorporates two core basic technologies: exergy recovery and process integration. Several operating parameters including target moisture content in drying module, operating pressure in chemical looping module, are observed in terms of their influence to energy efficiency. From process modeling and calculation, two integrated systems can realize high total energy efficiency, higher than 60%. However, the system employing coal direct chemical looping represents higher energy efficiency, including hydrogen production and power generation, which is about 83%. In addition, optimum target moisture content in drying and operating pressure in chemical looping also have been defined.

Thermodynamic efficiency analysis and cycle optimization of deeply precooled combined cycle engine in the air-breathing mode

NASA Astrophysics Data System (ADS)

Zhang, Jianqiang; Wang, Zhenguo; Li, Qinglian

2017-09-01

The efficiency calculation and cycle optimization were carried out for the Synergistic Air-Breathing Rocket Engine (SABRE) with deeply precooled combined cycle. A component-level model was developed for the engine, and exergy efficiency analysis based on the model was carried out. The methods to improve cycle efficiency have been proposed. The results indicate cycle efficiency of SABRE is between 29.7% and 41.7% along the flight trajectory, and most of the wasted exergy is occupied by the unburned hydrogen in exit gas. Exergy loss exists in each engine component, and the sum losses of main combustion chamber(CC), pre-burner(PB), precooler(PC) and 3# heat exchanger(HX3) are greater than 71.3% of the total loss. Equivalence ratio is the main influencing factor of cycle, and it can be regulated by adjusting parameters of helium loop. Increase the maximum helium outlet temperature of PC by 50 K, the total assumption of hydrogen will be saved by 4.8%, and the cycle efficiency is advanced by 3% averagely in the trajectory. Helium recirculation scheme introduces a helium recirculation loop to increase local helium flow rate of PC. It turns out the total assumption of hydrogen will be saved by 9%, that's about 1740 kg, and the cycle efficiency is advanced by 5.6% averagely.

Loop engineering reveals the importance of active-site-decorating loops and gating residue in substrate affinity modulation of arginine deiminase (an anti-tumor enzyme).

PubMed

Cheng, Feng; Yang, Jianhua; Bocola, Marco; Schwaneberg, Ulrich; Zhu, Leilei

2018-05-05

Protein engineering of enzyme loop regions is an effective strategy to improve enzymatic properties. Previous studies that aimed to boost the activity of PpADI (an arginine deiminase from Pseudomonas plecoglossicida) under physiological conditions yielded several significantly improved variants that harbor substitutions predominantly located in active-site-decorating loops. A multi-site saturation mutagenesis at four positions in loop 1 (37, 38, 42, and 43) and three positions in loop 4 (402, 403, and 404) was performed to elucidate the importance of these loops in modulating the substrate affinity of PpADI. The identified "best" variant (M6-L1-4) showed a decreased S 0.5 ('K M ') of 0.48 mM compared with the parent M6 (0.81 mM). Subsequently, a rational design to recombine beneficial substitutions within loops 1 and 4 yielded variant L6 with a substantially decreased S 0.5 value (0.17 mM). A comprehensive simulation analysis resulted in a conclusion that high loop flexibility (especially the gating residue Arg400) is beneficial for substrate affinity due to less efficient blocking of the active site. Copyright © 2018 Elsevier Inc. All rights reserved.

A wirelessly-powered homecage with animal behavior analysis and closed-loop power control.

PubMed

Yaoyao Jia; Zheyuan Wang; Canales, Daniel; Tinkler, Morgan; Chia-Chun Hsu; Madsen, Teresa E; Mirbozorgi, S Abdollah; Rainnie, Donald; Ghovanloo, Maysam

2016-08-01

This paper presents a new EnerCage-homecage system, EnerCage-HC2, for longitudinal electrophysiology data acquisition experiments on small freely moving animal subjects, such as rodents. EnerCage-HC2 is equipped with multi-coil wireless power transmission (WPT), closed-loop power control, bidirectional data communication via Bluetooth Low Energy (BLE), and Microsoft Kinect® based animal behavior tracking and analysis. The EnerCage-HC2 achieves a homogeneous power transfer efficiency (PTE) of 14% on average, with ~42 mW power delivered to the load (PDL) at a nominal height of 7 cm by the closed-loop power control mechanism. The Microsoft Kinect® behavioral analysis algorithm can not only track the animal position in real-time but also classify 5 different types of rodent behaviors: standstill, walking, grooming, rearing, and rotating. A proof-of-concept in vivo experiment was conducted on two awake freely behaving rats while successfully operating a one-channel stimulator and generating an ethogram.

Efficient dynamic coherence transfer relying on offset locking using optical phase-locked loop

NASA Astrophysics Data System (ADS)

Xie, Weilin; Dong, Yi; Bretenaker, Fabien; Shi, Hongxiao; Zhou, Qian; Xia, Zongyang; Qin, Jie; Zhang, Lin; Lin, Xi; Hu, Weisheng

2018-01-01

We design and experimentally demonstrate a highly efficient coherence transfer based on composite optical phaselocked loop comprising multiple feedback servo loops. The heterodyne offset-locking is achieved by conducting an acousto-optic frequency shifter in combination with the current tuning and the temperature controlling of the semiconductor laser. The adaptation of the composite optical phase-locked loop enables the tight coherence transfer from a frequency comb to a semiconductor laser in a fully dynamic manner.

Algorithmic design of a noise-resistant and efficient closed-loop deep brain stimulation system: A computational approach.

PubMed

Karamintziou, Sofia D; Custódio, Ana Luísa; Piallat, Brigitte; Polosan, Mircea; Chabardès, Stéphan; Stathis, Pantelis G; Tagaris, George A; Sakas, Damianos E; Polychronaki, Georgia E; Tsirogiannis, George L; David, Olivier; Nikita, Konstantina S

2017-01-01

Advances in the field of closed-loop neuromodulation call for analysis and modeling approaches capable of confronting challenges related to the complex neuronal response to stimulation and the presence of strong internal and measurement noise in neural recordings. Here we elaborate on the algorithmic aspects of a noise-resistant closed-loop subthalamic nucleus deep brain stimulation system for advanced Parkinson's disease and treatment-refractory obsessive-compulsive disorder, ensuring remarkable performance in terms of both efficiency and selectivity of stimulation, as well as in terms of computational speed. First, we propose an efficient method drawn from dynamical systems theory, for the reliable assessment of significant nonlinear coupling between beta and high-frequency subthalamic neuronal activity, as a biomarker for feedback control. Further, we present a model-based strategy through which optimal parameters of stimulation for minimum energy desynchronizing control of neuronal activity are being identified. The strategy integrates stochastic modeling and derivative-free optimization of neural dynamics based on quadratic modeling. On the basis of numerical simulations, we demonstrate the potential of the presented modeling approach to identify, at a relatively low computational cost, stimulation settings potentially associated with a significantly higher degree of efficiency and selectivity compared with stimulation settings determined post-operatively. Our data reinforce the hypothesis that model-based control strategies are crucial for the design of novel stimulation protocols at the backstage of clinical applications.

Real-time monitoring of CO2 storage sites: Application to Illinois Basin-Decatur Project

USGS Publications Warehouse

Picard, G.; Berard, T.; Chabora, E.; Marsteller, S.; Greenberg, S.; Finley, R.J.; Rinck, U.; Greenaway, R.; Champagnon, C.; Davard, J.

2011-01-01

Optimization of carbon dioxide (CO2) storage operations for efficiency and safety requires use of monitoring techniques and implementation of control protocols. The monitoring techniques consist of permanent sensors and tools deployed for measurement campaigns. Large amounts of data are thus generated. These data must be managed and integrated for interpretation at different time scales. A fast interpretation loop involves combining continuous measurements from permanent sensors as they are collected to enable a rapid response to detected events; a slower loop requires combining large datasets gathered over longer operational periods from all techniques. The purpose of this paper is twofold. First, it presents an analysis of the monitoring objectives to be performed in the slow and fast interpretation loops. Second, it describes the implementation of the fast interpretation loop with a real-time monitoring system at the Illinois Basin-Decatur Project (IBDP) in Illinois, USA. ?? 2011 Published by Elsevier Ltd.

Supercomputers for engineering analysis

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

Goudreau, G.L.; Benson, D.J.; Hallquist, J.O.

1986-07-01

The Cray-1 and Cray X-MP/48 experience in engineering computations at the Lawrence Livermore National Laboratory is surveyed. The fully vectorized explicit DYNA and implicit NIKE finite element codes are discussed with respect to solid and structural mechanics. The main efficiencies for production analyses are currently obtained by simple CFT compiler exploitation of pipeline architecture for inner do-loop optimization. Current developmet of outer-loop multitasking is also discussed. Applications emphasis will be on 3D examples spanning earth penetrator loads analysis, target lethality assessment, and crashworthiness. The use of a vectorized large deformation shell element in both DYNA and NIKE has substantially expandedmore » 3D nonlinear capability. 25 refs., 7 figs.« less

A decoupled recursive approach for constrained flexible multibody system dynamics

NASA Technical Reports Server (NTRS)

Lai, Hao-Jan; Kim, Sung-Soo; Haug, Edward J.; Bae, Dae-Sung

1989-01-01

A variational-vector calculus approach is employed to derive a recursive formulation for dynamic analysis of flexible multibody systems. Kinematic relationships for adjacent flexible bodies are derived in a companion paper, using a state vector notation that represents translational and rotational components simultaneously. Cartesian generalized coordinates are assigned for all body and joint reference frames, to explicitly formulate deformation kinematics under small deformation kinematics and an efficient flexible dynamics recursive algorithm is developed. Dynamic analysis of a closed loop robot is performed to illustrate efficiency of the algorithm.

Efficient Computation of Closed-loop Frequency Response for Large Order Flexible Systems

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Giesy, Daniel P.

1997-01-01

An efficient and robust computational scheme is given for the calculation of the frequency response function of a large order, flexible system implemented with a linear, time invariant control system. Advantage is taken of the highly structured sparsity of the system matrix of the plant based on a model of the structure using normal mode coordinates. The computational time per frequency point of the new computational scheme is a linear function of system size, a significant improvement over traditional, full-matrix techniques whose computational times per frequency point range from quadratic to cubic functions of system size. This permits the practical frequency domain analysis of systems of much larger order than by traditional, full-matrix techniques. Formulations are given for both open and closed loop loop systems. Numerical examples are presented showing the advantages of the present formulation over traditional approaches, both in speed and in accuracy. Using a model with 703 structural modes, a speed-up of almost two orders of magnitude was observed while accuracy improved by up to 5 decimal places.

Binding modes of phosphotriesterase-like lactonase complexed with δ-nonanoic lactone and paraoxon using molecular dynamics simulations.

PubMed

Guan, Shanshan; Zhao, Li; Jin, Hanyong; Shan, Ning; Han, Weiwei; Wang, Song; Shan, Yaming

2017-02-01

Phosphotriesterase-like lactonases (PLLs) have received much attention because of their physical and chemical properties. They may have widespread applications in various fields. For example, they show potential for quorum-sensing signaling pathways and organophosphorus (OP) detoxification in agricultural science. However, the mechanism by which PLLs hydrolyze, which involves OP compounds and lactones and a variety of distinct catalytic efficiencies, has only rarely been explored. In the present study, molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of DrPLL, a member of the PLL superfamily in Deinococcus radiodurans, bound to two substrates, δ-nonanoic lactone and paraoxon. It has been observed that there is a 16-fold increase in the catalytic efficiency of the two mutant strains of DrPLL (F26G/C72I) vs. the wild-type enzyme toward the hydrolysis of paraoxon, but an explanation for this behavior is currently lacking. The analysis of the molecular trajectories of DrPLL bound to δ-nonanoic lactone indicated that lactone-induced conformational changes take place in loop 8, which is near the active site. Binding to paraoxon may lead to conformational displacement of loop 1 residues, which could lead to the deformation of the active site and so trigger the entry of the paraoxon into the active site. The efficiency of the F26G/C72I mutant was increased by decreasing the displacement of loop 1 residues and increasing the flexibility of loop 8 residues. These results provide a molecular-level explanation for the experimental behavior.

The effect of compressive viscosity and thermal conduction on the longitudinal MHD waves

NASA Astrophysics Data System (ADS)

Bahari, K.; Shahhosaini, N.

2018-05-01

longitudinal Magnetohydrodynamic (MHD) oscillations have been studied in a slowly cooling coronal loop, in the presence of thermal conduction and compressive viscosity, in the linear MHD approximation. WKB method has been used to solve the governing equations. In the leading order approximation the dispersion relation has been obtained, and using the first order approximation the time dependent amplitude has been determined. Cooling causes the oscillations to amplify and damping mechanisms are more efficient in hot loops. In cool loops the oscillation amplitude increases with time but in hot loops the oscillation amplitude decreases with time. Our conclusion is that in hot loops the efficiency of the compressive viscosity in damping longitudinal waves is comparable to that of the thermal conduction.

The effect of compressive viscosity and thermal conduction on the longitudinal MHD waves

NASA Astrophysics Data System (ADS)

Bahari, K.; Shahhosaini, N.

2018-07-01

Longitudinal magnetohydrodynamic (MHD) oscillations have been studied in a slowly cooling coronal loop, in the presence of thermal conduction and compressive viscosity, in the linear MHD approximation. The WKB method has been used to solve the governing equations. In the leading order approximation the dispersion relation has been obtained, and using the first-order approximation the time-dependent amplitude has been determined. Cooling causes the oscillations to amplify and damping mechanisms are more efficient in hot loops. In cool loops the oscillation amplitude increases with time but in hot loops the oscillation amplitude decreases with time. Our conclusion is that in hot loops the efficiency of the compressive viscosity in damping longitudinal waves is comparable to that of the thermal conduction.

Algorithmic design of a noise-resistant and efficient closed-loop deep brain stimulation system: A computational approach

PubMed Central

Karamintziou, Sofia D.; Custódio, Ana Luísa; Piallat, Brigitte; Polosan, Mircea; Chabardès, Stéphan; Stathis, Pantelis G.; Tagaris, George A.; Sakas, Damianos E.; Polychronaki, Georgia E.; Tsirogiannis, George L.; David, Olivier; Nikita, Konstantina S.

2017-01-01

Advances in the field of closed-loop neuromodulation call for analysis and modeling approaches capable of confronting challenges related to the complex neuronal response to stimulation and the presence of strong internal and measurement noise in neural recordings. Here we elaborate on the algorithmic aspects of a noise-resistant closed-loop subthalamic nucleus deep brain stimulation system for advanced Parkinson’s disease and treatment-refractory obsessive-compulsive disorder, ensuring remarkable performance in terms of both efficiency and selectivity of stimulation, as well as in terms of computational speed. First, we propose an efficient method drawn from dynamical systems theory, for the reliable assessment of significant nonlinear coupling between beta and high-frequency subthalamic neuronal activity, as a biomarker for feedback control. Further, we present a model-based strategy through which optimal parameters of stimulation for minimum energy desynchronizing control of neuronal activity are being identified. The strategy integrates stochastic modeling and derivative-free optimization of neural dynamics based on quadratic modeling. On the basis of numerical simulations, we demonstrate the potential of the presented modeling approach to identify, at a relatively low computational cost, stimulation settings potentially associated with a significantly higher degree of efficiency and selectivity compared with stimulation settings determined post-operatively. Our data reinforce the hypothesis that model-based control strategies are crucial for the design of novel stimulation protocols at the backstage of clinical applications. PMID:28222198

Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue 96 in the Plasmodial Enzyme.

PubMed

Pareek, Vidhi; Samanta, Moumita; Joshi, Niranjan V; Balaram, Hemalatha; Murthy, Mathur R N; Balaram, Padmanabhan

2016-04-01

Despite extensive research into triosephosphate isomerases (TIMs), there exists a gap in understanding of the remarkable conjunction between catalytic loop-6 (residues 166-176) movement and the conformational flip of Glu165 (catalytic base) upon substrate binding that primes the active site for efficient catalysis. The overwhelming occurrence of serine at position 96 (98% of the 6277 unique TIM sequences), spatially proximal to E165 and the loop-6 residues, raises questions about its role in catalysis. Notably, Plasmodium falciparum TIM has an extremely rare residue--phenylalanine--at this position whereas, curiously, the mutant F96S was catalytically defective. We have obtained insights into the influence of residue 96 on the loop-6 conformational flip and E165 positioning by combining kinetic and structural studies on the PfTIM F96 mutants F96Y, F96A, F96S/S73A, and F96S/L167V with sequence conservation analysis and comparative analysis of the available apo and holo structures of the enzyme from diverse organisms. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Space Life Support Engineering Program

NASA Technical Reports Server (NTRS)

Seagrave, Richard C.

1993-01-01

This report covers the second year of research relating to the development of closed-loop long-term life support systems. Emphasis was directed toward concentrating on the development of dynamic simulation techniques and software and on performing a thermodynamic systems analysis in an effort to begin optimizing the system needed for water purification. Four appendices are attached. The first covers the ASPEN modeling of the closed loop Environmental Control Life Support System (ECLSS) and its thermodynamic analysis. The second is a report on the dynamic model development for water regulation in humans. The third regards the development of an interactive computer-based model for determining exercise limitations. The fourth attachment is an estimate of the second law thermodynamic efficiency of the various units comprising an ECLSS.

Structural tailoring of counter rotation propfans

NASA Technical Reports Server (NTRS)

Brown, Kenneth W.; Hopkins, D. A.

1989-01-01

The STAT program was designed for the optimization of single rotation, tractor propfan designs. New propfan designs, however, generally consist of two counter rotating propfan rotors. STAT is constructed to contain two levels of analysis. An interior loop, consisting of accurate, efficient approximate analyses, is used to perform the primary propfan optimization. Once an optimum design has been obtained, a series of refined analyses are conducted. These analyses, while too computer time expensive for the optimization loop, are of sufficient accuracy to validate the optimized design. Should the design prove to be unacceptable, provisions are made for recalibration of the approximate analyses, for subsequent reoptimization.

Enhanced Microchip Electrophoresis Separations Combined with Electrochemical Detection Utilizing a Capillary Embedded in Polystyrene.

PubMed

Mehl, Benjamin T; Martin, R Scott

2018-01-07

The ability to use microchip-based electrophoresis for fast, high-throughput separations provides researchers with a tool for close-to real time analysis of biological systems. While PDMS-based electrophoresis devices are popular, the separation efficiency is often an issue due to the hydrophobic nature of PDMS. In this study, a hybrid microfluidic capillary device was fabricated to utilize the positive features of PDMS along with the electrophoretic performance of fused silica. A capillary loop was embedded in a polystyrene base that can be coupled with PDMS microchannels at minimal dead volume interconnects. A method for cleaning out the capillaries after a wet-polishing step was devised through the use of 3D printed syringe attachment. By comparing the separation efficiency of fluorescein and CBI-glycine with both a PDMS-based serpentine device and the embedded capillary loop device, it was shown that the embedded capillary loop device maintained higher theoretical plates for both analytes. A Pd decoupler with a carbon or Pt detection electrode were embedded along with the loop allowing integration of the electrophoretic separation with electrochemical detection. A series of catecholamines were separated to show the ability to resolve similar analytes and detect redox active species. The release of dopamine and norepinephrine from PC 12 cells was also analyzed showing the compatibility of these improved microchip separations with high ionic cell buffers associated with cell culture.

Nonlinear predictive control for adaptive adjustments of deep brain stimulation parameters in basal ganglia-thalamic network.

PubMed

Su, Fei; Wang, Jiang; Niu, Shuangxia; Li, Huiyan; Deng, Bin; Liu, Chen; Wei, Xile

2018-02-01

The efficacy of deep brain stimulation (DBS) for Parkinson's disease (PD) depends in part on the post-operative programming of stimulation parameters. Closed-loop stimulation is one method to realize the frequent adjustment of stimulation parameters. This paper introduced the nonlinear predictive control method into the online adjustment of DBS amplitude and frequency. This approach was tested in a computational model of basal ganglia-thalamic network. The autoregressive Volterra model was used to identify the process model based on physiological data. Simulation results illustrated the efficiency of closed-loop stimulation methods (amplitude adjustment and frequency adjustment) in improving the relay reliability of thalamic neurons compared with the PD state. Besides, compared with the 130Hz constant DBS the closed-loop stimulation methods can significantly reduce the energy consumption. Through the analysis of inter-spike-intervals (ISIs) distribution of basal ganglia neurons, the evoked network activity by the closed-loop frequency adjustment stimulation was closer to the normal state. Copyright © 2017 Elsevier Ltd. All rights reserved.

Printed Multi-Turn Loop Antenna for RF Bio-Telemetry

NASA Technical Reports Server (NTRS)

Simons, Rainee N.; Hall, David G.; Miranda, Felix A.

2004-01-01

In this paper, a novel printed multi-turn loop antenna for contact-less powering and RF telemetry from implantable bio- MEMS sensors at a design frequency of 300 MHz is demonstrated. In addition, computed values of input reactance, radiation resistance, skin effect resistance, and radiation efficiency for the printed multi-turn loop antenna are presented. The computed input reactance is compared with the measured values and shown to be in fair agreement. The computed radiation efficiency at the design frequency is about 24 percent.

Convection equation modeling: A non-iterative direct matrix solution algorithm for use with SINDA

NASA Technical Reports Server (NTRS)

Schrage, Dean S.

1993-01-01

The determination of the boundary conditions for a component-level analysis, applying discrete finite element and finite difference modeling techniques often requires an analysis of complex coupled phenomenon that cannot be described algebraically. For example, an analysis of the temperature field of a coldplate surface with an integral fluid loop requires a solution to the parabolic heat equation and also requires the boundary conditions that describe the local fluid temperature. However, the local fluid temperature is described by a convection equation that can only be solved with the knowledge of the locally-coupled coldplate temperatures. Generally speaking, it is not computationally efficient, and sometimes, not even possible to perform a direct, coupled phenomenon analysis of the component-level and boundary condition models within a single analysis code. An alternative is to perform a disjoint analysis, but transmit the necessary information between models during the simulation to provide an indirect coupling. For this approach to be effective, the component-level model retains full detail while the boundary condition model is simplified to provide a fast, first-order prediction of the phenomenon in question. Specifically for the present study, the coldplate structure is analyzed with a discrete, numerical model (SINDA) while the fluid loop convection equation is analyzed with a discrete, analytical model (direct matrix solution). This indirect coupling allows a satisfactory prediction of the boundary condition, while not subjugating the overall computational efficiency of the component-level analysis. In the present study a discussion of the complete analysis of the derivation and direct matrix solution algorithm of the convection equation is presented. Discretization is analyzed and discussed to extend of solution accuracy, stability and computation speed. Case studies considering a pulsed and harmonic inlet disturbance to the fluid loop are analyzed to assist in the discussion of numerical dissipation and accuracy. In addition, the issues of code melding or integration with standard class solvers such as SINDA are discussed to advise the user of the potential problems to be encountered.

First cytoplasmic loop of glucagon-like peptide-1 receptor can function at the third cytoplasmic loop position of rhodopsin.

PubMed

Yamashita, Takahiro; Tose, Koji; Shichida, Yoshinori

2008-01-01

G protein-coupled receptors (GPCRs) are classified into several families based on their amino acid sequences. In family 1, GPCRs such as rhodopsin and adrenergic receptor, the structure-function relationship has been extensively investigated to demonstrate that exposure of the third cytoplasmic loop is essential for selective G protein activation. In contrast, much less is known about other families. Here we prepared chimeric mutants between Gt-coupled rhodopsin and Gi/Go- and Gs-coupled glucagon-like peptide-1 (GLP-1) receptor of family 2 and tried to identify the loop region that functions at the third cytoplasmic loop position of rhodopsin. We succeeded in expressing a mutant having the first cytoplasmic loop of GLP-1 receptor and found that this mutant activated Gi and Go efficiently but did not activate Gt. Moreover, the rhodopsin mutant having the first loop of Gs-coupled secretin receptor of family 2 decreased the Gi and Go activation efficiencies. Therefore, the first loop of GLP-1 receptor would share a similar role to the third loop of rhodopsin in G protein activation. This result strongly suggested that different families of GPCRs have maintained molecular architectures of their ancestral types to generate a common mechanism, namely exposure of the cytoplasmic loop, to activate peripheral G protein.

Energy Conversion Alternatives Study (ECAS), Westinghouse phase 1. Volume 9: Closed-cycle MHD. [energy conversion efficiency of electric power plants using magnetohydrodynamics

NASA Technical Reports Server (NTRS)

Tsu, T. C.

1976-01-01

A closed-cycle MHD system for an electric power plant was studied. It consists of 3 interlocking loops, an external heating loop, a closed-cycle cesium seeded argon nonequilibrium ionization MHD loop, and a steam bottomer. A MHD duct maximum temperature of 2366 K (3800 F), a pressure of 0.939 MPa (9.27 atm) and a Mach number of 0.9 are found to give a topping cycle efficiency of 59.3%; however when combined with an integrated gasifier and optimistic steam bottomer the coal to bus bar efficiency drops to 45.5%. A 1978 K (3100 F) cycle has an efficiency of 55.1% and a power plant efficiency of 42.2%. The high cost of the external heating loop components results in a cost of electricity of 21.41 mills/MJ (77.07 mills/kWh) for the high temperature system and 19.0 mills/MJ (68.5 mills/kWh) for the lower temperature system. It is, therefore, thought that this cycle may be more applicable to internally heated systems such as some futuristic high temperature gas cooled reactor.

Feedback Regulation and Its Efficiency in Biochemical Networks

NASA Astrophysics Data System (ADS)

Kobayashi, Tetsuya J.; Yokota, Ryo; Aihara, Kazuyuki

2016-03-01

Intracellular biochemical networks fluctuate dynamically due to various internal and external sources of fluctuation. Dissecting the fluctuation into biologically relevant components is important for understanding how a cell controls and harnesses noise and how information is transferred over apparently noisy intracellular networks. While substantial theoretical and experimental advancement on the decomposition of fluctuation was achieved for feedforward networks without any loop, we still lack a theoretical basis that can consistently extend such advancement to feedback networks. The main obstacle that hampers is the circulative propagation of fluctuation by feedback loops. In order to define the relevant quantity for the impact of feedback loops for fluctuation, disentanglement of the causally interlocked influences between the components is required. In addition, we also lack an approach that enables us to infer non-perturbatively the influence of the feedback to fluctuation in the same way as the dual reporter system does in the feedforward networks. In this work, we address these problems by extending the work on the fluctuation decomposition and the dual reporter system. For a single-loop feedback network with two components, we define feedback loop gain as the feedback efficiency that is consistent with the fluctuation decomposition for feedforward networks. Then, we clarify the relation of the feedback efficiency with the fluctuation propagation in an open-looped FF network. Finally, by extending the dual reporter system, we propose a conjugate feedback and feedforward system for estimating the feedback efficiency non-perturbatively only from the statistics of the system.

A high-speed, tunable silicon photonic ring modulator integrated with ultra-efficient active wavelength control.

PubMed

Zheng, Xuezhe; Chang, Eric; Amberg, Philip; Shubin, Ivan; Lexau, Jon; Liu, Frankie; Thacker, Hiren; Djordjevic, Stevan S; Lin, Shiyun; Luo, Ying; Yao, Jin; Lee, Jin-Hyoung; Raj, Kannan; Ho, Ron; Cunningham, John E; Krishnamoorthy, Ashok V

2014-05-19

We report the first complete 10G silicon photonic ring modulator with integrated ultra-efficient CMOS driver and closed-loop wavelength control. A selective substrate removal technique was used to improve the ring tuning efficiency. Limited by the thermal tuner driver output power, a maximum open-loop tuning range of about 4.5nm was measured with about 14mW of total tuning power including the heater driver circuit power consumption. Stable wavelength locking was achieved with a low-power mixed-signal closed-loop wavelength controller. An active wavelength tracking range of > 500GHz was demonstrated with controller energy cost of only 20fJ/bit.

Plate with decentralised velocity feedback loops: Power absorption and kinetic energy considerations

NASA Astrophysics Data System (ADS)

Gardonio, P.; Miani, S.; Blanchini, F.; Casagrande, D.; Elliott, S. J.

2012-04-01

This paper is focused on the vibration effects produced by an array of decentralised velocity feedback loops that are evenly distributed over a rectangular thin plate to minimise its flexural response. The velocity feedback loops are formed by collocated ideal velocity sensor and point force actuator pairs, which are unconditionally stable and produce 'sky-hook' damping on the plate. The study compares how the overall flexural vibration of the plate and the local absorption of vibration power by the feedback loops vary with the control gains. The analysis is carried out both considering a typical frequency-domain formulation based on kinetic energy and structural power physical quantities, which is normally used to study vibration and noise problems, and a time-domain formulation also based on kinetic energy and structural power, which is usually implemented to investigate control problems. The time-domain formulation shows to be much more computationally efficient and robust with reference to truncation errors. Thus it has been used to perform a parametric study to assess if, and under which conditions, the minimum of the kinetic energy and the maximum of the absorbed power cost functions match with reference to: (a) the number of feedback control loops, (b) the structural damping in the plate, (c) the mutual distance of a pair of control loops and (d) the mutual gains implemented in a pair of feedback loops.

Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B.

PubMed

Li, Zhu; Duan, Xuguo; Chen, Sheng; Wu, Jing

2017-01-01

The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase.

Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B

PubMed Central

Li, Zhu; Duan, Xuguo; Chen, Sheng; Wu, Jing

2017-01-01

The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase. PMID:28253342

La-CTP: Loop-Aware Routing for Energy-Harvesting Wireless Sensor Networks.

PubMed

Sun, Guodong; Shang, Xinna; Zuo, Yan

2018-02-02

In emerging energy-harvesting wireless sensor networks (EH-WSN), the sensor nodes can harvest environmental energy to drive their operation, releasing the user's burden in terms of frequent battery replacement, and even enabling perpetual sensing systems. In EH-WSN applications, usually, the node in energy-harvesting or recharging state has to stop working until it completes the energy replenishment. However, such temporary departures of recharging nodes severely impact the packet routing, and one immediate result is the routing loop problem. Controlling loops in connectivity-intermittent EH-WSN in an efficient way is a big challenge in practice, and so far, users still lack of effective and practicable routing protocols with loop handling. Based on the Collection Tree Protocol (CTP) widely used in traditional wireless sensor networks, this paper proposes a loop-aware routing protocol for real-world EH-WSNs, called La-CTP, which involves a new parent updating metric and a proactive, adaptive beaconing scheme to effectively suppress the occurrence of loops and unlock unavoidable loops, respectively. We constructed a 100-node testbed to evaluate La-CTP, and the experimental results showed its efficacy and efficiency.

High-Performance Computing Data Center Cooling System Energy Efficiency |

Science.gov Websites

approaches involve a cooling distribution unit (CDU) (2), which interfaces with the facility cooling loop and to the energy recovery water (ERW) loop (5), which is a closed-loop system. There are three heat rejection options for this IT load: When possible, heat energy from the energy recovery loop is transferred

Fission Surface Power Technology Demonstration Unit Test Results

NASA Technical Reports Server (NTRS)

Briggs, Maxwell H.; Gibson, Marc A.; Geng, Steven M.; Sanzi, James L.

2016-01-01

The Fission Surface Power (FSP) Technology Demonstration Unit (TDU) is a system-level demonstration of fission power technology intended for use on manned missions to Mars. The Baseline FSP systems consists of a 190 kWt UO2 fast-spectrum reactor cooled by a primary pumped liquid metal loop. This liquid metal loop transfers heat to two intermediate liquid metal loops designed to isolate fission products in the primary loop from the balance of plant. The intermediate liquid metal loops transfer heat to four Stirling Power Conversion Units (PCU), each of which produce 12 kWe (48 kW total) and reject waste heat to two pumped water loops, which transfer the waste heat to titanium-water heat pipe radiators. The FSP TDU simulates a single leg of the baseline FSP system using an electrically heater core simulator, a single liquid metal loop, a single PCU, and a pumped water loop which rejects the waste heat to a Facility Cooling System (FCS). When operated at the nominal operating conditions (modified for low liquid metal flow) during TDU testing the PCU produced 8.9 kW of power at an efficiency of 21.7 percent resulting in a net system power of 8.1 kW and a system level efficiency of 17.2 percent. The reduction in PCU power from levels seen during electrically heated testing is the result of insufficient heat transfer from the NaK heater head to the Stirling acceptor, which could not be tested at Sunpower prior to delivery to the NASA Glenn Research Center (GRC). The maximum PCU power of 10.4 kW was achieved at the maximum liquid metal temperature of 875 K, minimum water temperature of 350 K, 1.1 kg/s liquid metal flow, 0.39 kg/s water flow, and 15.0 mm amplitude at an efficiency of 23.3 percent. This resulted in a system net power of 9.7 kW and a system efficiency of 18.7 percent.

Fission Surface Power Technology Demonstration Unit Test Results

NASA Technical Reports Server (NTRS)

Briggs, Maxwell H.; Gibson, Marc A.; Geng, Steven; Sanzi, James

2016-01-01

The Fission Surface Power (FSP) Technology Demonstration Unit (TDU) is a system-level demonstration of fission power technology intended for use on manned missions to Mars. The Baseline FSP systems consists of a 190 kWt UO2 fast-spectrum reactor cooled by a primary pumped liquid metal loop. This liquid metal loop transfers heat to two intermediate liquid metal loops designed to isolate fission products in the primary loop from the balance of plant. The intermediate liquid metal loops transfer heat to four Stirling Power Conversion Units (PCU), each of which produce 12 kWe (48 kW total) and reject waste heat to two pumped water loops, which transfer the waste heat to titanium-water heat pipe radiators. The FSP TDU simulates a single leg of the baseline FSP system using an electrically heater core simulator, a single liquid metal loop, a single PCU, and a pumped water loop which rejects the waste heat to a Facility Cooling System (FCS). When operated at the nominal operating conditions (modified for low liquid metal flow) during TDU testing the PCU produced 8.9 kW of power at an efficiency of 21.7% resulting in a net system power of 8.1 kW and a system level efficiency of 17.2%. The reduction in PCU power from levels seen during electrically heated testing is the result of insufficient heat transfer from the NaK heater head to the Stirling acceptor, which could not be tested at Sunpower prior to delivery to GRC. The maximum PCU power of 10.4 kW was achieved at the maximum liquid metal temperature of 875 K, minimum water temperature of 350 K, 1.1 kg/s liquid metal flow, 0.39 kg/s water flow, and 15.0 mm amplitude at an efficiency of 23.3%. This resulted in a system net power of 9.7 kW and a system efficiency of 18.7 %.

Detection of Shigella in Milk and Clinical Samples by Magnetic Immunocaptured-Loop-Mediated Isothermal Amplification Assay

PubMed Central

Zhang, Liding; Wei, Qiujiang; Han, Qinqin; Chen, Qiang; Tai, Wenlin; Zhang, Jinyang; Song, Yuzhu; Xia, Xueshan

2018-01-01

Shigella is an important human food-borne zoonosis bacterial pathogen, and can cause clinically severe diarrhea. There is an urgent need to develop a specific, sensitive, and rapid methodology for detection of this pathogen. In this study, loop-mediated isothermal amplification (LAMP) combined with magnetic immunocapture assay (IC-LAMP) was first developed for the detection of Shigella in pure culture, artificial milk, and clinical stool samples. This method exhibited a detection limit of 8.7 CFU/mL. Compared with polymerase chain reaction, IC-LAMP is sensitive, specific, and reliable for monitoring Shigella. Additionally, IC-LAMP is more convenient, efficient, and rapid than ordinary LAMP, as it is more efficiently enriches pathogen cells without extraction of genomic DNA. Under isothermal conditions, the amplification curves and the green fluorescence were detected within 30 min in the presence of genomic DNA template. The overall analysis time was approximately 1 h, including the enrichment and lysis of the bacterial cells, a significantly short detection time. Therefore, the IC-LAMP methodology described here is potentially useful for the efficient detection of Shigella in various samples. PMID:29467730

Discrete Event Command & Control for Networked Teams with Multiple Missions

DTIC Science & Technology

2009-03-16

Architecture for Unmanned Ground Systems ( JAUGS )10, and is an efficient means to realize the high-level OODA loops (observe, orient, decide, act) of 4D...for Unmanned Ground systems ( JAUGS )10, and is an efficient means to realize the OODA loops (observe, orient, decide, act) of 4D/RCS11. DEC is able to

A Graphical Method for Estimation of Barometric Efficiency from Continuous Data - Concepts and Application to a Site in the Piedmont, Air Force Plant 6, Marietta, Georgia

USGS Publications Warehouse

Gonthier, Gerard

2007-01-01

A graphical method that uses continuous water-level and barometric-pressure data was developed to estimate barometric efficiency. A plot of nearly continuous water level (on the y-axis), as a function of nearly continuous barometric pressure (on the x-axis), will plot as a line curved into a series of connected elliptical loops. Each loop represents a barometric-pressure fluctuation. The negative of the slope of the major axis of an elliptical loop will be the ratio of water-level change to barometric-pressure change, which is the sum of the barometric efficiency plus the error. The negative of the slope of the preferred orientation of many elliptical loops is an estimate of the barometric efficiency. The slope of the preferred orientation of many elliptical loops is approximately the median of the slopes of the major axes of the elliptical loops. If water-level change that is not caused by barometric-pressure change does not correlate with barometric-pressure change, the probability that the error will be greater than zero will be the same as the probability that it will be less than zero. As a result, the negative of the median of the slopes for many loops will be close to the barometric efficiency. The graphical method provided a rapid assessment of whether a well was affected by barometric-pressure change and also provided a rapid estimate of barometric efficiency. The graphical method was used to assess which wells at Air Force Plant 6, Marietta, Georgia, had water levels affected by barometric-pressure changes during a 2003 constant-discharge aquifer test. The graphical method was also used to estimate barometric efficiency. Barometric-efficiency estimates from the graphical method were compared to those of four other methods: average of ratios, median of ratios, Clark, and slope. The two methods (the graphical and median-of-ratios methods) that used the median values of water-level change divided by barometric-pressure change appeared to be most resistant to error caused by barometric-pressure-independent water-level change. The graphical method was particularly resistant to large amounts of barometric-pressure-independent water-level change, having an average and standard deviation of error for control wells that was less than one-quarter that of the other four methods. When using the graphical method, it is advisable that more than one person select the slope or that the same person fits the same data several times to minimize the effect of subjectivity. Also, a long study period should be used (at least 60 days) to ensure that loops affected by large amounts of barometric-pressure-independent water-level change do not significantly contribute to error in the barometric-efficiency estimate.

Unravelling the active microbial community in a thermophilic anaerobic digester-microbial electrolysis cell coupled system under different conditions.

PubMed

Cerrillo, Míriam; Viñas, Marc; Bonmatí, August

2017-03-01

Thermophilic anaerobic digestion (AD) of pig slurry coupled to a microbial electrolysis cell (MEC) with a recirculation loop was studied at lab-scale as a strategy to increase AD stability when submitted to organic and nitrogen overloads. The system performance was studied, with the recirculation loop both connected and disconnected, in terms of AD methane production, chemical oxygen demand removal (COD) and volatile fatty acid (VFA) concentrations. Furthermore, the microbial population was quantitatively and qualitatively assessed through DNA and RNA-based qPCR and high throughput sequencing (MiSeq), respectively to identify the RNA-based active microbial populations from the total DNA-based microbial community composition both in the AD and MEC reactors under different operational conditions. Suppression of the recirculation loop reduced the AD COD removal efficiency (from 40% to 22%) and the methane production (from 0.32 to 0.03 m 3  m -3  d -1 ). Restoring the recirculation loop led to a methane production of 0.55 m 3  m -3  d -1 concomitant with maximum MEC COD and ammonium removal efficiencies of 29% and 34%, respectively. Regarding microbial analysis, the composition of the AD and MEC anode populations differed from really active microorganisms. Desulfuromonadaceae was revealed as the most active family in the MEC (18%-19% of the RNA relative abundance), while hydrogenotrophic methanogens (Methanobacteriaceae) dominated the AD biomass. Copyright © 2016 Elsevier Ltd. All rights reserved.

Binary phase locked loops for Omega receivers

NASA Technical Reports Server (NTRS)

Chamberlin, K.

1974-01-01

An all-digital phase lock loop (PLL) is considered because of a number of problems inherent in an employment of analog PLL. The digital PLL design presented solves these problems. A single loop measures all eight Omega time slots. Memory-aiding leads to the name of this design, the memory-aided phase lock loop (MAPLL). Basic operating principles are discussed and the superiority of MAPLL over the conventional digital phase lock loop with regard to the operational efficiency for Omega applications is demonstrated.

RECQ-like helicases Sgs1 and BLM regulate R-loop–associated genome instability

PubMed Central

Chang, Emily Yun-Chia; Novoa, Carolina A.; Aristizabal, Maria J.; Coulombe, Yan; Segovia, Romulo; Shen, Yaoqing; Keong, Christelle; Tam, Annie S.; Jones, Steven J.M.; Masson, Jean-Yves; Kobor, Michael S.

2017-01-01

Sgs1, the orthologue of human Bloom’s syndrome helicase BLM, is a yeast DNA helicase functioning in DNA replication and repair. We show that SGS1 loss increases R-loop accumulation and sensitizes cells to transcription–replication collisions. Yeast lacking SGS1 accumulate R-loops and γ-H2A at sites of Sgs1 binding, replication pausing regions, and long genes. The mutation signature of sgs1Δ reveals copy number changes flanked by repetitive regions with high R-loop–forming potential. Analysis of BLM in Bloom’s syndrome fibroblasts or by depletion of BLM from human cancer cells confirms a role for Sgs1/BLM in suppressing R-loop–associated genome instability across species. In support of a potential direct effect, BLM is found physically proximal to DNA:RNA hybrids in human cells, and can efficiently unwind R-loops in vitro. Together, our data describe a conserved role for Sgs1/BLM in R-loop suppression and support an increasingly broad view of DNA repair and replication fork stabilizing proteins as modulators of R-loop–mediated genome instability. PMID:29042409

Kinking and Torsion Can Significantly Improve the Efficiency of Valveless Pumping in Periodically Compressed Tubular Conduits. Implications for Understanding of the Form-Function Relationship of Embryonic Heart Tubes.

PubMed

Hiermeier, Florian; Männer, Jörg

2017-11-19

Valveless pumping phenomena (peristalsis, Liebau-effect) can generate unidirectional fluid flow in periodically compressed tubular conduits. Early embryonic hearts are tubular conduits acting as valveless pumps. It is unclear whether such hearts work as peristaltic or Liebau-effect pumps. During the initial phase of its pumping activity, the originally straight embryonic heart is subjected to deforming forces that produce bending, twisting, kinking, and coiling. This deformation process is called cardiac looping. Its function is traditionally seen as generating a configuration needed for establishment of correct alignments of pulmonary and systemic flow pathways in the mature heart of lung-breathing vertebrates. This idea conflicts with the fact that cardiac looping occurs in all vertebrates, including gill-breathing fishes. We speculate that looping morphogenesis may improve the efficiency of valveless pumping. To test the physical plausibility of this hypothesis, we analyzed the pumping performance of a Liebau-effect pump in straight and looped (kinked) configurations. Compared to the straight configuration, the looped configuration significantly improved the pumping performance of our pump. This shows that looping can improve the efficiency of valveless pumping driven by the Liebau-effect. Further studies are needed to clarify whether this finding may have implications for understanding of the form-function relationship of embryonic hearts.

Kinking and Torsion Can Significantly Improve the Efficiency of Valveless Pumping in Periodically Compressed Tubular Conduits. Implications for Understanding of the Form-Function Relationship of Embryonic Heart Tubes

PubMed Central

Hiermeier, Florian; Männer, Jörg

2017-01-01

Valveless pumping phenomena (peristalsis, Liebau-effect) can generate unidirectional fluid flow in periodically compressed tubular conduits. Early embryonic hearts are tubular conduits acting as valveless pumps. It is unclear whether such hearts work as peristaltic or Liebau-effect pumps. During the initial phase of its pumping activity, the originally straight embryonic heart is subjected to deforming forces that produce bending, twisting, kinking, and coiling. This deformation process is called cardiac looping. Its function is traditionally seen as generating a configuration needed for establishment of correct alignments of pulmonary and systemic flow pathways in the mature heart of lung-breathing vertebrates. This idea conflicts with the fact that cardiac looping occurs in all vertebrates, including gill-breathing fishes. We speculate that looping morphogenesis may improve the efficiency of valveless pumping. To test the physical plausibility of this hypothesis, we analyzed the pumping performance of a Liebau-effect pump in straight and looped (kinked) configurations. Compared to the straight configuration, the looped configuration significantly improved the pumping performance of our pump. This shows that looping can improve the efficiency of valveless pumping driven by the Liebau-effect. Further studies are needed to clarify whether this finding may have implications for understanding of the form-function relationship of embryonic hearts. PMID:29367548

Decision feedback loop for tracking a polyphase modulated carrier

NASA Technical Reports Server (NTRS)

Simon, M. K. (Inventor)

1974-01-01

A multiple phase modulated carrier tracking loop for use in a frequency shift keying system is described in which carrier tracking efficiency is improved by making use of the decision signals made on the data phase transmitted in each T-second interval. The decision signal is used to produce a pair of decision-feedback quadrature signals for enhancing the loop's performance in developing a loop phase error signal.

La-CTP: Loop-Aware Routing for Energy-Harvesting Wireless Sensor Networks

PubMed Central

Sun, Guodong; Shang, Xinna; Zuo, Yan

2018-01-01

In emerging energy-harvesting wireless sensor networks (EH-WSN), the sensor nodes can harvest environmental energy to drive their operation, releasing the user’s burden in terms of frequent battery replacement, and even enabling perpetual sensing systems. In EH-WSN applications, usually, the node in energy-harvesting or recharging state has to stop working until it completes the energy replenishment. However, such temporary departures of recharging nodes severely impact the packet routing, and one immediate result is the routing loop problem. Controlling loops in connectivity-intermittent EH-WSN in an efficient way is a big challenge in practice, and so far, users still lack of effective and practicable routing protocols with loop handling. Based on the Collection Tree Protocol (CTP) widely used in traditional wireless sensor networks, this paper proposes a loop-aware routing protocol for real-world EH-WSNs, called La-CTP, which involves a new parent updating metric and a proactive, adaptive beaconing scheme to effectively suppress the occurrence of loops and unlock unavoidable loops, respectively. We constructed a 100-node testbed to evaluate La-CTP, and the experimental results showed its efficacy and efficiency. PMID:29393876

The Perceived Ease of Use and Usefulness of Loop: Evaluation and Content Analysis of a Web-Based Clinical Collaboration System

PubMed Central

Kurahashi, Allison M; Stinson, Jennifer N; van Wyk, Margaret; Luca, Stephanie; Jamieson, Trevor; Weinstein, Peter; Cafazzo, Joseph A; Lokuge, Bhadra; Cohen, Eyal; Rapoport, Adam

2018-01-01

Background Patients with complex health care needs require the expertise of many health care providers. Communication, collaboration, and patient-centered care positively impact care quality and patient outcomes. Few technologies exist that facilitate collaboration between providers across settings of care and also engage the patient. We developed a Web-based clinical collaboration system, Loop, to address this gap. The likelihood of a technological system’s uptake is associated with its perceived ease of use and perceived usefulness. We engaged stakeholders in the conceptualization and development of Loop in an effort to maximize its intuitiveness and utility. Objective This study aimed to report end users’ perceptions about the ease of use and usefulness of Loop captured during usability tests of Loop. Methods Participants represented three user types (patients, caregivers, and health care providers) recruited from three populations (adults with cancer, adolescents and young adults with cancer, and children with medical complexity). We conducted usability testing over three iterative cycles of testing and development in both laboratory-based and off-site environments. We performed a content analysis of usability testing transcripts to summarize and describe participant perceptions about the ease of use and usefulness of Loop. Results Participants enjoyed testing Loop and were able to use the core functions—composing, posting, and reading messages—with little difficulty. They had difficulty interpreting certain visual cues and design elements or the purpose of some features. This difficulty negatively impacted perceived ease of use but was primarily limited to auxiliary features. Participants predicted that Loop could improve the efficiency and effectiveness of communication between care team members; however, this perceived usefulness could be compromised by disruptions to personal workflow such as additional time or task requirements. Conclusions Loop was perceived to have value as a collaboration system; however, usability testing findings indicate that some design and functional elements need to be addressed to improve ease of use. Additionally, participant concerns highlight the need to consider how a system can be implemented so as to minimize impact on workflow and optimize usefulness. PMID:29317386

An open-loop system design for deep space signal processing applications

NASA Astrophysics Data System (ADS)

Tang, Jifei; Xia, Lanhua; Mahapatra, Rabi

2018-06-01

A novel open-loop system design with high performance is proposed for space positioning and navigation signal processing. Divided by functions, the system has four modules, bandwidth selectable data recorder, narrowband signal analyzer, time-delay difference of arrival estimator and ANFIS supplement processor. A hardware-software co-design approach is made to accelerate computing capability and improve system efficiency. Embedded with the proposed signal processing algorithms, the designed system is capable of handling tasks with high accuracy over long period of continuous measurements. The experiment results show the Doppler frequency tracking root mean square error during 3 h observation is 0.0128 Hz, while the TDOA residue analysis in correlation power spectrum is 0.1166 rad.

Dynamic Systems Analysis for Turbine Based Aero Propulsion Systems

NASA Technical Reports Server (NTRS)

Csank, Jeffrey T.

2016-01-01

The aircraft engine design process seeks to optimize the overall system-level performance, weight, and cost for a given concept. Steady-state simulations and data are used to identify trade-offs that should be balanced to optimize the system in a process known as systems analysis. These systems analysis simulations and data may not adequately capture the true performance trade-offs that exist during transient operation. Dynamic systems analysis provides the capability for assessing the dynamic tradeoffs at an earlier stage of the engine design process. The dynamic systems analysis concept, developed tools, and potential benefit are presented in this paper. To provide this capability, the Tool for Turbine Engine Closed-loop Transient Analysis (TTECTrA) was developed to provide the user with an estimate of the closed-loop performance (response time) and operability (high pressure compressor surge margin) for a given engine design and set of control design requirements. TTECTrA along with engine deterioration information, can be used to develop a more generic relationship between performance and operability that can impact the engine design constraints and potentially lead to a more efficient engine.

78 FR 58535 - Hydropower Regulatory Efficiency Act of 2013; Supplemental Notice of Workshop

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-24

... license for hydropower development at non-powered dams and closed-loop pumped storage projects in... for licensing hydropower development at non-powered dams and closed-loop pumped storage projects... closed- loop pumped storage) affect the steps included in a two-year process? 3.9 Should there be a...

In-loop flow [11 C]CO2 fixation and radiosynthesis of N,N'-[11 C]dibenzylurea.

PubMed

Downey, Joseph; Bongarzone, Salvatore; Hader, Stefan; Gee, Antony D

2018-03-01

Cyclotron-produced carbon-11 is a highly valuable radionuclide for the production of positron emission tomography (PET) radiotracers. It is typically produced as relatively unreactive carbon-11 carbon dioxide ([ 11 C]CO 2 ), which is most commonly converted into a more reactive precursor for synthesis of PET radiotracers. The development of [ 11 C]CO 2 fixation methods has more recently enabled the direct radiolabelling of a diverse array of structures directly from [ 11 C]CO 2 , and the advantages afforded by the use of a loop-based system used in 11 C-methylation and 11 C-carboxylation reactions inspired us to apply the [ 11 C]CO 2 fixation "in-loop." In this work, we developed and investigated a new ethylene tetrafluoroethylene (ETFE) loop-based [ 11 C]CO 2 fixation method, enabling the fast and efficient, direct-from-cyclotron, in-loop trapping of [ 11 C]CO 2 using mixed DBU/amine solutions. An optimised protocol was integrated into a proof-of-concept in-loop flow radiosynthesis of N,N'-[ 11 C]dibenzylurea. This reaction exhibited an average 78% trapping efficiency and a crude radiochemical purity of 83% (determined by radio-HPLC), giving an overall nonisolated radiochemical yield of 72% (decay-corrected) within just 3 minutes from end of bombardment. This proof-of-concept reaction has demonstrated that efficient [ 11 C]CO 2 fixation can be achieved in a low-volume (150 μL) ETFE loop and that this can be easily integrated into a rapid in-loop flow radiosynthesis of carbon-11-labelled products. This new in-loop methodology will allow fast radiolabelling reactions to be performed using cheap/disposable ETFE tubing setup (ideal for good manufacturing practice production) thereby contributing to the widespread usage of [ 11 C]CO 2 trapping/fixation reactions for the production of PET radiotracers. © 2017 The Authors. Journal of Labelled Compounds and Radiopharmaceuticals Published by John Wiley & Sons, Ltd.

High precision locating control system based on VCM for Talbot lithography

NASA Astrophysics Data System (ADS)

Yao, Jingwei; Zhao, Lixin; Deng, Qian; Hu, Song

2016-10-01

Aiming at the high precision and efficiency requirements of Z-direction locating in Talbot lithography, a control system based on Voice Coil Motor (VCM) was designed. In this paper, we built a math model of VCM and its moving characteristic was analyzed. A double-closed loop control strategy including position loop and current loop were accomplished. The current loop was implemented by driver, in order to achieve the rapid follow of the system current. The position loop was completed by the digital signal processor (DSP) and the position feedback was achieved by high precision linear scales. Feed forward control and position feedback Proportion Integration Differentiation (PID) control were applied in order to compensate for dynamic lag and improve the response speed of the system. And the high precision and efficiency of the system were verified by simulation and experiments. The results demonstrated that the performance of Z-direction gantry was obviously improved, having high precision, quick responses, strong real-time and easily to expend for higher precision.

78 FR 62322 - Hydropower Regulatory Efficiency Act of 2013; Notice of Rescheduled Two-Year Licensing Process...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-16

... at non-powered dams and closed-loop pumped storage projects in compliance with section 6 of the... process for licensing hydropower development at non-powered dams and closed-loop pumped storage projects...-powered dam versus closed- loop pumped storage) affect the steps included in a two-year process? 3.9...

Modular high-voltage bias generator powered by dual-looped self-adaptive wireless power transmission.

PubMed

Xie, Kai; Huang, An-Feng; Li, Xiao-Ping; Guo, Shi-Zhong; Zhang, Han-Lu

2015-04-01

We proposed a modular high-voltage (HV) bias generator powered by a novel transmitter-sharing inductive coupled wireless power transmission technology, aimed to extend the generator's flexibility and configurability. To solve the problems caused through an uncertain number of modules, a dual-looped self-adaptive control method is proposed that is capable of tracking resonance frequency while maintaining a relatively stable induction voltage for each HV module. The method combines a phase-locked loop and a current feedback loop, which ensures an accurate resonance state and a relatively constant boost ratio for each module, simplifying the architecture of the boost stage and improving the total efficiency. The prototype was built and tested. The input voltage drop of each module is less than 14% if the module number varies from 3 to 10; resonance tracking is completed within 60 ms. The efficiency of the coupling structure reaches up to 95%, whereas the total efficiency approaches 73% for a rated output. Furthermore, this technology can be used in various multi-load wireless power supply applications.

A multi-objective model for closed-loop supply chain optimization and efficient supplier selection in a competitive environment considering quantity discount policy

NASA Astrophysics Data System (ADS)

Jahangoshai Rezaee, Mustafa; Yousefi, Samuel; Hayati, Jamileh

2017-06-01

Supplier selection and allocation of optimal order quantity are two of the most important processes in closed-loop supply chain (CLSC) and reverse logistic (RL). So that providing high quality raw material is considered as a basic requirement for a manufacturer to produce popular products, as well as achieve more market shares. On the other hand, considering the existence of competitive environment, suppliers have to offer customers incentives like discounts and enhance the quality of their products in a competition with other manufacturers. Therefore, in this study, a model is presented for CLSC optimization, efficient supplier selection, as well as orders allocation considering quantity discount policy. It is modeled using multi-objective programming based on the integrated simultaneous data envelopment analysis-Nash bargaining game. In this study, maximizing profit and efficiency and minimizing defective and functions of delivery delay rate are taken into accounts. Beside supplier selection, the suggested model selects refurbishing sites, as well as determining the number of products and parts in each network's sector. The suggested model's solution is carried out using global criteria method. Furthermore, based on related studies, a numerical example is examined to validate it.

Comparison of Iron and Tungsten Based Oxygen Carriers for Hydrogen Production Using Chemical Looping Reforming

NASA Astrophysics Data System (ADS)

Khan, M. N.; Shamim, T.

2017-08-01

Hydrogen production by using a three reactor chemical looping reforming (TRCLR) technology is an innovative and attractive process. Fossil fuels such as methane are the feedstocks used. This process is similar to a conventional steam-methane reforming but occurs in three steps utilizing an oxygen carrier. As the oxygen carrier plays an important role, its selection should be done carefully. In this study, two oxygen carrier materials of base metal iron (Fe) and tungsten (W) are analysed using a thermodynamic model of a three reactor chemical looping reforming plant in Aspen plus. The results indicate that iron oxide has moderate oxygen carrying capacity and is cheaper since it is abundantly available. In terms of hydrogen production efficiency, tungsten oxide gives 4% better efficiency than iron oxide. While in terms of electrical power efficiency, iron oxide gives 4.6% better results than tungsten oxide. Overall, a TRCLR system with iron oxide is 2.6% more efficient and is cost effective than the TRCLR system with tungsten oxide.

Automatic temperature adjustment apparatus

DOEpatents

Chaplin, James E.

1985-01-01

An apparatus for increasing the efficiency of a conventional central space heating system is disclosed. The temperature of a fluid heating medium is adjusted based on a measurement of the external temperature, and a system parameter. The system parameter is periodically modified based on a closed loop process that monitors the operation of the heating system. This closed loop process provides a heating medium temperature value that is very near the optimum for energy efficiency.

Harnessing the power of emerging petascale platforms

NASA Astrophysics Data System (ADS)

Mellor-Crummey, John

2007-07-01

As part of the US Department of Energy's Scientific Discovery through Advanced Computing (SciDAC-2) program, science teams are tackling problems that require computational simulation and modeling at the petascale. A grand challenge for computer science is to develop software technology that makes it easier to harness the power of these systems to aid scientific discovery. As part of its activities, the SciDAC-2 Center for Scalable Application Development Software (CScADS) is building open source software tools to support efficient scientific computing on the emerging leadership-class platforms. In this paper, we describe two tools for performance analysis and tuning that are being developed as part of CScADS: a tool for analyzing scalability and performance, and a tool for optimizing loop nests for better node performance. We motivate these tools by showing how they apply to S3D, a turbulent combustion code under development at Sandia National Laboratory. For S3D, our node performance analysis tool helped uncover several performance bottlenecks. Using our loop nest optimization tool, we transformed S3D's most costly loop nest to reduce execution time by a factor of 2.94 for a processor working on a 503 domain.

Stability analysis and compensation of a boost regulator with two-loop control

NASA Technical Reports Server (NTRS)

Wester, G. W.

1974-01-01

A useful stability measure has been demonstrated by Wester (1973) for switching regulators with a single feedback loop by applying the Nyquist criterion to the approximate loop gain determined by a time-averaging technique. This approach is extended and applied to the characterization, stability analysis, and compensation design of a switching regulator with two-loop control. The role and relative significance of each control loop is clarified on the basis of a description of circuit operation, and the major and minor loops are identified. In view of the inapplicability of linear feedback theory, describing functions of the feedback loops and power stage are derived, using small-signal analysis. Several phenomena revealed from an analysis of the major loop gain are discussed.

The bifurcated stem loop 4 (SL4) is crucial for efficient packaging of mouse mammary tumor virus (MMTV) genomic RNA.

PubMed

Mustafa, Farah; Vivet-Boudou, Valérie; Jabeen, Ayesha; Ali, Lizna M; Kalloush, Rawan M; Marquet, Roland; Rizvi, Tahir A

2018-06-21

Packaging the mouse mammary tumor virus (MMTV) genomic RNA (gRNA) requires the entire 5' untranslated region (UTR) in conjunction with the first 120 nucleotides of the gag gene. This region includes several palindromic (pal) sequence(s) and stable stem loops (SLs). Among these, stem loop 4 (SL4) adopts a bifurcated structure consisting of three stems, two apical loops, and an internal loop. Pal II, located in one of the apical loops, mediates gRNA dimerization, a process intricately linked to packaging. We thus hypothesized that the bifurcated SL4 structure could constitute the major gRNA packaging determinant. To test this hypothesis, the two apical loops and the flanking sequences forming the bifurcated SL4 were individually mutated. These mutations all had deleterious effects on gRNA packaging and propagation. Next, single and compensatory mutants were designed to destabilize then recreate the bifurcated SL4 structure. A structure-function analysis using bioinformatics predictions and RNA chemical probing revealed that mutations that led to the loss of the SL4 bifurcated structure abrogated RNA packaging and propagation, while compensatory mutations that recreated the native SL4 structure restored RNA packaging and propagation to wild type levels. Altogether, our results demonstrate that SL4 constitutes the principal packaging determinant of MMTV gRNA. Our findings further suggest that SL4 acts as a structural switch that can not only differentiate between RNA for translation versus packaging/dimerization, but its location also allows differentiation between spliced and unspliced RNAs during gRNA encapsidation.

Fast Bayesian experimental design: Laplace-based importance sampling for the expected information gain

NASA Astrophysics Data System (ADS)

Beck, Joakim; Dia, Ben Mansour; Espath, Luis F. R.; Long, Quan; Tempone, Raúl

2018-06-01

In calculating expected information gain in optimal Bayesian experimental design, the computation of the inner loop in the classical double-loop Monte Carlo requires a large number of samples and suffers from underflow if the number of samples is small. These drawbacks can be avoided by using an importance sampling approach. We present a computationally efficient method for optimal Bayesian experimental design that introduces importance sampling based on the Laplace method to the inner loop. We derive the optimal values for the method parameters in which the average computational cost is minimized according to the desired error tolerance. We use three numerical examples to demonstrate the computational efficiency of our method compared with the classical double-loop Monte Carlo, and a more recent single-loop Monte Carlo method that uses the Laplace method as an approximation of the return value of the inner loop. The first example is a scalar problem that is linear in the uncertain parameter. The second example is a nonlinear scalar problem. The third example deals with the optimal sensor placement for an electrical impedance tomography experiment to recover the fiber orientation in laminate composites.

Closed loop statistical performance analysis of N-K knock controllers

NASA Astrophysics Data System (ADS)

Peyton Jones, James C.; Shayestehmanesh, Saeed; Frey, Jesse

2017-09-01

The closed loop performance of engine knock controllers cannot be rigorously assessed from single experiments or simulations because knock behaves as a random process and therefore the response belongs to a random distribution also. In this work a new method is proposed for computing the distributions and expected values of the closed loop response, both in steady state and in response to disturbances. The method takes as its input the control law, and the knock propensity characteristic of the engine which is mapped from open loop steady state tests. The method is applicable to the 'n-k' class of knock controllers in which the control action is a function only of the number of cycles n since the last control move, and the number k of knock events that have occurred in this time. A Cumulative Summation (CumSum) based controller falls within this category, and the method is used to investigate the performance of the controller in a deeper and more rigorous way than has previously been possible. The results are validated using onerous Monte Carlo simulations, which confirm both the validity of the method and its high computational efficiency.

Emergy analysis of the recycling options for construction and demolition waste.

PubMed

Yuan, Fang; Shen, Li-yin; Li, Qi-ming

2011-12-01

Construction and demolition (C&D) waste is becoming a major contributor to environmental pollution. In Shanghai, China, the quantity of C&D waste is 2.11E+07 t/yr, which accounts for 45% of the total quantity of solid waste. There has been a growing promotion of recycling C&D waste as an effective way to solve this waste problem. However, the evaluation of the efficiency of recycling C&D waste as a potential source of resources is largely based on traditional economic analysis. The economic analysis emphasizes money instead of the harmony between economic benefit and environmental effects. There is a need for a new strategic approach to investigate the efficiency of recycling C&D waste to achieve the integration between economic, social and environmental effects. Emergy theory can be employed to analyze different recycling options for C&D waste. With reference to the Chinese construction industry, this paper demonstrates that the close-loop recycling option is better than the open-loop recycling option for C&D waste in terms of the integration of social, environmental and sustainable aspects. To evaluate different technology solutions for C&D waste recycling, the emergy theory and method is not limited to a cost-benefit balance but can include economic, social, environmental and sustainable effects. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

Bodenheimer, Annette M.; Meilleur, Flora

Trichoderma reesei Cel7A efficiently hydrolyses cellulose. We report here the crystallographic structures of the wild-type TrCel7A catalytic domain (CD) in an open state and, for the first time, in a closed state. Molecular dynamics (MD) simulations indicate that the loops along the CD tunnel move in concerted motions. Together, the crystallographic and MD data suggest that the CD cycles between the tense and relaxed forms that are characteristic of work producing enzymes. Analysis of the interactions formed by R251 provides a structural rationale for the concurrent decrease in product inhibition and catalytic efficiency measured for product-binding site mutants.

A Triple-Loop Inductive Power Transmission System for Biomedical Applications.

PubMed

Lee, Byunghun; Kiani, Mehdi; Ghovanloo, Maysam

2016-02-01

A triple-loop wireless power transmission (WPT) system equipped with closed-loop global power control, adaptive transmitter (Tx) resonance compensation (TRC), and automatic receiver (Rx) resonance tuning (ART) is presented. This system not only opposes coupling and load variations but also compensates for changes in the environment surrounding the inductive link to enhance power transfer efficiency (PTE) in applications such as implantable medical devices (IMDs). The Tx was built around a commercial off-the-shelf (COTS) radio-frequency identification (RFID) reader, operating at 13.56 MHz. A local Tx loop finds the optimal capacitance in parallel with the Tx coil by adjusting a varactor. A global power control loop maintains the received power at a desired level in the presence of changes in coupling distance, coil misalignments, and loading. Moreover, a local Rx loop is implemented inside a power management integrated circuit (PMIC) to avoid PTE degradation due to the Rx coil surrounding environment and process variations. The PMIC was fabricated in a 0.35- μm 4M2P standard CMOS process with 2.54 mm(2) active area. Measurement results show that the proposed triple-loop system improves the overall PTE by up to 10.5% and 4.7% compared to a similar open- and single closed-loop system, respectively, at nominal coil distance of 2 cm. The added TRC and ART loops contribute 2.3% and 1.4% to the overall PTE of 13.5%, respectively. This is the first WPT system to include three loops to dynamically compensate for environment and circuit variations and improve the overall power efficiency all the way from the driver output in Tx to the load in Rx.

Analysis of the link between the redox state and enzymatic activity of the HtrA (DegP) protein from Escherichia coli.

PubMed

Koper, Tomasz; Polit, Agnieszka; Sobiecka-Szkatula, Anna; Wegrzyn, Katarzyna; Scire, Andrea; Figaj, Donata; Kadzinski, Leszek; Zarzecka, Urszula; Zurawa-Janicka, Dorota; Banecki, Bogdan; Lesner, Adam; Tanfani, Fabio; Lipinska, Barbara; Skorko-Glonek, Joanna

2015-01-01

Bacterial HtrAs are proteases engaged in extracytoplasmic activities during stressful conditions and pathogenesis. A model prokaryotic HtrA (HtrA/DegP from Escherichia coli) requires activation to cleave its substrates efficiently. In the inactive state of the enzyme, one of the regulatory loops, termed LA, forms inhibitory contacts in the area of the active center. Reduction of the disulfide bond located in the middle of LA stimulates HtrA activity in vivo suggesting that this S-S bond may play a regulatory role, although the mechanism of this stimulation is not known. Here, we show that HtrA lacking an S-S bridge cleaved a model peptide substrate more efficiently and exhibited a higher affinity for a protein substrate. An LA loop lacking the disulfide was more exposed to the solvent; hence, at least some of the interactions involving this loop must have been disturbed. The protein without S-S bonds demonstrated lower thermal stability and was more easily converted to a dodecameric active oligomeric form. Thus, the lack of the disulfide within LA affected the stability and the overall structure of the HtrA molecule. In this study, we have also demonstrated that in vitro human thioredoxin 1 is able to reduce HtrA; thus, reduction of HtrA can be performed enzymatically.

Dynamic impedance compensation for wireless power transfer using conjugate power

NASA Astrophysics Data System (ADS)

Liu, Suqi; Tan, Jianping; Wen, Xue

2018-02-01

Wireless power transfer (WPT) via coupled magnetic resonances has been in development for over a decade. However, the frequency splitting phenomenon occurs in the over-coupled region. Thus, the output power of the two-coil system achieves the maximum output power at the two splitting angular frequencies, and not at the natural resonant angular frequency. According to the maximum power transfer theorem, the impedance compensation method was adopted in many WPT projects. However, it remains a challenge to achieve the maximum output power and transmission efficiency in a fixed-frequency mode. In this study, dynamic impedance compensation for WPT was presented by utilizing the compensator within a virtual three-coil WPT system. First, the circuit model was established and transfer characteristics of a system were studied by utilizing circuit theories. Second, the power superposition of the WPT system was carefully researched. When a pair of compensating coils was inserted into the transmitter loop, the conjugate power of the compensator loop was created via magnetic coupling of the two compensating coils that insert into the transmitter loop. The mechanism for dynamic impedance compensation for wireless power transfer was then provided by investigating a virtual three-coil WPT system. Finally, the experimental circuit of a virtual three-coil WPT system was designed, and experimental results are consistent with the theoretical analysis, which achieves the maximum output power and transmission efficiency.

Reducing full one-loop amplitudes to scalar integrals at the integrand level

NASA Astrophysics Data System (ADS)

Ossola, Giovanni; Papadopoulos, Costas G.; Pittau, Roberto

2007-02-01

We show how to extract the coefficients of the 4-, 3-, 2- and 1-point one-loop scalar integrals from the full one-loop amplitude of arbitrary scattering processes. In a similar fashion, also the rational terms can be derived. Basically no information on the analytical structure of the amplitude is required, making our method appealing for an efficient numerical implementation.

[Deletion of a dynamic surface loop improves thermostability of (R)-selective amine transaminase from Aspergillus terreus].

PubMed

Xie, Dongfang; Lv, Changjiang; Fang, Hui; Yang, Weikang; Hu, Sheng; Zhao, Weirui; Huang, Jun; Mei, Lehe

2017-12-25

Chiral amines are important building blocks for the synthesis of pharmaceutical products and fine chemicals. Highly stereoselective synthesis of chiral amines compounds through asymmetric amination has attracted more and more attention. ω-transaminases (ω-TAs) are a promising class of natural biocatalysts which provide an efficient and environment-friendly access to production of chiral amines with stringent enantioselectivity and excellent catalytic efficiency. Compared with (S)-ω-TA, the research focused on (R)-ω-TA was relatively less. However, increasing demand for chiral (R)-amines as pharmaceutical intermediates has rendered industrial applications of (R)-ω-TA more attractive. Improving the thermostability of (R)-ω-TA with potential biotechnological application will facilitate the preparation of chiral amines. In this study, the dynamic surface loop with higher B-factor from Aspergillus terreus (R)-ω-TA was predicted by two computer softwares (PyMOL and YASARA). Then mutant enzymes were obtained by deleting amino acid residues of a dynamic surface loop using site-directed mutagenesis. The results showed that the best two mutants R131del and P132-E133del improved thermostability by 2.6 ℃ and 0.9 ℃ in T₅₀¹⁰ (41.1 ℃ and 39.4 ℃, respectively), and 2.2-fold and 1.5-fold in half-life (t1/2) at 40 ℃ (15.0 min and 10.0 min, respectively), compared to that of wild type. Furtherly, the thermostability mechanism of the mutant enzymes was investigated by molecular dynamics (MD) simulation and intermolecular interaction analysis. R131del in the loop region has lower root mean square fluctuation (RMSF) than the wild type at 400 K for 10 ns, and mutant enzyme P132-E133del increases four hydrogen bonds in the loop region. In this study, we obtain two stability-increased mutants of (R)-ω-TA from A. terreus by deleting its dynamic surface loop and also provide methodological guidance for the use of rational design to enhance the thermal stability of other enzymes.

Network efficient power control for wireless communication systems.

PubMed

Campos-Delgado, Daniel U; Luna-Rivera, Jose Martin; Martinez-Sánchez, C J; Gutierrez, Carlos A; Tecpanecatl-Xihuitl, J L

2014-01-01

We introduce a two-loop power control that allows an efficient use of the overall power resources for commercial wireless networks based on cross-layer optimization. This approach maximizes the network's utility in the outer-loop as a function of the averaged signal to interference-plus-noise ratio (SINR) by considering adaptively the changes in the network characteristics. For this purpose, the concavity property of the utility function was verified with respect to the SINR, and an iterative search was proposed with guaranteed convergence. In addition, the outer-loop is in charge of selecting the detector that minimizes the overall power consumption (transmission and detection). Next the inner-loop implements a feedback power control in order to achieve the optimal SINR in the transmissions despite channel variations and roundtrip delays. In our proposal, the utility maximization process and detector selection and feedback power control are decoupled problems, and as a result, these strategies are implemented at two different time scales in the two-loop framework. Simulation results show that substantial utility gains may be achieved by improving the power management in the wireless network.

Network Efficient Power Control for Wireless Communication Systems

PubMed Central

Campos-Delgado, Daniel U.; Luna-Rivera, Jose Martin; Martinez-Sánchez, C. J.; Gutierrez, Carlos A.; Tecpanecatl-Xihuitl, J. L.

2014-01-01

We introduce a two-loop power control that allows an efficient use of the overall power resources for commercial wireless networks based on cross-layer optimization. This approach maximizes the network's utility in the outer-loop as a function of the averaged signal to interference-plus-noise ratio (SINR) by considering adaptively the changes in the network characteristics. For this purpose, the concavity property of the utility function was verified with respect to the SINR, and an iterative search was proposed with guaranteed convergence. In addition, the outer-loop is in charge of selecting the detector that minimizes the overall power consumption (transmission and detection). Next the inner-loop implements a feedback power control in order to achieve the optimal SINR in the transmissions despite channel variations and roundtrip delays. In our proposal, the utility maximization process and detector selection and feedback power control are decoupled problems, and as a result, these strategies are implemented at two different time scales in the two-loop framework. Simulation results show that substantial utility gains may be achieved by improving the power management in the wireless network. PMID:24683350

Chemical Looping Technology: Oxygen Carrier Characteristics.

PubMed

Luo, Siwei; Zeng, Liang; Fan, Liang-Shih

2015-01-01

Chemical looping processes are characterized as promising carbonaceous fuel conversion technologies with the advantages of manageable CO2 capture and high energy conversion efficiency. Depending on the chemical looping reaction products generated, chemical looping technologies generally can be grouped into two types: chemical looping full oxidation (CLFO) and chemical looping partial oxidation (CLPO). In CLFO, carbonaceous fuels are fully oxidized to CO2 and H2O, as typically represented by chemical looping combustion with electricity as the primary product. In CLPO, however, carbonaceous fuels are partially oxidized, as typically represented by chemical looping gasification with syngas or hydrogen as the primary product. Both CLFO and CLPO share similar operational features; however, the optimum process configurations and the specific oxygen carriers used between them can vary significantly. Progress in both CLFO and CLPO is reviewed and analyzed with specific focus on oxygen carrier developments that characterize these technologies.

Closed-Loop- and Decision-Assist-Guided Fluid Therapy of Human Hemorrhage.

PubMed

Hundeshagen, Gabriel; Kramer, George C; Ribeiro Marques, Nicole; Salter, Michael G; Koutrouvelis, Aristides K; Li, Husong; Solanki, Daneshvari R; Indrikovs, Alexander; Seeton, Roger; Henkel, Sheryl N; Kinsky, Michael P

2017-10-01

We sought to evaluate the efficacy, efficiency, and physiologic consequences of automated, endpoint-directed resuscitation systems and compare them to formula-based bolus resuscitation. Experimental human hemorrhage and resuscitation. Clinical research laboratory. Healthy volunteers. Subjects (n = 7) were subjected to hemorrhage and underwent a randomized fluid resuscitation scheme on separate visits 1) formula-based bolus resuscitation; 2) semiautonomous (decision assist) fluid administration; and 3) fully autonomous (closed loop) resuscitation. Hemodynamic variables, volume shifts, fluid balance, and cardiac function were monitored during hemorrhage and resuscitation. Treatment modalities were compared based on resuscitation efficacy and efficiency. All approaches achieved target blood pressure by 60 minutes. Following hemorrhage, the total amount of infused fluid (bolus resuscitation: 30 mL/kg, decision assist: 5.6 ± 3 mL/kg, closed loop: 4.2 ± 2 mL/kg; p < 0.001), plasma volume, extravascular volume (bolus resuscitation: 17 ± 4 mL/kg, decision assist: 3 ± 1 mL/kg, closed loop: -0.3 ± 0.3 mL/kg; p < 0.001), body weight, and urinary output remained stable under decision assist and closed loop and were significantly increased under bolus resuscitation. Mean arterial pressure initially decreased further under bolus resuscitation (-10 mm Hg; p < 0.001) and was lower under bolus resuscitation than closed loop at 20 minutes (bolus resuscitation: 57 ± 2 mm Hg, closed loop: 69 ± 4 mm Hg; p = 0.036). Colloid osmotic pressure (bolus resuscitation: 19.3 ± 2 mm Hg, decision assist, closed loop: 24 ± 0.4 mm Hg; p < 0.05) and hemoglobin concentration were significantly decreased after bolus fluid administration. We define efficacy of decision-assist and closed-loop resuscitation in human hemorrhage. In comparison with formula-based bolus resuscitation, both semiautonomous and autonomous approaches were more efficient in goal-directed resuscitation of hemorrhage. They provide favorable conditions for the avoidance of over-resuscitation and its adverse clinical sequelae. Decision-assist and closed-loop resuscitation algorithms are promising technological solutions for constrained environments and areas of limited resources.

Efficient dynamic modeling of manipulators containing closed kinematic loops

NASA Astrophysics Data System (ADS)

Ferretti, Gianni; Rocco, Paolo

An approach to efficiently solve the forward dynamics problem for manipulators containing closed chains is proposed. The two main distinctive features of this approach are: the dynamics of the equivalent open loop tree structures (any closed loop can be in general modeled by imposing some additional kinematic constraints to a suitable tree structure) is computed through an efficient Newton Euler formulation; the constraint equations relative to the most commonly adopted closed chains in industrial manipulators are explicitly solved, thus, overcoming the redundancy of Lagrange's multipliers method while avoiding the inefficiency due to a numerical solution of the implicit constraint equations. The constraint equations considered for an explicit solution are those imposed by articulated gear mechanisms and planar closed chains (pantograph type structures). Articulated gear mechanisms are actually used in all industrial robots to transmit motion from actuators to links, while planar closed chains are usefully employed to increase the stiffness of the manipulators and their load capacity, as well to reduce the kinematic coupling of joint axes. The accuracy and the efficiency of the proposed approach are shown through a simulation test.

In silico Analysis of HIV-1 Env-gp120 Reveals Structural Bases for Viral Adaptation in Growth-Restrictive Cells

PubMed Central

Yokoyama, Masaru; Nomaguchi, Masako; Doi, Naoya; Kanda, Tadahito; Adachi, Akio; Sato, Hironori

2016-01-01

Variable V1/V2 and V3 loops on human immunodeficiency virus type 1 (HIV-1) envelope-gp120 core play key roles in modulating viral competence to recognize two infection receptors, CD4 and chemokine-receptors. However, molecular bases for the modulation largely remain unclear. To address these issues, we constructed structural models for a full-length gp120 in CD4-free and -bound states. The models showed topologies of gp120 surface loop that agree with those in reported structural data. Molecular dynamics simulation showed that in the unliganded state, V1/V2 loop settled into a thermodynamically stable arrangement near V3 loop for conformational masking of V3 tip, a potent neutralization epitope. In the CD4-bound state, however, V1/V2 loop was rearranged near the bound CD4 to support CD4 binding. In parallel, cell-based adaptation in the absence of anti-viral antibody pressures led to the identification of amino acid substitutions that individually enhance viral entry and growth efficiencies in association with reduced sensitivity to CCR5 antagonist TAK-779. Notably, all these substitutions were positioned on the receptors binding surfaces in V1/V2 or V3 loop. In silico structural studies predicted some physical changes of gp120 by substitutions with alterations in viral replication phenotypes. These data suggest that V1/V2 loop is critical for creating a gp120 structure that masks co-receptor binding site compatible with maintenance of viral infectivity, and for tuning a functional balance of gp120 between immune escape ability and infectivity to optimize HIV-1 replication fitness. PMID:26903989

Efficient Ligation of the Schistosoma Hammerhead Ribozyme †

PubMed Central

Canny, Marella D.; Jucker, Fiona M.; Pardi, Arthur

2011-01-01

The hammerhead ribozyme from Schistosoma mansoni is the best characterized of the natural hammerhead ribozymes. Biophysical, biochemical, and structural studies have shown that the formation of the loop-loop tertiary interaction between stems I and II alters the global folding, cleavage kinetics, and conformation of the catalytic core of this hammerhead, leading to a ribozyme that is readily cleaved under physiological conditions. This study investigates the ligation kinetics and the internal equilibrium between cleavage and ligation for the Schistosoma hammerhead. Single turnover kinetic studies on a construct where the ribozyme cleaves and ligates substrate(s) in trans showed up to 23% ligation when starting from fully cleaved products. This was achieved by a ~2,000-fold increase in the rate of ligation compared to a minimal hammerhead without the loop-loop tertiary interaction, yielding an internal equilibrium that ranges from 2–3 at physiological Mg2+ ion concentrations (0.1 –1 mM). Thus, the natural Schistosoma hammerhead ribozyme is almost as efficient at ligation as it is at cleavage. The results here are consistent with a model where formation of the loop-loop tertiary interaction leads to a higher population of catalytically active molecules, and where formation of this tertiary interaction has a much larger effect on the ligation than the cleavage activity of the Schistosoma hammerhead ribozyme. PMID:17319693

Conformational trapping of mismatch recognition complex MSH2/MSH3 on repair-resistant DNA loops.

PubMed

Lang, Walter H; Coats, Julie E; Majka, Jerzy; Hura, Greg L; Lin, Yuyen; Rasnik, Ivan; McMurray, Cynthia T

2011-10-18

Insertion and deletion of small heteroduplex loops are common mutations in DNA, but why some loops are prone to mutation and others are efficiently repaired is unknown. Here we report that the mismatch recognition complex, MSH2/MSH3, discriminates between a repair-competent and a repair-resistant loop by sensing the conformational dynamics of their junctions. MSH2/MSH3 binds, bends, and dissociates from repair-competent loops to signal downstream repair. Repair-resistant Cytosine-Adenine-Guanine (CAG) loops adopt a unique DNA junction that traps nucleotide-bound MSH2/MSH3, and inhibits its dissociation from the DNA. We envision that junction dynamics is an active participant and a conformational regulator of repair signaling, and governs whether a loop is removed by MSH2/MSH3 or escapes to become a precursor for mutation.

The GSFC NASTRAN thermal analyzer new capabilities

NASA Technical Reports Server (NTRS)

Lee, H. P.; Harder, R. L.

1976-01-01

An overview of four analysis capabilities, which developed and integrated into the NASTRAN Thermal Analyzer, is given. To broaden the scope of applications, these additions provide the NTA users with the following capabilities: (1) simulating a thermal louver as a means of the passive thermal control, (2) simulating a fluid loop for transporting energy as a means of the active thermal control, (3) condensing a large sized finite element model for an efficient transient thermal analysis, and (4) entering multiple boundary condition sets in a single submission for execution in steady state thermal analyses.

Efficiently computing exact geodesic loops within finite steps.

PubMed

Xin, Shi-Qing; He, Ying; Fu, Chi-Wing

2012-06-01

Closed geodesics, or geodesic loops, are crucial to the study of differential topology and differential geometry. Although the existence and properties of closed geodesics on smooth surfaces have been widely studied in mathematics community, relatively little progress has been made on how to compute them on polygonal surfaces. Most existing algorithms simply consider the mesh as a graph and so the resultant loops are restricted only on mesh edges, which are far from the actual geodesics. This paper is the first to prove the existence and uniqueness of geodesic loop restricted on a closed face sequence; it contributes also with an efficient algorithm to iteratively evolve an initial closed path on a given mesh into an exact geodesic loop within finite steps. Our proposed algorithm takes only an O(k) space complexity and an O(mk) time complexity (experimentally), where m is the number of vertices in the region bounded by the initial loop and the resultant geodesic loop, and k is the average number of edges in the edge sequences that the evolving loop passes through. In contrast to the existing geodesic curvature flow methods which compute an approximate geodesic loop within a predefined threshold, our method is exact and can apply directly to triangular meshes without needing to solve any differential equation with a numerical solver; it can run at interactive speed, e.g., in the order of milliseconds, for a mesh with around 50K vertices, and hence, significantly outperforms existing algorithms. Actually, our algorithm could run at interactive speed even for larger meshes. Besides the complexity of the input mesh, the geometric shape could also affect the number of evolving steps, i.e., the performance. We motivate our algorithm with an interactive shape segmentation example shown later in the paper.

Stability of a stem-loop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA.

PubMed Central

Honda, M; Brown, E A; Lemon, S M

1996-01-01

The initiation of translation on the positive-sense RNA genome of hepatitis C virus (HCV) is directed by an internal ribosomal entry site (IRES) that occupies most of the 341-nt 5' nontranslated RNA (5'NTR). Previous studies indicate that this IRES differs from picornaviral IRESs in that its activity is dependent upon RNA sequence downstream of the initiator AUG. Here, we demonstrate that the initiator AUG of HCV is located within a stem-loop (stem-loop IV) involving nt -12 to +12 (with reference to the AUG). This structure is conserved among HCV strains, and is present in the 5'NTR of the phylogenetically distant GB virus B. Mutant, nearly genome-length RNAs containing nucleotide substitutions predicted to enhance the stability of stem-loop IV were generally deficient in cap-independent translation both in vitro and in vivo. Additional mutations that destabilize the stem-loop restored translation to normal. Thus, the stability of the stem-loop is strongly but inversely correlated with the efficiency of internal initiation of translation. In contrast, mutations that stabilize this stem-loop had comparatively little effect on translation of 5' truncated RNAs by scanning ribosomes, suggesting that internal initiation of translation follows binding of the 40S ribosome directly at the site of stem-loop IV. Because stem-loop IV is not required for internal entry of ribosomes but is able to regulate this process, we speculate that it may be stabilized by interactions with a viral protein, providing a mechanism for feedback regulation of translation, which may be important for viral persistence. PMID:8849773

Efficient micromagnetics for magnetic storage devices

NASA Astrophysics Data System (ADS)

Escobar Acevedo, Marco Antonio

Micromagnetics is an important component for advancing the magnetic nanostructures understanding and design. Numerous existing and prospective magnetic devices rely on micromagnetic analysis, these include hard disk drives, magnetic sensors, memories, microwave generators, and magnetic logic. The ability to examine, describe, and predict the magnetic behavior, and macroscopic properties of nanoscale magnetic systems is essential for improving the existing devices, for progressing in their understanding, and for enabling new technologies. This dissertation describes efficient micromagnetic methods as required for magnetic storage analysis. Their performance and accuracy is demonstrated by studying realistic, complex, and relevant micromagnetic system case studies. An efficient methodology for dynamic micromagnetics in large scale simulations is used to study the writing process in a full scale model of a magnetic write head. An efficient scheme, tailored for micromagnetics, to find the minimum energy state on a magnetic system is presented. This scheme can be used to calculate hysteresis loops. An efficient scheme, tailored for micromagnetics, to find the minimum energy path between two stable states on a magnetic system is presented. This minimum energy path is intimately related to the thermal stability.

Displacement Fields and Self-Energies of Circular and Polygonal Dislocation Loops in Homogeneous and Layered Anisotropic Solids

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

Gao, Yanfei; Larson, Ben C.

There are large classes of materials problems that involve the solutions of stress, displacement, and strain energy of dislocation loops in elastically anisotropic solids, including increasingly detailed investigations of the generation and evolution of irradiation induced defect clusters ranging in sizes from the micro- to meso-scopic length scales. Based on a two-dimensional Fourier transform and Stroh formalism that are ideal for homogeneous and layered anisotropic solids, we have developed robust and computationally efficient methods to calculate the displacement fields for circular and polygonal dislocation loops. Using the homogeneous nature of the Green tensor of order -1, we have shown thatmore » the displacement and stress fields of dislocation loops can be obtained by numerical quadrature of a line integral. In addition, it is shown that the sextuple integrals associated with the strain energy of loops can be represented by the product of a pre-factor containing elastic anisotropy effects and a universal term that is singular and equal to that for elastic isotropic case. Furthermore, we have found that the self-energy pre-factor of prismatic loops is identical to the effective modulus of normal contact, and the pre-factor of shear loops differs from the effective indentation modulus in shear by only a few percent. These results provide a convenient method for examining dislocation reaction energetic and efficient procedures for numerical computation of local displacements and stresses of dislocation loops, both of which play integral roles in quantitative defect analyses within combined experimental–theoretical investigations.« less

Displacement Fields and Self-Energies of Circular and Polygonal Dislocation Loops in Homogeneous and Layered Anisotropic Solids

DOE PAGES

Gao, Yanfei; Larson, Ben C.

2015-06-19

There are large classes of materials problems that involve the solutions of stress, displacement, and strain energy of dislocation loops in elastically anisotropic solids, including increasingly detailed investigations of the generation and evolution of irradiation induced defect clusters ranging in sizes from the micro- to meso-scopic length scales. Based on a two-dimensional Fourier transform and Stroh formalism that are ideal for homogeneous and layered anisotropic solids, we have developed robust and computationally efficient methods to calculate the displacement fields for circular and polygonal dislocation loops. Using the homogeneous nature of the Green tensor of order -1, we have shown thatmore » the displacement and stress fields of dislocation loops can be obtained by numerical quadrature of a line integral. In addition, it is shown that the sextuple integrals associated with the strain energy of loops can be represented by the product of a pre-factor containing elastic anisotropy effects and a universal term that is singular and equal to that for elastic isotropic case. Furthermore, we have found that the self-energy pre-factor of prismatic loops is identical to the effective modulus of normal contact, and the pre-factor of shear loops differs from the effective indentation modulus in shear by only a few percent. These results provide a convenient method for examining dislocation reaction energetic and efficient procedures for numerical computation of local displacements and stresses of dislocation loops, both of which play integral roles in quantitative defect analyses within combined experimental–theoretical investigations.« less

Hippocampal closed-loop modeling and implications for seizure stimulation design

NASA Astrophysics Data System (ADS)

Sandler, Roman A.; Song, Dong; Hampson, Robert E.; Deadwyler, Sam A.; Berger, Theodore W.; Marmarelis, Vasilis Z.

2015-10-01

Objective. Traditional hippocampal modeling has focused on the series of feedforward synapses known as the trisynaptic pathway. However, feedback connections from CA1 back to the hippocampus through the entorhinal cortex (EC) actually make the hippocampus a closed-loop system. By constructing a functional closed-loop model of the hippocampus, one may learn how both physiological and epileptic oscillations emerge and design efficient neurostimulation patterns to abate such oscillations. Approach. Point process input-output models where estimated from recorded rodent hippocampal data to describe the nonlinear dynamical transformation from CA3 → CA1, via the schaffer-collateral synapse, and CA1 → CA3 via the EC. Each Volterra-like subsystem was composed of linear dynamics (principal dynamic modes) followed by static nonlinearities. The two subsystems were then wired together to produce the full closed-loop model of the hippocampus. Main results. Closed-loop connectivity was found to be necessary for the emergence of theta resonances as seen in recorded data, thus validating the model. The model was then used to identify frequency parameters for the design of neurostimulation patterns to abate seizures. Significance. Deep-brain stimulation (DBS) is a new and promising therapy for intractable seizures. Currently, there is no efficient way to determine optimal frequency parameters for DBS, or even whether periodic or broadband stimuli are optimal. Data-based computational models have the potential to be used as a testbed for designing optimal DBS patterns for individual patients. However, in order for these models to be successful they must incorporate the complex closed-loop structure of the seizure focus. This study serves as a proof-of-concept of using such models to design efficient personalized DBS patterns for epilepsy.

Hippocampal closed-loop modeling and implications for seizure stimulation design.

PubMed

Sandler, Roman A; Song, Dong; Hampson, Robert E; Deadwyler, Sam A; Berger, Theodore W; Marmarelis, Vasilis Z

2015-10-01

Traditional hippocampal modeling has focused on the series of feedforward synapses known as the trisynaptic pathway. However, feedback connections from CA1 back to the hippocampus through the entorhinal cortex (EC) actually make the hippocampus a closed-loop system. By constructing a functional closed-loop model of the hippocampus, one may learn how both physiological and epileptic oscillations emerge and design efficient neurostimulation patterns to abate such oscillations. Point process input-output models where estimated from recorded rodent hippocampal data to describe the nonlinear dynamical transformation from CA3 → CA1, via the schaffer-collateral synapse, and CA1 → CA3 via the EC. Each Volterra-like subsystem was composed of linear dynamics (principal dynamic modes) followed by static nonlinearities. The two subsystems were then wired together to produce the full closed-loop model of the hippocampus. Closed-loop connectivity was found to be necessary for the emergence of theta resonances as seen in recorded data, thus validating the model. The model was then used to identify frequency parameters for the design of neurostimulation patterns to abate seizures. Deep-brain stimulation (DBS) is a new and promising therapy for intractable seizures. Currently, there is no efficient way to determine optimal frequency parameters for DBS, or even whether periodic or broadband stimuli are optimal. Data-based computational models have the potential to be used as a testbed for designing optimal DBS patterns for individual patients. However, in order for these models to be successful they must incorporate the complex closed-loop structure of the seizure focus. This study serves as a proof-of-concept of using such models to design efficient personalized DBS patterns for epilepsy.

Hippocampal Closed-Loop Modeling and Implications for Seizure Stimulation Design

PubMed Central

Sandler, Roman A.; Song, Dong; Hampson, Robert E.; Deadwyler, Sam A.; Berger, Theodore W.; Marmarelis, Vasilis Z.

2016-01-01

Objective Traditional hippocampal modeling has focused on the series of feedforward synapses known as the trisynaptic pathway. However, feedback connections from CA1 back to the hippocampus through the Entorhinal Cortex (EC) actually make the hippocampus a closed-loop system. By constructing a functional closed-loop model of the hippocampus, one may learn how both physiological and epileptic oscillations emerge and design efficient neurostimulation patterns to abate such oscillations. Approach Point process input-output models where estimated from recorded rodent hippocampal data to describe the nonlinear dynamical transformation from CA3→CA1, via the Schaffer-Collateral synapse, and CA1→CA3 via the EC. Each Volterra-like subsystem was composed of linear dynamics (Principal Dynamic Modes) followed by static nonlinearities. The two subsystems were then wired together to produce the full closed-loop model of the hippocampus. Main Results Closed-loop connectivity was found to be necessary for the emergence of theta resonances as seen in recorded data, thus validating the model. The model was then used to identify frequency parameters for the design of neurostimulation patterns to abate seizures. Significance DBS is a new and promising therapy for intractable seizures. Currently, there is no efficient way to determine optimal frequency parameters for DBS, or even whether periodic or broadband stimuli are optimal. Data-based computational models have the potential to be used as a testbed for designing optimal DBS patterns for individual patients. However, in order for these models to be successful they must incorporate the complex closed-loop structure of the seizure focus. This study serves as a proof-of-concept of using such models to design efficient personalized DBS patterns for epilepsy. PMID:26355815

Constrained Combinatorial Libraries of Gp2 Proteins Enhance Discovery of PD-L1 Binders.

PubMed

Kruziki, Max A; Sarma, Vidur; Hackel, Benjamin J

2018-06-05

Engineered protein ligands are used for molecular therapy, diagnostics, and industrial biotechnology. The Gp2 domain is a 45-amino acid scaffold that has been evolved for specific, high-affinity binding to multiple targets by diversification of two solvent-exposed loops. Inspired by sitewise enrichment of select amino acids, including cysteine pairs, in earlier Gp2 discovery campaigns, we hypothesized that the breadth and efficiency of de novo Gp2 discovery will be aided by sitewise amino acid constraint within combinatorial library design. We systematically constructed eight libraries and comparatively evaluated their efficacy for binder discovery via yeast display against a panel of targets. Conservation of a cysteine pair at the termini of the first diversified paratope loop increased binder discovery 16-fold ( p < 0.001). Yet two other libraries with conserved cysteine pairs, within the second loop or an interloop pair, did not aid discovery thereby indicating site-specific impact. Via a yeast display protease resistance assay, Gp2 variants from the loop one cysteine pair library were 3.3 ± 2.1-fold ( p = 0.005) more stable than nonconstrained variants. Sitewise constraint of noncysteine residues-guided by previously evolved binders, natural Gp2 homology, computed stability, and structural analysis-did not aid discovery. A panel of binders to programmed death ligand 1 (PD-L1), a key target in cancer immunotherapy, were discovered from the loop 1 cysteine constraint library. Affinity maturation via loop walking resulted in strong, specific cellular PD-L1 affinity ( K d = 6-9 nM).

In‐loop flow [11C]CO2 fixation and radiosynthesis of N,N′‐[11C]dibenzylurea

PubMed Central

Downey, Joseph; Bongarzone, Salvatore; Hader, Stefan

2017-01-01

Cyclotron‐produced carbon‐11 is a highly valuable radionuclide for the production of positron emission tomography (PET) radiotracers. It is typically produced as relatively unreactive carbon‐11 carbon dioxide ([11C]CO2), which is most commonly converted into a more reactive precursor for synthesis of PET radiotracers. The development of [11C]CO2 fixation methods has more recently enabled the direct radiolabelling of a diverse array of structures directly from [11C]CO2, and the advantages afforded by the use of a loop‐based system used in 11C‐methylation and 11C‐carboxylation reactions inspired us to apply the [11C]CO2 fixation “in‐loop.” In this work, we developed and investigated a new ethylene tetrafluoroethylene (ETFE) loop‐based [11C]CO2 fixation method, enabling the fast and efficient, direct‐from‐cyclotron, in‐loop trapping of [11C]CO2 using mixed DBU/amine solutions. An optimised protocol was integrated into a proof‐of‐concept in‐loop flow radiosynthesis of N,N′‐[11C]dibenzylurea. This reaction exhibited an average 78% trapping efficiency and a crude radiochemical purity of 83% (determined by radio‐HPLC), giving an overall nonisolated radiochemical yield of 72% (decay‐corrected) within just 3 minutes from end of bombardment. This proof‐of‐concept reaction has demonstrated that efficient [11C]CO2 fixation can be achieved in a low‐volume (150 μL) ETFE loop and that this can be easily integrated into a rapid in‐loop flow radiosynthesis of carbon‐11–labelled products. This new in‐loop methodology will allow fast radiolabelling reactions to be performed using cheap/disposable ETFE tubing setup (ideal for good manufacturing practice production) thereby contributing to the widespread usage of [11C]CO2 trapping/fixation reactions for the production of PET radiotracers. PMID:28977686

Solar Tutorial and Annotation Resource (STAR)

NASA Astrophysics Data System (ADS)

Showalter, C.; Rex, R.; Hurlburt, N. E.; Zita, E. J.

2009-12-01

We have written a software suite designed to facilitate solar data analysis by scientists, students, and the public, anticipating enormous datasets from future instruments. Our “STAR" suite includes an interactive learning section explaining 15 classes of solar events. Users learn software tools that exploit humans’ superior ability (over computers) to identify many events. Annotation tools include time slice generation to quantify loop oscillations, the interpolation of event shapes using natural cubic splines (for loops, sigmoids, and filaments) and closed cubic splines (for coronal holes). Learning these tools in an environment where examples are provided prepares new users to comfortably utilize annotation software with new data. Upon completion of our tutorial, users are presented with media of various solar events and asked to identify and annotate the images, to test their mastery of the system. Goals of the project include public input into the data analysis of very large datasets from future solar satellites, and increased public interest and knowledge about the Sun. In 2010, the Solar Dynamics Observatory (SDO) will be launched into orbit. SDO’s advancements in solar telescope technology will generate a terabyte per day of high-quality data, requiring innovation in data management. While major projects develop automated feature recognition software, so that computers can complete much of the initial event tagging and analysis, still, that software cannot annotate features such as sigmoids, coronal magnetic loops, coronal dimming, etc., due to large amounts of data concentrated in relatively small areas. Previously, solar physicists manually annotated these features, but with the imminent influx of data it is unrealistic to expect specialized researchers to examine every image that computers cannot fully process. A new approach is needed to efficiently process these data. Providing analysis tools and data access to students and the public have proven efficient in similar astrophysical projects (e.g. the “Galaxy Zoo.”) For “crowdsourcing” to be effective for solar research, the public needs knowledge and skills to recognize and annotate key events on the Sun. Our tutorial can provide this training, with over 200 images and 18 movies showing examples of active regions, coronal dimmings, coronal holes, coronal jets, coronal waves, emerging flux, sigmoids, coronal magnetic loops, filaments, filament eruption, flares, loop oscillation, plage, surges, and sunspots. Annotation tools are provided for many of these events. Many features of the tutorial, such as mouse-over definitions and interactive annotation examples, are designed to assist people without previous experience in solar physics. After completing the tutorial, the user is presented with an interactive quiz: a series of movies and images to identify and annotate. The tutorial teaches the user, with feedback on correct and incorrect answers, until the user develops appropriate confidence and skill. This prepares users to annotate new data, based on their experience with event recognition and annotation tools. Trained users can contribute significantly to our data analysis tasks, even as our training tool contributes to public science literacy and interest in solar physics.

A 7T Spine Array Based on Electric Dipole Transmitters

PubMed Central

Duan, Qi; Nair, Govind; Gudino, Natalia; de Zwart, Jacco A.; van Gelderen, Peter; Murphy-Boesch, Joe; Reich, Daniel S.; Duyn, Jeff H.; Merkle, Hellmut

2015-01-01

Purpose In this work the feasibility of using an array of electric dipole antennas for RF transmission in spine MRI at high field is explored. Method A 2-channel transmit array based on an electric dipole design was quantitatively optimized for 7T spine imaging and integrated with a receive array combining 8 loop coils. Using B1+ mapping, the transmit efficiency of the dipole array was compared to a design using quadrature loop pairs. The radio-frequency (RF) energy deposition for each array was measured using a home-built dielectric phantom and MR thermometry. The performance of the proposed array was qualitatively demonstrated in human studies. Results The results indicate dramatically improved transmit efficiency for the dipole design as compared to the loop excitation. Up to 76% gain was achieved within the spinal region. Conclusion For imaging of the spine, electric-dipole based transmitters provided an attractive alternative to the traditional loop-based design. Easy integration with existing receive array technology facilitates practical use at high field. PMID:26190585

High-throughput sample adaptive offset hardware architecture for high-efficiency video coding

NASA Astrophysics Data System (ADS)

Zhou, Wei; Yan, Chang; Zhang, Jingzhi; Zhou, Xin

2018-03-01

A high-throughput hardware architecture for a sample adaptive offset (SAO) filter in the high-efficiency video coding video coding standard is presented. First, an implementation-friendly and simplified bitrate estimation method of rate-distortion cost calculation is proposed to reduce the computational complexity in the mode decision of SAO. Then, a high-throughput VLSI architecture for SAO is presented based on the proposed bitrate estimation method. Furthermore, multiparallel VLSI architecture for in-loop filters, which integrates both deblocking filter and SAO filter, is proposed. Six parallel strategies are applied in the proposed in-loop filters architecture to improve the system throughput and filtering speed. Experimental results show that the proposed in-loop filters architecture can achieve up to 48% higher throughput in comparison with prior work. The proposed architecture can reach a high-operating clock frequency of 297 MHz with TSMC 65-nm library and meet the real-time requirement of the in-loop filters for 8 K × 4 K video format at 132 fps.

A system architecture for online data interpretation and reduction in fluorescence microscopy

NASA Astrophysics Data System (ADS)

Röder, Thorsten; Geisbauer, Matthias; Chen, Yang; Knoll, Alois; Uhl, Rainer

2010-01-01

In this paper we present a high-throughput sample screening system that enables real-time data analysis and reduction for live cell analysis using fluorescence microscopy. We propose a novel system architecture capable of analyzing a large amount of samples during the experiment and thus greatly minimizing the post-analysis phase that is the common practice today. By utilizing data reduction algorithms, relevant information of the target cells is extracted from the online collected data stream, and then used to adjust the experiment parameters in real-time, allowing the system to dynamically react on changing sample properties and to control the microscope setup accordingly. The proposed system consists of an integrated DSP-FPGA hybrid solution to ensure the required real-time constraints, to execute efficiently the underlying computer vision algorithms and to close the perception-action loop. We demonstrate our approach by addressing the selective imaging of cells with a particular combination of markers. With this novel closed-loop system the amount of superfluous collected data is minimized, while at the same time the information entropy increases.

Computer simulation of magnetic resonance spectra employing homotopy.

PubMed

Gates, K E; Griffin, M; Hanson, G R; Burrage, K

1998-11-01

Multidimensional homotopy provides an efficient method for accurately tracing energy levels and hence transitions in the presence of energy level anticrossings and looping transitions. Herein we describe the application and implementation of homotopy to the analysis of continuous wave electron paramagnetic resonance spectra. The method can also be applied to electron nuclear double resonance, electron spin echo envelope modulation, solid-state nuclear magnetic resonance, and nuclear quadrupole resonance spectra. Copyright 1998 Academic Press.

LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures.

PubMed

Kadumuri, Rajashekar Varma; Vadrevu, Ramakrishna

2017-10-01

Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops. Two new features (i) conservation of the polar/nonpolar environment and (ii) conservation of sequence and conformation of specific residues within the loops have also been incorporated in the search and retrieval of compatible loops for a chosen target loop. Thus, the LoopX server not only serves as a database and visualization tool for sequence and structural analysis of protein loops but also aids in extracting and comparing candidate loops for a given target loop based on user-defined search options.

Optimal frequency-response sensitivity of compressible flow over roughness elements

NASA Astrophysics Data System (ADS)

Fosas de Pando, Miguel; Schmid, Peter J.

2017-04-01

Compressible flow over a flat plate with two localised and well-separated roughness elements is analysed by global frequency-response analysis. This analysis reveals a sustained feedback loop consisting of a convectively unstable shear-layer instability, triggered at the upstream roughness, and an upstream-propagating acoustic wave, originating at the downstream roughness and regenerating the shear-layer instability at the upstream protrusion. A typical multi-peaked frequency response is recovered from the numerical simulations. In addition, the optimal forcing and response clearly extract the components of this feedback loop and isolate flow regions of pronounced sensitivity and amplification. An efficient parametric-sensitivity framework is introduced and applied to the reference case which shows that first-order increases in Reynolds number and roughness height act destabilising on the flow, while changes in Mach number or roughness separation cause corresponding shifts in the peak frequencies. This information is gained with negligible effort beyond the reference case and can easily be applied to more complex flows.

FPGA-Based Efficient Hardware/Software Co-Design for Industrial Systems with Consideration of Output Selection

NASA Astrophysics Data System (ADS)

Deliparaschos, Kyriakos M.; Michail, Konstantinos; Zolotas, Argyrios C.; Tzafestas, Spyros G.

2016-05-01

This work presents a field programmable gate array (FPGA)-based embedded software platform coupled with a software-based plant, forming a hardware-in-the-loop (HIL) that is used to validate a systematic sensor selection framework. The systematic sensor selection framework combines multi-objective optimization, linear-quadratic-Gaussian (LQG)-type control, and the nonlinear model of a maglev suspension. A robustness analysis of the closed-loop is followed (prior to implementation) supporting the appropriateness of the solution under parametric variation. The analysis also shows that quantization is robust under different controller gains. While the LQG controller is implemented on an FPGA, the physical process is realized in a high-level system modeling environment. FPGA technology enables rapid evaluation of the algorithms and test designs under realistic scenarios avoiding heavy time penalty associated with hardware description language (HDL) simulators. The HIL technique facilitates significant speed-up in the required execution time when compared to its software-based counterpart model.

Conceptual design of a thermalhydraulic loop for multiple test geometries at supercritical conditions named Supercritical Phenomena Experimental Test Apparatus (SPETA)

NASA Astrophysics Data System (ADS)

Adenariwo, Adepoju

The efficiency of nuclear reactors can be improved by increasing the operating pressure of current nuclear reactors. Current CANDU-type nuclear reactors use heavy water as coolant at an outlet pressure of up to 11.5 MPa. Conceptual SuperCritical Water Reactors (SCWRs) will operate at a higher coolant outlet pressure of 25 MPa. Supercritical water technology has been used in advanced coal plants and its application proves promising to be employed in nuclear reactors. To better understand how supercritical water technology can be applied in nuclear power plants, supercritical water loops are used to study the heat transfer phenomena as it applies to CANDU-type reactors. A conceptual design of a loop known as the Supercritical Phenomena Experimental Apparatus (SPETA) has been done. This loop has been designed to fit in a 9 m by 2 m by 2.8 m enclosure that will be installed at the University of Ontario Institute of Technology Energy Research Laboratory. The loop include components to safely start up and shut down various test sections, produce a heat source to the test section, and to remove reject heat. It is expected that loop will be able to investigate the behaviour of supercritical water in various geometries including bare tubes, annulus tubes, and multi-element-type bundles. The experimental geometries are designed to match the fluid properties of Canadian SCWR fuel channel designs so that they are representative of a practical application of supercritical water technology in nuclear plants. This loop will investigate various test section orientations which are the horizontal, vertical, and inclined to investigate buoyancy effects. Frictional pressure drop effects and satisfactory methods of estimating hydraulic resistances in supercritical fluid shall also be estimated with the loop. Operating limits for SPETA have been established to be able to capture the important heat transfer phenomena at supercritical conditions. Heat balance and flow calculations have been done to appropriately size components in the loop. Sensitivity analysis has been done to find the optimum design for the loop.

Electron cyclotron wave acceleration outside a flaring loop

NASA Technical Reports Server (NTRS)

Sprangle, P.; Vlahos, L.

1983-01-01

A model for the secondary acceleration of electrons outside a flaring loop is proposed. The results suggest that the narrow bandwidth radiation emitted by the unstable electron distribution inside a flaring loop can become the driver for secondary electron acceleration outside the loop. It is shown that a system of electrons gyrating about and streaming along an adiabatically spatially varying, static magnetic field can be efficiently accelerated to high energies by an electromagnetic wave propagating along and polarized transverse to the static magnetic field. The predictions from our model appear to be in general agreement with existing observations.

Substituting Tyr138 in the active site loop of human phenylalanine hydroxylase affects catalysis and substrate activation.

PubMed

Leandro, João; Stokka, Anne J; Teigen, Knut; Andersen, Ole A; Flatmark, Torgeir

2017-07-01

Mammalian phenylalanine hydroxylase (PAH) is a key enzyme in l-phenylalanine (l-Phe) metabolism and is active as a homotetramer. Biochemical and biophysical work has demonstrated that it cycles between two states with a variably low and a high activity, and that the substrate l-Phe is the key player in this transition. X-ray structures of the catalytic domain have shown mobility of a partially intrinsically disordered Tyr 138 -loop to the active site in the presence of l-Phe. The mechanism by which the loop dynamics are coupled to substrate binding at the active site in tetrameric PAH is not fully understood. We have here conducted functional studies of four Tyr 138 point mutants. A high linear correlation ( r 2 = 0.99) was observed between their effects on the catalytic efficiency of the catalytic domain dimers and the corresponding effect on the catalytic efficiency of substrate-activated full-length tetramers. In the tetramers, a correlation ( r 2 = 0.96) was also observed between the increase in catalytic efficiency (activation) and the global conformational change (surface plasmon resonance signal response) at the same l-Phe concentration. The new data support a similar functional importance of the Tyr 138 -loop in the catalytic domain and the full-length enzyme homotetramer.

Simultaneous pressure-volume measurements using optical sensors and MRI for left ventricle function assessment during animal experiment.

PubMed

Abi-Abdallah Rodriguez, Dima; Durand, Emmanuel; de Rochefort, Ludovic; Boudjemline, Younes; Mousseaux, Elie

2015-01-01

Simultaneous pressure and volume measurements enable the extraction of valuable parameters for left ventricle function assessment. Cardiac MR has proven to be the most accurate method for volume estimation. Nonetheless, measuring pressure simultaneously during MRI acquisitions remains a challenge given the magnetic nature of the widely used pressure transducers. In this study we show the feasibility of simultaneous in vivo pressure-volume acquisitions with MRI using optical pressure sensors. Pressure-volume loops were calculated while inducing three inotropic states in a sheep and functional indices were extracted, using single beat loops, to characterize systolic and diastolic performance. Functional indices evolved as expected in response to positive inotropic stimuli. The end-systolic elastance, representing the contractility index, the diastolic myocardium compliance, and the cardiac work efficiency all increased when inducing inotropic state enhancement. The association of MRI and optical pressure sensors within the left ventricle successfully enabled pressure-volume loop analysis after having respective data simultaneously recorded during the experimentation without the need to move the animal between each inotropic state. Copyright © 2014 IPEM. Published by Elsevier Ltd. All rights reserved.

Two-Stage Design Method for Enhanced Inductive Energy Transmission with Q-Constrained Planar Square Loops.

PubMed

Eteng, Akaa Agbaeze; Abdul Rahim, Sharul Kamal; Leow, Chee Yen; Chew, Beng Wah; Vandenbosch, Guy A E

2016-01-01

Q-factor constraints are usually imposed on conductor loops employed as proximity range High Frequency Radio Frequency Identification (HF-RFID) reader antennas to ensure adequate data bandwidth. However, pairing such low Q-factor loops in inductive energy transmission links restricts the link transmission performance. The contribution of this paper is to assess the improvement that is reached with a two-stage design method, concerning the transmission performance of a planar square loop relative to an initial design, without compromise to a Q-factor constraint. The first stage of the synthesis flow is analytical in approach, and determines the number and spacing of turns by which coupling between similar paired square loops can be enhanced with low deviation from the Q-factor limit presented by an initial design. The second stage applies full-wave electromagnetic simulations to determine more appropriate turn spacing and widths to match the Q-factor constraint, and achieve improved coupling relative to the initial design. Evaluating the design method in a test scenario yielded a more than 5% increase in link transmission efficiency, as well as an improvement in the link fractional bandwidth by more than 3%, without violating the loop Q-factor limit. These transmission performance enhancements are indicative of a potential for modifying proximity HF-RFID reader antennas for efficient inductive energy transfer and data telemetry links.

Loop Evolution Observed with AIA and Hi-C

NASA Technical Reports Server (NTRS)

Mulu-Moore, Fana; Winebarger, Amy R.; Cirtain, Jonathan W.; Kobayashi, Ken; Korreck, Kelly E.; Golub, Leon; Kuzin, Sergei; Walsh, Robert William; DeForest, Craig E.; De Pontieu, Bart;

Loop-bed combustion apparatus

DOEpatents

Shang, Jer-Yu; Mei, Joseph S.; Slagle, Frank D.; Notestein, John E.

1984-01-01

The present invention is directed to a combustion apparatus in the configuration of a oblong annulus defining a closed loop. Particulate coal together with a sulfur sorbent such as sulfur or dolomite is introduced into the closed loop, ignited, and propelled at a high rate of speed around the loop. Flue gas is withdrawn from a location in the closed loop in close proximity to an area in the loop where centrifugal force imposed upon the larger particulate material maintains these particulates at a location spaced from the flue gas outlet. Only flue gas and smaller particulates resulting from the combustion and innerparticle grinding are discharged from the combustor. This structural arrangement provides increased combustion efficiency due to the essentially complete combustion of the coal particulates as well as increased sulfur absorption due to the innerparticle grinding of the sorbent which provides greater particle surface area.

Design and Evaluation of the Terminal Area Precision Scheduling and Spacing System

NASA Technical Reports Server (NTRS)

Swenson, Harry N.; Thipphavong, Jane; Sadovsky, Alex; Chen, Liang; Sullivan, Chris; Martin, Lynne

2011-01-01

This paper describes the design, development and results from a high fidelity human-in-the-loop simulation of an integrated set of trajectory-based automation tools providing precision scheduling, sequencing and controller merging and spacing functions. These integrated functions are combined into a system called the Terminal Area Precision Scheduling and Spacing (TAPSS) system. It is a strategic and tactical planning tool that provides Traffic Management Coordinators, En Route and Terminal Radar Approach Control air traffic controllers the ability to efficiently optimize the arrival capacity of a demand-impacted airport while simultaneously enabling fuel-efficient descent procedures. The TAPSS system consists of four-dimensional trajectory prediction, arrival runway balancing, aircraft separation constraint-based scheduling, traffic flow visualization and trajectory-based advisories to assist controllers in efficient metering, sequencing and spacing. The TAPSS system was evaluated and compared to today's ATC operation through extensive series of human-in-the-loop simulations for arrival flows into the Los Angeles International Airport. The test conditions included the variation of aircraft demand from a baseline of today's capacity constrained periods through 5%, 10% and 20% increases. Performance data were collected for engineering and human factor analysis and compared with similar operations both with and without the TAPSS system. The engineering data indicate operations with the TAPSS show up to a 10% increase in airport throughput during capacity constrained periods while maintaining fuel-efficient aircraft descent profiles from cruise to landing.

A hierarchical structure for automatic meshing and adaptive FEM analysis

NASA Technical Reports Server (NTRS)

Kela, Ajay; Saxena, Mukul; Perucchio, Renato

1987-01-01

A new algorithm for generating automatically, from solid models of mechanical parts, finite element meshes that are organized as spatially addressable quaternary trees (for 2-D work) or octal trees (for 3-D work) is discussed. Because such meshes are inherently hierarchical as well as spatially addressable, they permit efficient substructuring techniques to be used for both global analysis and incremental remeshing and reanalysis. The global and incremental techniques are summarized and some results from an experimental closed loop 2-D system in which meshing, analysis, error evaluation, and remeshing and reanalysis are done automatically and adaptively are presented. The implementation of 3-D work is briefly discussed.

Livermore Compiler Analysis Loop Suite

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

Hornung, R. D.

2013-03-01

LCALS is designed to evaluate compiler optimizations and performance of a variety of loop kernels and loop traversal software constructs. Some of the loop kernels are pulled directly from "Livermore Loops Coded in C", developed at LLNL (see item 11 below for details of earlier code versions). The older suites were used to evaluate floating-point performances of hardware platforms prior to porting larger application codes. The LCALS suite is geared toward assissing C++ compiler optimizations and platform performance related to SIMD vectorization, OpenMP threading, and advanced C++ language features. LCALS contains 20 of 24 loop kernels from the older Livermoremore » Loop suites, plus various others representative of loops found in current production appkication codes at LLNL. The latter loops emphasize more diverse loop constructs and data access patterns than the others, such as multi-dimensional difference stencils. The loops are included in a configurable framework, which allows control of compilation, loop sampling for execution timing, which loops are run and their lengths. It generates timing statistics for analysis and comparing variants of individual loops. Also, it is easy to add loops to the suite as desired.« less

Design of a high altitude long endurance flying-wing solar-powered unmanned air vehicle

NASA Astrophysics Data System (ADS)

Alsahlani, A. A.; Johnston, L. J.; Atcliffe, P. A.

2017-06-01

The low-Reynolds number environment of high-altitude §ight places severe demands on the aerodynamic design and stability and control of a high altitude, long endurance (HALE) unmanned air vehicle (UAV). The aerodynamic efficiency of a §ying-wing configuration makes it an attractive design option for such an application and is investigated in the present work. The proposed configuration has a high-aspect ratio, swept-wing planform, the wing sweep being necessary to provide an adequate moment arm for outboard longitudinal and lateral control surfaces. A design optimization framework is developed under a MATLAB environment, combining aerodynamic, structural, and stability analysis. Low-order analysis tools are employed to facilitate efficient computations, which is important when there are multiple optimization loops for the various engineering analyses. In particular, a vortex-lattice method is used to compute the wing planform aerodynamics, coupled to a twodimensional (2D) panel method to derive aerofoil sectional characteristics. Integral boundary-layer methods are coupled to the panel method in order to predict §ow separation boundaries during the design iterations. A quasi-analytical method is adapted for application to flyingwing con¦gurations to predict the wing weight and a linear finite-beam element approach is used for structural analysis of the wing-box. Stability is a particular concern in the low-density environment of high-altitude flight for flying-wing aircraft and so provision of adequate directional stability and control power forms part of the optimization process. At present, a modified Genetic Algorithm is used in all of the optimization loops. Each of the low-order engineering analysis tools is validated using higher-order methods to provide con¦dence in the use of these computationally-efficient tools in the present design-optimization framework. This paper includes the results of employing the present optimization tools in the design of a HALE, flying-wing UAV to indicate that this is a viable design configuration option.

Mining protein loops using a structural alphabet and statistical exceptionality

PubMed Central

2010-01-01

Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. Conclusions We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/. PMID:20132552

Mining protein loops using a structural alphabet and statistical exceptionality.

PubMed

Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

2010-02-04

Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.

Assisted closed-loop optimization of SSVEP-BCI efficiency

PubMed Central

Fernandez-Vargas, Jacobo; Pfaff, Hanns U.; Rodríguez, Francisco B.; Varona, Pablo

2012-01-01

We designed a novel assisted closed-loop optimization protocol to improve the efficiency of brain-computer interfaces (BCI) based on steady state visually evoked potentials (SSVEP). In traditional paradigms, the control over the BCI-performance completely depends on the subjects' ability to learn from the given feedback cues. By contrast, in the proposed protocol both the subject and the machine share information and control over the BCI goal. Generally, the innovative assistance consists in the delivery of online information together with the online adaptation of BCI stimuli properties. In our case, this adaptive optimization process is realized by (1) a closed-loop search for the best set of SSVEP flicker frequencies and (2) feedback of actual SSVEP magnitudes to both the subject and the machine. These closed-loop interactions between subject and machine are evaluated in real-time by continuous measurement of their efficiencies, which are used as online criteria to adapt the BCI control parameters. The proposed protocol aims to compensate for variability in possibly unknown subjects' state and trait dimensions. In a study with N = 18 subjects, we found significant evidence that our protocol outperformed classic SSVEP-BCI control paradigms. Evidence is presented that it takes indeed into account interindividual variabilities: e.g., under the new protocol, baseline resting state EEG measures predict subjects' BCI performances. This paper illustrates the promising potential of assisted closed-loop protocols in BCI systems. Probably their applicability might be expanded to innovative uses, e.g., as possible new diagnostic/therapeutic tools for clinical contexts and as new paradigms for basic research. PMID:23443214

Assisted closed-loop optimization of SSVEP-BCI efficiency.

PubMed

Fernandez-Vargas, Jacobo; Pfaff, Hanns U; Rodríguez, Francisco B; Varona, Pablo

2013-01-01

We designed a novel assisted closed-loop optimization protocol to improve the efficiency of brain-computer interfaces (BCI) based on steady state visually evoked potentials (SSVEP). In traditional paradigms, the control over the BCI-performance completely depends on the subjects' ability to learn from the given feedback cues. By contrast, in the proposed protocol both the subject and the machine share information and control over the BCI goal. Generally, the innovative assistance consists in the delivery of online information together with the online adaptation of BCI stimuli properties. In our case, this adaptive optimization process is realized by (1) a closed-loop search for the best set of SSVEP flicker frequencies and (2) feedback of actual SSVEP magnitudes to both the subject and the machine. These closed-loop interactions between subject and machine are evaluated in real-time by continuous measurement of their efficiencies, which are used as online criteria to adapt the BCI control parameters. The proposed protocol aims to compensate for variability in possibly unknown subjects' state and trait dimensions. In a study with N = 18 subjects, we found significant evidence that our protocol outperformed classic SSVEP-BCI control paradigms. Evidence is presented that it takes indeed into account interindividual variabilities: e.g., under the new protocol, baseline resting state EEG measures predict subjects' BCI performances. This paper illustrates the promising potential of assisted closed-loop protocols in BCI systems. Probably their applicability might be expanded to innovative uses, e.g., as possible new diagnostic/therapeutic tools for clinical contexts and as new paradigms for basic research.

Rotating elastic string loops in flat and black hole spacetimes: stability, cosmic censorship and the Penrose process

NASA Astrophysics Data System (ADS)

Natário, José; Queimada, Leonel; Vicente, Rodrigo

2018-04-01

We rederive the equations of motion for relativistic strings, that is, one-dimensional elastic bodies whose internal energy depends only on their stretching, and use them to study circular string loops rotating in the equatorial plane of flat and black hole spacetimes. We start by obtaining the conditions for equilibrium, and find that: (i) if the string’s longitudinal speed of sound does not exceed the speed of light then its radius when rotating in Minkowski’s spacetime is always larger than its radius when at rest; (ii) in Minkowski’s spacetime, equilibria are linearly stable for rotation speeds below a certain threshold, higher than the string’s longitudinal speed of sound, and linearly unstable for some rotation speeds above it; (iii) equilibria are always linearly unstable in Schwarzschild’s spacetime. Moreover, we study interactions of a rotating string loop with a Kerr black hole, namely in the context of the weak cosmic censorship conjecture and the Penrose process. We find that: (i) elastic string loops that satisfy the null energy condition cannot overspin extremal black holes; (ii) elastic string loops that satisfy the dominant energy condition cannot increase the maximum efficiency of the usual particle Penrose process; (iii) if the dominant energy condition (but not the weak energy condition) is violated then the efficiency can be increased. This last result hints at the interesting possibility that the dominant energy condition may underlie the well known upper bounds for the efficiencies of energy extraction processes (including, for example, superradiance).

THE CORONAL LOOP INVENTORY PROJECT: EXPANDED ANALYSIS AND RESULTS

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

Schmelz, J. T.; Christian, G. M.; Chastain, R. A., E-mail: jschmelz@usra.edu

We have expanded upon earlier work that investigates the relative importance of coronal loops with isothermal versus multithermal cross-field temperature distributions. These results are important for determining if loops have substructure in the form of unresolved magnetic strands. We have increased the number of loops targeted for temperature analysis from 19 to 207 with the addition of 188 new loops from multiple regions. We selected all loop segments visible in the 171 Å images of the Atmospheric Imaging Assembly (AIA) that had a clean background. Eighty-six of the new loops were rejected because they could not be reliably separated frommore » the background in other AIA filters. Sixty-one loops required multithermal models to reproduce the observations. Twenty-eight loops were effectively isothermal, that is, the plasma emission to which AIA is sensitive could not be distinguished from isothermal emission, within uncertainties. Ten loops were isothermal. Also, part of our inventory was one small flaring loop, one very cool loop whose temperature distribution could not be constrained by the AIA data, and one loop with inconclusive results. Our survey can confirm an unexpected result from the pilot study: we found no isothermal loop segments where we could properly use the 171-to-193 ratio method, which would be similar to the analysis done for many loops observed with TRACE and EIT. We recommend caution to observers who assume the loop plasma is isothermal, and hope that these results will influence the direction of coronal heating models and the effort modelers spend on various heating scenarios.« less

Stopped-in-loop flow analysis of trace vanadium in water.

PubMed

Teshima, Norio; Ohno, Shinsuke; Sakai, Tadao

2007-01-01

The new concept of stopped-in-loop flow analysis (SIL-FA) is proposed, and an SIL-FA method for the catalytic determination of vanadium is demonstrated. In an SIL format, a sample solution merges with reagent(s), and the well-mixed solution is loaded into a loop. The solution in the loop is separated by a six-way switching valve from the main stream. While the reaction proceeds in the stationary loop, the SIL-FA system does not need to establish a baseline continuously. This leads to a reduction in reagent consumption and waste generation compared with traditional flow injection analysis.

Novel sensors to enable closed-loop active clearance control in gas turbine engines

NASA Astrophysics Data System (ADS)

Geisheimer, Jonathan; Holst, Tom

2014-06-01

Active clearance control within the turbine section of gas turbine engines presents and opportunity within aerospace and industrial applications to improve operating efficiencies and the life of downstream components. Open loop clearance control is currently employed during the development of all new large core aerospace engines; however, the ability to measure the gap between the blades and the case and close down the clearance further presents as opportunity to gain even greater efficiencies. The turbine area is one of the harshest environments for long term placement of a sensor in addition to the extreme accuracy requirements required to enable closed loop clearance control. This paper gives an overview of the challenges of clearance measurements within the turbine as well as discusses the latest developments of a microwave sensor designed for this application.

Energy Efficiency and Environmental Impact Analyses of Supermarket Refrigeration Systems

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

Fricke, Brian A; Bansal, Pradeep; Zha, Shitong

This paper presents energy and life cycle climate performance (LCCP) analyses of a variety of supermarket refrigeration systems to identify designs that exhibit low environmental impact and high energy efficiency. EnergyPlus was used to model refrigeration systems in a variety of climate zones across the United States. The refrigeration systems that were modeled include the traditional multiplex DX system, cascade systems with secondary loops and the transcritical CO2 system. Furthermore, a variety of refrigerants were investigated, including R-32, R-134a, R-404A, R-1234yf, R-717, and R-744. LCCP analysis was used to determine the direct and indirect carbon dioxide emissions resulting from themore » operation of the various refrigeration systems over their lifetimes. Our analysis revealed that high-efficiency supermarket refrigeration systems may result in up to 44% less energy consumption and 78% reduced carbon dioxide emissions compared to the baseline multiplex DX system. This is an encouraging result for legislators, policy makers and supermarket owners to select low emission, high-efficiency commercial refrigeration system designs for future retrofit and new projects.« less

Replacing the Axial Ligand Tyrosine 75 or Its Hydrogen Bond Partner Histidine 83 Minimally Affects Hemin Acquisition by the Hemophore HasAp from Pseudomonas aeruginosa

PubMed Central

2015-01-01

Hemophores from Pseudomonas aeruginosa (HasAp), Serratia marcescens (HasAsm), and Yersinia pestis (HasAyp) bind hemin between two loops. One of the loops harbors conserved axial ligand Tyr75 (Y75 loop) in all three structures, whereas the second loop (H32 loop) contains axial ligand His32 in HasAp and HasAsm, but a noncoordinating Gln32 in HasAyp. Binding of hemin to the Y75 loop of HasAp or HasAsm causes a large rearrangement of the H32 loop that allows His32 coordination. The Q32 loop in apo-HasAyp is already in the closed conformation, such that binding of hemin to the conserved Y75 loop occurs with minimal structural rearrangement and without coordinative interaction with the Q32 loop. In this study, structural and spectroscopic investigations of the hemophore HasAp were conducted to probe (i) the role of the conserved Tyr75 loop in hemin binding and (ii) the proposed requirement of the His83–Tyr75 hydrogen bond to allow the coordination of hemin by Tyr75. High-resolution crystal structures of H83A holo-HasAp obtained at pH 6.5 (0.89 Å) and pH 5.4 (1.25 Å) show that Tyr75 remains coordinated to the heme iron, and that a water molecule can substitute for Nδ of His83 to interact with the Oη atom of Tyr75, likely stabilizing the Tyr75–Fe interaction. Nuclear magnetic resonance spectroscopy revealed that in apo-Y75A and apo-H83A HasAp, the Y75 loop is disordered, and that disorder propagates to nearby elements of secondary structure, suggesting that His83 Nδ–Tyr75 Oη interaction is important to the organization of the Y75 loop in apo-HasA. Kinetic analysis of hemin loading conducted via stopped-flow UV–vis and rapid-freeze-quench resonance Raman shows that both mutants load hemin with biphasic kinetic parameters that are not significantly dissimilar from those previously observed for wild-type HasAp. When the structural and kinetic data are taken together, a tentative model emerges, which suggests that HasA hemophores utilize hydrophobic, π–π stacking, and van der Waals interactions to load hemin efficiently, while axial ligation likely functions to slow hemin release, thus allowing the hemophore to meet the challenge of capturing hemin under inhospitable conditions and delivering it selectively to its cognate receptor. PMID:24625274

Reduced Moment-Based Models for Oxygen Precipitates and Dislocation Loops in Silicon

NASA Astrophysics Data System (ADS)

Trzynadlowski, Bart

The demand for ever smaller, higher-performance integrated circuits and more efficient, cost-effective solar cells continues to push the frontiers of process technology. Fabrication of silicon devices requires extremely precise control of impurities and crystallographic defects. Failure to do so not only reduces performance, efficiency, and yield, it threatens the very survival of commercial enterprises in today's fiercely competitive and price-sensitive global market. The presence of oxygen in silicon is an unavoidable consequence of the Czochralski process, which remains the most popular method for large-scale production of single-crystal silicon. Oxygen precipitates that form during thermal processing cause distortion of the surrounding silicon lattice and can lead to the formation of dislocation loops. Localized deformation caused by both of these defects introduces potential wells that trap diffusing impurities such as metal atoms, which is highly desirable if done far away from sensitive device regions. Unfortunately, dislocations also reduce the mechanical strength of silicon, which can cause wafer warpage and breakage. Engineers must negotiate this and other complex tradeoffs when designing fabrication processes. Accomplishing this in a complex, modern process involving a large number of thermal steps is impossible without the aid of computational models. In this dissertation, new models for oxygen precipitation and dislocation loop evolution are described. An oxygen model using kinetic rate equations to evolve the complete precipitate size distribution was developed first. This was then used to create a reduced model tracking only the moments of the size distribution. The moment-based model was found to run significantly faster than its full counterpart while accurately capturing the evolution of oxygen precipitates. The reduced model was fitted to experimental data and a sensitivity analysis was performed to assess the robustness of the results. Source code for both models is included. A moment-based model for dislocation loop formation from {311} defects in ion-implanted silicon was also developed and validated against experimental data. Ab initio density functional theory calculations of stacking faults and edge dislocations were performed to extract energies and elastic properties. This allowed the effect of applied stress on the evolution of {311} defects and dislocation loops to be investigated.

Antenna theory: Analysis and design

NASA Astrophysics Data System (ADS)

Balanis, C. A.

The book's main objective is to introduce the fundamental principles of antenna theory and to apply them to the analysis, design, and measurements of antennas. In a description of antennas, the radiation mechanism is discussed along with the current distribution on a thin wire. Fundamental parameters of antennas are examined, taking into account the radiation pattern, radiation power density, radiation intensity, directivity, numerical techniques, gain, antenna efficiency, half-power beamwidth, beam efficiency, bandwidth, polarization, input impedance, and antenna temperature. Attention is given to radiation integrals and auxiliary potential functions, linear wire antennas, loop antennas, linear and circular arrays, self- and mutual impedances of linear elements and arrays, broadband dipoles and matching techniques, traveling wave and broadband antennas, frequency independent antennas and antenna miniaturization, the geometrical theory of diffraction, horns, reflectors and lens antennas, antenna synthesis and continuous sources, and antenna measurements.

Battle for Climate and Scarcity Rents: Beyond the Linear-Quadratic Case.

PubMed

Kagan, Mark; van der Ploeg, Frederick; Withagen, Cees

Industria imports oil, produces final goods and wishes to mitigate global warming. Oilrabia exports oil and buys final goods from the other country. Industria uses the carbon tax to impose an import tariff on oil and steal some of Oilrabia's scarcity rent. Conversely, Oilrabia has monopoly power and sets the oil price to steal some of Industria's climate rent. We analyze the relative speeds of oil extraction and carbon accumulation under these strategic interactions for various production function specifications and compare these with the efficient and competitive outcomes. We prove that for the class of HARA production functions, the oil price is initially higher and subsequently lower in the open-loop Nash equilibrium than in the efficient outcome. The oil extraction rate is thus initially too low and in later stages too high. The HARA class includes linear, loglinear and semi-loglinear demand functions as special cases. For non-HARA production functions, Oilrabia may in the open-loop Nash equilibrium initially price oil lower than the efficient level, thus resulting in more oil extraction and climate damages. We also contrast the open-loop Nash and efficient outcomes numerically with the feedback Nash outcomes. We find that the optimal carbon tax path in the feedback Nash equilibrium is flatter than in the open-loop Nash equilibrium. It turns out that for certain demand functions using the carbon tax as an import tariff may hurt consumers' welfare as the resulting user cost of oil is so high that the fall in welfare wipes out the gain from higher tariff revenues.

Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators.

PubMed

Penno, Christophe; Sharma, Virag; Coakley, Arthur; O'Connell Motherway, Mary; van Sinderen, Douwe; Lubkowska, Lucyna; Kireeva, Maria L; Kashlev, Mikhail; Baranov, Pavel V; Atkins, John F

2015-04-21

Escherichia coli and yeast DNA-dependent RNA polymerases are shown to mediate efficient nascent transcript stem loop formation-dependent RNA-DNA hybrid realignment. The realignment was discovered on the heteropolymeric sequence T5C5 and yields transcripts lacking a C residue within a corresponding U5C4. The sequence studied is derived from a Roseiflexus insertion sequence (IS) element where the resulting transcriptional slippage is required for transposase synthesis. The stability of the RNA structure, the proximity of the stem loop to the slippage site, the length and composition of the slippage site motif, and the identity of its 3' adjacent nucleotides (nt) are crucial for transcripts lacking a single C. In many respects, the RNA structure requirements for this slippage resemble those for hairpin-dependent transcription termination. In a purified in vitro system, the slippage efficiency ranges from 5% to 75% depending on the concentration ratios of the nucleotides specified by the slippage sequence and the 3' nt context. The only previous proposal of stem loop mediated slippage, which was in Ebola virus expression, was based on incorrect data interpretation. We propose a mechanical slippage model involving the RNAP translocation state as the main motor in slippage directionality and efficiency. It is distinct from previously described models, including the one proposed for paramyxovirus, where following random movement efficiency is mainly dependent on the stability of the new realigned hybrid. In broadening the scope for utilization of transcription slippage for gene expression, the stimulatory structure provides parallels with programmed ribosomal frameshifting at the translation level.

Coordinated gripping of substrate by subunits of a AAA+ proteolytic machine

PubMed Central

Iosefson, Ohad; Nager, Andrew R.; Baker, Tania A.; Sauer, Robert T.

2014-01-01

Hexameric AAA+ unfoldases of ATP-dependent proteases and protein-remodeling machines use conserved loops that line the axial pore to apply force to substrates during the mechanical processes of protein unfolding and translocation. Whether loops from multiple subunits act independently or coordinately in these processes is a critical aspect of mechanism but is currently unknown for any AAA+ machine. By studying covalently linked hexamers of the E. coli ClpX unfoldase bearing different numbers and configurations of wild-type and mutant pore loops, we show that loops function synergistically, with the number of wild-type loops required for efficient degradation depending upon the stability of the protein substrate. Our results support a mechanism in which a power stroke initiated in one subunit of the ClpX hexamer results in the concurrent movement of all six pore loops, which coordinately grip and apply force to the substrate. PMID:25599533

Development of a novel loop-mediated isothermal amplification (LAMP) assay for the detection of Salmonella ser. Enteritidis from egg products

USDA-ARS?s Scientific Manuscript database

Salmonella ser. Enteritidis is a major public health concern worldwide. Loop-mediated isothermal amplification (LAMP) is a novel simple, easy-to-operate detection technology that amplifies DNA with high speed, efficiency, and specificity under isothermal conditions. The objective of this study was t...

A 7T spine array based on electric dipole transmitters.

PubMed

Duan, Qi; Nair, Govind; Gudino, Natalia; de Zwart, Jacco A; van Gelderen, Peter; Murphy-Boesch, Joe; Reich, Daniel S; Duyn, Jeff H; Merkle, Hellmut

2015-10-01

The goal of this study was to explore the feasibility of using an array of electric dipole antennas for RF transmission in spine MRI at high fields. A two-channel transmit array based on an electric dipole design was quantitatively optimized for 7T spine imaging and integrated with a receive array combining eight loop coils. Using B1+ mapping, the transmit efficiency of the dipole array was compared with a design using quadrature loop pairs. The radiofrequency energy deposition for each array was measured using a home-built dielectric phantom and MR thermometry. The performance of the proposed array was qualitatively demonstrated in human studies. The results indicate dramatically improved transmit efficiency for the dipole design compared with the loop excitation. A gain of up to 76% was achieved within the spinal region. For imaging of the spine, electric dipole-based transmitters provide an attractive alternative to the traditional loop-based design. Easy integration with existing receive array technology facilitates practical use at high fields. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner.

PubMed

Wiedemann, Eva-Maria; Peycheva, Mihaela; Pavri, Rushad

2016-12-13

Class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) locus generates antibody isotypes. CSR depends on double-strand breaks (DSBs) induced by activation-induced cytidine deaminase (AID). Although DSB formation and repair machineries are active in G1 phase, efficient CSR is dependent on cell proliferation and S phase entry; however, the underlying mechanisms are obscure. Here, we show that efficient CSR requires the replicative helicase, the Mcm complex. Mcm proteins are enriched at IgH switch regions during CSR, leading to assembly of facultative replication origins that require Mcm helicase function for productive CSR. Assembly of CSR-associated origins is facilitated by R loops and promotes the physical proximity (synapsis) of recombining switch regions, which is reduced by R loop inhibition or Mcm complex depletion. Thus, R loops contribute to replication origin specification that promotes DSB resolution in CSR. This suggests a mechanism for the dependence of CSR on S phase and cell division. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Efficient HIV-1 inhibition by a 16 nt-long RNA aptamer designed by combining in vitro selection and in silico optimisation strategies

PubMed Central

Sánchez-Luque, Francisco J.; Stich, Michael; Manrubia, Susanna; Briones, Carlos; Berzal-Herranz, Alfredo

2014-01-01

The human immunodeficiency virus type-1 (HIV-1) genome contains multiple, highly conserved structural RNA domains that play key roles in essential viral processes. Interference with the function of these RNA domains either by disrupting their structures or by blocking their interaction with viral or cellular factors may seriously compromise HIV-1 viability. RNA aptamers are amongst the most promising synthetic molecules able to interact with structural domains of viral genomes. However, aptamer shortening up to their minimal active domain is usually necessary for scaling up production, what requires very time-consuming, trial-and-error approaches. Here we report on the in vitro selection of 64 nt-long specific aptamers against the complete 5′-untranslated region of HIV-1 genome, which inhibit more than 75% of HIV-1 production in a human cell line. The analysis of the selected sequences and structures allowed for the identification of a highly conserved 16 nt-long stem-loop motif containing a common 8 nt-long apical loop. Based on this result, an in silico designed 16 nt-long RNA aptamer, termed RNApt16, was synthesized, with sequence 5′-CCCCGGCAAGGAGGGG-3′. The HIV-1 inhibition efficiency of such an aptamer was close to 85%, thus constituting the shortest RNA molecule so far described that efficiently interferes with HIV-1 replication. PMID:25175101

Efficient ECH-assisted plasma start-up using trapped particle configuration in the versatile experiment spherical torus

NASA Astrophysics Data System (ADS)

An, YoungHwa; Lee, Jeongwon; Jo, JongGab; Jung, Bong-Ki; Lee, HyunYeong; Chung, Kyoung-Jae; Na, Yong-Su; Hahm, T. S.; Hwang, Y. S.

2017-01-01

An efficient and robust ECH (electron cyclotron heating)-assisted plasma start-up scheme with a low loop voltage and low volt-second consumption utilizing the trapped particle configuration (TPC) has been developed in the versatile experiment spherical torus (VEST). The TPC is a mirror-like magnetic field configuration providing a vertical magnetic field in the same direction as the equilibrium field. It significantly enhances ECH pre-ionization with enhanced particle confinement due to its mirror effect, and intrinsically provides an equilibrium field with a stable decay index enabling prompt plasma current initiation. Consequently, the formation of TPC before the onset of the loop voltage allows the plasma to start up with a lower loop voltage and lower volt-second consumption as well as a wider operation range in terms of ECH pre-ionization power and H2 filling pressure. The TPC can improve the widely-used field null configuration significantly for more efficient start-up when ECH pre-ionization is used. This can then be utilized in superconducting tokamaks requiring a low loop voltage start-up, such as ITER, or in spherical tori with limited volt-seconds. The TPC can be particularly useful in superconducting tokamaks with a limited current slew-rate of superconducting PF coils, as it can save volt-second consumption before plasma current initiation by providing prompt initiation with an intrinsic stable equilibrium field.

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

Fathi, Nima; McDaniel, Patrick; Vorobieff, Peter

The aim of this paper is evaluating the efficiency of a novel combined solar-nuclear cycle. CFD-Thermal analysis is performed to apply the available surplus heat from the nuclear cycle and measure the available kinetic energy of air for the turbine of a solar chimney power plant system (SCPPS). The presented idea helps to decrease the thermal pollution and handle the water shortage supply for water plant by replacing the cooling tower by solar chimney power plant to get the surplus heat from the available warm air in the secondary loop of the reactor. By applying this idea to a typicalmore » 1000 MW nuclear power plant with a 0.33 thermal efficiency, we can increase it to 0.39.« less

Design and simulation of permanent magnet synchronous motor control system

NASA Astrophysics Data System (ADS)

Li, Li; Liu, Yongqiu

2018-06-01

In recent years, with the development of power electronics, microelectronics, new motor control theory and rare earth permanent magnet materials, permanent magnet synchronous motors have been rapidly applied. Permanent magnet synchronous motors have the advantages of small size, low loss and high efficiency. Today, energy conservation and environmental protection are increasingly valued. It is very necessary to study them. Permanent magnet synchronous motor control system has a wide range of application prospects in the fields of electric vehicles, ships and other transportation. Using the simulation function of MATLAB/SIMULINK, a modular design structure was used to simulate the whole system model of speed loop adjustment, current PI modulation, SVPWM (Space Vector Pulse Width Module) wave generation and double closed loop. The results show that this control method has good robustness, and this method can improve the design efficiency and shorten the system design time. In this article, the analysis of the control principle of modern permanent magnet synchronous motor and the various processes of MATLAB simulation application will be analyzed in detail. The basic theory, basic method and application technology of the permanent magnet synchronous motor control system are systematically introduced.

Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1

PubMed Central

Nguyen, Hai Dang; Yadav, Tribhuwan; Giri, Sumanprava; Saez, Borja; Graubert, Timothy A.; Zou, Lee

2017-01-01

R loop, a transcription intermediate containing RNA:DNA hybrids and displaced single-stranded DNA (ssDNA), has emerged as a major source of genomic instability. RNaseH1, which cleaves the RNA in RNA:DNA hybrids, plays an important role in R loop suppression. Here, we show that replication protein A (RPA), a ssDNA-binding protein, interacts with RNaseH1 and colocalizes with both RNaseH1 and R loops in cells. In vitro, purified RPA directly enhances the association of RNaseH1 with RNA:DNA hybrids and stimulates the activity of RNaseH1 on R loops. An RPA binding-defective RNaseH1 mutant is not efficiently stimulated by RPA in vitro, fails to accumulate at R loops in cells, and loses the ability to suppress R loops and associated genomic instability. Thus, in addition to sensing DNA damage and replication stress, RPA is a sensor of R loops and a regulator of RNaseH1, extending the versatile role of RPA in suppression of genomic instability. PMID:28257700

Analysis of first and second order binary quantized digital phase-locked loops for ideal and white Gaussian noise inputs

NASA Technical Reports Server (NTRS)

Blasche, P. R.

1980-01-01

Specific configurations of first and second order all digital phase locked loops are analyzed for both ideal and additive white gaussian noise inputs. In addition, a design for a hardware digital phase locked loop capable of either first or second order operation is presented along with appropriate experimental data obtained from testing of the hardware loop. All parameters chosen for the analysis and the design of the digital phase locked loop are consistent with an application to an Omega navigation receiver although neither the analysis nor the design are limited to this application.

DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

PubMed Central

Laurens, Niels; Rusling, David A.; Pernstich, Christian; Brouwer, Ineke; Halford, Stephen E.; Wuite, Gijs J. L.

2012-01-01

Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond. PMID:22373924

Interprocedural Analysis and the Verification of Concurrent Programs

DTIC Science & Technology

2009-01-01

SSPE ) problem is to compute a regular expression that represents paths(s, v) for all vertices v in the graph. The syntax of regular expressions is as...follows: r ::= ∅ | ε | e | r1 ∪ r2 | r1.r2 | r∗, where e stands for an edge in G. We can use any algorithm for SSPE to compute regular expressions for...a closed representation of loops provides an exponential speedup.2 Tarjan’s path-expression algorithm solves the SSPE problem efficiently. It uses

Loop transfer recovery for general nonminimum phase discrete time systems. I - Analysis

NASA Technical Reports Server (NTRS)

Chen, Ben M.; Saberi, Ali; Sannuti, Peddapullaiah; Shamash, Yacov

1992-01-01

A complete analysis of loop transfer recovery (LTR) for general nonstrictly proper, not necessarily minimum phase discrete time systems is presented. Three different observer-based controllers, namely, `prediction estimator' and full or reduced-order type `current estimator' based controllers, are used. The analysis corresponding to all these three controllers is unified into a single mathematical framework. The LTR analysis given here focuses on three fundamental issues: (1) the recoverability of a target loop when it is arbitrarily given, (2) the recoverability of a target loop while taking into account its specific characteristics, and (3) the establishment of necessary and sufficient conditions on the given system so that it has at least one recoverable target loop transfer function or sensitivity function. Various differences that arise in LTR analysis of continuous and discrete systems are pointed out.

Transcript Lifetime Is Balanced between Stabilizing Stem-Loop Structures and Degradation-Promoting Polyadenylation in Plant Mitochondria

PubMed Central

Kuhn, Josef; Tengler, Ulrike; Binder, Stefan

2001-01-01

To determine the influence of posttranscriptional modifications on 3′ end processing and RNA stability in plant mitochondria, pea atp9 and Oenothera atp1 transcripts were investigated for the presence and function of 3′ nonencoded nucleotides. A 3′ rapid amplification of cDNA ends approach initiated at oligo(dT)-adapter primers finds the expected poly(A) tails predominantly attached within the second stem or downstream of the double stem-loop structures at sites of previously mapped 3′ ends. Functional studies in a pea mitochondrial in vitro processing system reveal a rapid removal of the poly(A) tails up to termini at the stem-loop structure but little if any influence on further degradation of the RNA. In contrast 3′ poly(A) tracts at RNAs without such stem-loop structures significantly promote total degradation in vitro. To determine the in vivo identity of 3′ nonencoded nucleotides more accurately, pea atp9 transcripts were analyzed by a direct anchor primer ligation-reverse transcriptase PCR approach. This analysis identified maximally 3-nucleotide-long nonencoded extensions most frequently of adenosines combined with cytidines. Processing assays with substrates containing homopolymer stretches of different lengths showed that 10 or more adenosines accelerate RNA processivity, while 3 adenosines have no impact on RNA life span. Thus polyadenylation can generally stimulate the decay of RNAs, but processivity of degradation is almost annihilated by the stabilizing effect of the stem-loop structures. These antagonistic actions thus result in the efficient formation of 3′ processed and stable transcripts. PMID:11154261

Dual allosteric activation mechanisms in monomeric human glucokinase

PubMed Central

Whittington, A. Carl; Larion, Mioara; Bowler, Joseph M.; Ramsey, Kristen M.; Brüschweiler, Rafael; Miller, Brian G.

2015-01-01

Cooperativity in human glucokinase (GCK), the body’s primary glucose sensor and a major determinant of glucose homeostatic diseases, is fundamentally different from textbook models of allostery because GCK is monomeric and contains only one glucose-binding site. Prior work has demonstrated that millisecond timescale order-disorder transitions within the enzyme’s small domain govern cooperativity. Here, using limited proteolysis, we map the site of disorder in unliganded GCK to a 30-residue active-site loop that closes upon glucose binding. Positional randomization of the loop, coupled with genetic selection in a glucokinase-deficient bacterium, uncovers a hyperactive GCK variant with substantially reduced cooperativity. Biochemical and structural analysis of this loop variant and GCK variants associated with hyperinsulinemic hypoglycemia reveal two distinct mechanisms of enzyme activation. In α-type activation, glucose affinity is increased, the proteolytic susceptibility of the active site loop is suppressed and the 1H-13C heteronuclear multiple quantum coherence (HMQC) spectrum of 13C-Ile–labeled enzyme resembles the glucose-bound state. In β-type activation, glucose affinity is largely unchanged, proteolytic susceptibility of the loop is enhanced, and the 1H-13C HMQC spectrum reveals no perturbation in ensemble structure. Leveraging both activation mechanisms, we engineer a fully noncooperative GCK variant, whose functional properties are indistinguishable from other hexokinase isozymes, and which displays a 100-fold increase in catalytic efficiency over wild-type GCK. This work elucidates specific structural features responsible for generating allostery in a monomeric enzyme and suggests a general strategy for engineering cooperativity into proteins that lack the structural framework typical of traditional allosteric systems. PMID:26283387

Dual allosteric activation mechanisms in monomeric human glucokinase.

PubMed

Whittington, A Carl; Larion, Mioara; Bowler, Joseph M; Ramsey, Kristen M; Brüschweiler, Rafael; Miller, Brian G

2015-09-15

Cooperativity in human glucokinase (GCK), the body's primary glucose sensor and a major determinant of glucose homeostatic diseases, is fundamentally different from textbook models of allostery because GCK is monomeric and contains only one glucose-binding site. Prior work has demonstrated that millisecond timescale order-disorder transitions within the enzyme's small domain govern cooperativity. Here, using limited proteolysis, we map the site of disorder in unliganded GCK to a 30-residue active-site loop that closes upon glucose binding. Positional randomization of the loop, coupled with genetic selection in a glucokinase-deficient bacterium, uncovers a hyperactive GCK variant with substantially reduced cooperativity. Biochemical and structural analysis of this loop variant and GCK variants associated with hyperinsulinemic hypoglycemia reveal two distinct mechanisms of enzyme activation. In α-type activation, glucose affinity is increased, the proteolytic susceptibility of the active site loop is suppressed and the (1)H-(13)C heteronuclear multiple quantum coherence (HMQC) spectrum of (13)C-Ile-labeled enzyme resembles the glucose-bound state. In β-type activation, glucose affinity is largely unchanged, proteolytic susceptibility of the loop is enhanced, and the (1)H-(13)C HMQC spectrum reveals no perturbation in ensemble structure. Leveraging both activation mechanisms, we engineer a fully noncooperative GCK variant, whose functional properties are indistinguishable from other hexokinase isozymes, and which displays a 100-fold increase in catalytic efficiency over wild-type GCK. This work elucidates specific structural features responsible for generating allostery in a monomeric enzyme and suggests a general strategy for engineering cooperativity into proteins that lack the structural framework typical of traditional allosteric systems.

Yeast Inner-Subunit PA-NZ-1 Labeling Strategy for Accurate Subunit Identification in a Macromolecular Complex through Cryo-EM Analysis.

PubMed

Wang, Huping; Han, Wenyu; Takagi, Junichi; Cong, Yao

2018-05-11

Cryo-electron microscopy (cryo-EM) has been established as one of the central tools in the structural study of macromolecular complexes. Although intermediate- or low-resolution structural information through negative staining or cryo-EM analysis remains highly valuable, we lack general and efficient ways to achieve unambiguous subunit identification in these applications. Here, we took advantage of the extremely high affinity between a dodecapeptide "PA" tag and the NZ-1 antibody Fab fragment to develop an efficient "yeast inner-subunit PA-NZ-1 labeling" strategy that when combined with cryo-EM could precisely identify subunits in macromolecular complexes. Using this strategy combined with cryo-EM 3D reconstruction, we were able to visualize the characteristic NZ-1 Fab density attached to the PA tag inserted into a surface-exposed loop in the middle of the sequence of CCT6 subunit present in the Saccharomyces cerevisiae group II chaperonin TRiC/CCT. This procedure facilitated the unambiguous localization of CCT6 in the TRiC complex. The PA tag was designed to contain only 12 amino acids and a tight turn configuration; when inserted into a loop, it usually has a high chance of maintaining the epitope structure and low likelihood of perturbing the native structure and function of the target protein compared to other tagging systems. We also found that the association between PA and NZ-1 can sustain the cryo freezing conditions, resulting in very high occupancy of the Fab in the final cryo-EM images. Our study demonstrated the robustness of this strategy combined with cryo-EM in efficient and accurate subunit identification in challenging multi-component complexes. Copyright © 2018 Elsevier Ltd. All rights reserved.

Markov chain sampling of the O(n) loop models on the infinite plane

NASA Astrophysics Data System (ADS)

Herdeiro, Victor

2017-07-01

A numerical method was recently proposed in Herdeiro and Doyon [Phys. Rev. E 94, 043322 (2016), 10.1103/PhysRevE.94.043322] showing a precise sampling of the infinite plane two-dimensional critical Ising model for finite lattice subsections. The present note extends the method to a larger class of models, namely the O(n) loop gas models for n ∈(1 ,2 ] . We argue that even though the Gibbs measure is nonlocal, it is factorizable on finite subsections when sufficient information on the loops touching the boundaries is stored. Our results attempt to show that provided an efficient Markov chain mixing algorithm and an improved discrete lattice dilation procedure the planar limit of the O(n) models can be numerically studied with efficiency similar to the Ising case. This confirms that scale invariance is the only requirement for the present numerical method to work.

A novel actin binding site of myosin required for effective muscle contraction.

PubMed

Várkuti, Boglárka H; Yang, Zhenhui; Kintses, Bálint; Erdélyi, Péter; Bárdos-Nagy, Irén; Kovács, Attila L; Hári, Péter; Kellermayer, Miklós; Vellai, Tibor; Málnási-Csizmadia, András

2012-02-12

F-actin serves as a track for myosin's motor functions and activates its ATPase activity by several orders of magnitude, enabling actomyosin to produce effective force against load. Although actin activation is a ubiquitous property of all myosin isoforms, the molecular mechanism and physiological role of this activation are unclear. Here we describe a conserved actin-binding region of myosin named the 'activation loop', which interacts with the N-terminal segment of actin. We demonstrate by biochemical, biophysical and in vivo approaches using transgenic Caenorhabditis elegans strains that the interaction between the activation loop and actin accelerates the movement of the relay, stimulating myosin's ATPase activity. This interaction results in efficient force generation, but it is not essential for the unloaded motility. We conclude that the binding of actin to myosin's activation loop specifically increases the ratio of mechanically productive to futile myosin heads, leading to efficient muscle contraction.

Efficient laser noise reduction method via actively stabilized optical delay line.

PubMed

Li, Dawei; Qian, Cheng; Li, Ye; Zhao, Jianye

2017-04-17

We report a fiber laser noise reduction method by locking it to an actively stabilized optical delay line, specifically a fiber-based Mach-Zehnder interferometer with a 10 km optical fiber spool. The fiber spool is used to achieve large arm imbalance. The heterodyne signal of the two arms converts the laser noise from the optical domain to several megahertz, and it is used in laser noise reduction by a phase-locked loop. An additional phase-locked loop is induced in the system to compensate the phase noise due to environmentally induced length fluctuations of the optical fiber spool. A major advantage of this structure is the efficient reduction of out-of-loop frequency noise, particularly at low Fourier frequency. The frequency noise reaches -30 dBc/Hz at 1 Hz, which is reduced by more than 90 dB compared with that of the laser in its free-running state.

Estimation of joint stiffness with a compliant load.

PubMed

Ludvig, Daniel; Kearney, Robert E

2009-01-01

Joint stiffness defines the dynamic relationship between the position of the joint and the torque acting about it. It consists of two components: intrinsic and reflex stiffness. Many previous studies have investigated joint stiffness in an open-loop environment, because the current algorithm in use is an open-loop algorithm. This paper explores issues related to the estimation of joint stiffness when subjects interact with compliant loads. First, we show analytically how the bias in closed-loop estimates of joint stiffness depends on the properties of the load, the noise power, and length of the estimated impulse response functions (IRF). We then demonstrate with simulations that the open-loop analysis will fail completely for an elastic load but may succeed for an inertial load. We further show that the open-loop analysis can yield unbiased results with an inertial load and document IRF length, signal-to-noise ratio needed, and minimum inertia needed for the analysis to succeed. Thus, by using a load with a properly selected inertia, open-loop analysis can be used under closed-loop conditions.

Nicotiana alata Defensin Chimeras Reveal Differences in the Mechanism of Fungal and Tumor Cell Killing and an Enhanced Antifungal Variant

PubMed Central

Payne, Jennifer A. E.; Hayes, Brigitte M. E.; Durek, Thomas; Craik, David J.; Shafee, Thomas M. A.; Poon, Ivan K. H.; Hulett, Mark D.; van der Weerden, Nicole L.

2016-01-01

The plant defensin NaD1 is a potent antifungal molecule that also targets tumor cells with a high efficiency. We examined the features of NaD1 that contribute to these two activities by producing a series of chimeras with NaD2, a defensin that has relatively poor activity against fungi and no activity against tumor cells. All plant defensins have a common tertiary structure known as a cysteine-stabilized α-β motif which consists of an α helix and a triple-stranded β-sheet stabilized by four disulfide bonds. The chimeras were produced by replacing loops 1 to 7, the sequences between each of the conserved cysteine residues on NaD1, with the corresponding loops from NaD2. The loop 5 swap replaced the sequence motif (SKILRR) that mediates tight binding with phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] and is essential for the potent cytotoxic effect of NaD1 on tumor cells. Consistent with previous reports, there was a strong correlation between PI(4,5)P2 binding and the tumor cell killing activity of all of the chimeras. However, this correlation did not extend to antifungal activity. Some of the loop swap chimeras were efficient antifungal molecules, even though they bound poorly to PI(4,5)P2, suggesting that additional mechanisms operate against fungal cells. Unexpectedly, the loop 1B swap chimera was 10 times more active than NaD1 against filamentous fungi. This led to the conclusion that defensin loops have evolved as modular components that combine to make antifungal molecules with variable mechanisms of action and that artificial combinations of loops can increase antifungal activity compared to that of the natural variants. PMID:27503651

THE EFFECT OF THE {sup 14}N(p, {gamma}){sup 15}O REACTION ON THE BLUE LOOPS IN INTERMEDIATE-MASS STARS

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

Halabi, Ghina M.; El Eid, Mounib F.; Champagne, Arthur

2012-12-10

We present stellar evolutionary sequences of stars in the mass range 5-12 M{sub Sun }, having solar-like initial composition. The stellar models are obtained using updated input physics, including recent rates of thermonuclear reactions. We investigate the effects of a modification of the {sup 14}N(p, {gamma}){sup 15}O reaction rate, as suggested by recent evaluations, on the formation and extension of the blue loops encountered during the evolution of the stars in the above mass range. We find that a reduced {sup 14}N(p, {gamma}){sup 15}O rate, as described in the text, has a striking impact on the physical conditions of burningmore » and mixing during shell hydrogen burning when the blue loops are formed. In particular, we find that the efficiency of shell hydrogen burning is crucial for the formation of an extended blue loop. We show that a significantly reduced {sup 14}N(p, {gamma}){sup 15}O rate affects severely the extension of the blue loops and the time spent by the star in the blue part of the Hertzsprung-Russell diagram in the mass range 5-7 M{sub Sun} if the treatment of convection is based on the Schwarzschild criterion only. In this case, envelope overshooting helps to restore well-extended blue loops as supported by the observations of the Cepheid stars. If core overshooting is included during the core hydrogen and core helium burning phases, the loop formation and its properties depend on how this overshooting is treated for a given stellar mass range, as well as on its efficiency.« less

Microinterventional endocapsular nucleus disassembly: novel technique and results of first-in-human randomised controlled study.

PubMed

Ianchulev, Tsontcho; Chang, David F; Koo, Edward; MacDonald, Susan; Calvo, Ernesto; Tyson, Farrell Toby; Vasquez, Andrea; Ahmed, Iqbal Ike K

2018-04-18

To assess the safety and efficacy of microinterventional endocapsular nuclear fragmentation in moderate to severe cataracts. This was a prospective single-masked multisurgeon interventional randomised controlled trial (ClinicalTrials.gov NCT02843594) where 101 eyes of 101 subjects with grade 3-4+ nuclear cataracts were randomised to torsional phacoemulsification alone (controls) or torsional phacoemulsification with adjunctive endocapsular nuclear fragmentation using a manual microinterventional nitinol filament loop device (miLOOP group). Outcome measures were phacoemulsification efficiency as measured by ultrasound energy (cumulative dispersed energy (CDE) units) and fluidics requirements (total irrigation fluid used) as well as incidence of intraoperative and postoperative complications. Only high-grade advanced cataracts were enrolled with more than 85% of eyes with baseline best corrected visual acuity (BCVA) of 20/200 or worse in either group. Mean CDE was 53% higher in controls (32.8±24.9 vs 21.4±13.1 with miLOOP assistance) (p=0.004). Endothelial cell loss after surgery was low and similar between groups (7-8%, p=0.561) One-month BCVA averaged 20/27 Snellen in miLOOP eyes and 20/24 in controls. No direct complications were caused by the miLOOP. In two cases, capsular tears occurred during IOL implantation and in all remaining cases during phacoemulsification, with none occurring during the miLOOP nucleus disassembly part of the procedure. Microinterventional endocapsular fragmentation with the manual, disposable miLOOP device achieved consistent, ultrasound-free, full-thickness nucleus disassembly and significantly improved overall phaco efficiency in advanced cataracts. NCT02843594. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Correlation filtering in financial time series (Invited Paper)

NASA Astrophysics Data System (ADS)

Aste, T.; Di Matteo, Tiziana; Tumminello, M.; Mantegna, R. N.

2005-05-01

We apply a method to filter relevant information from the correlation coefficient matrix by extracting a network of relevant interactions. This method succeeds to generate networks with the same hierarchical structure of the Minimum Spanning Tree but containing a larger amount of links resulting in a richer network topology allowing loops and cliques. In Tumminello et al.,1 we have shown that this method, applied to a financial portfolio of 100 stocks in the USA equity markets, is pretty efficient in filtering relevant information about the clustering of the system and its hierarchical structure both on the whole system and within each cluster. In particular, we have found that triangular loops and 4 element cliques have important and significant relations with the market structure and properties. Here we apply this filtering procedure to the analysis of correlation in two different kind of interest rate time series (16 Eurodollars and 34 US interest rates).

A novel approach for evaluating the performance of real time quantitative loop-mediated isothermal amplification-based methods.

PubMed

Nixon, Gavin J; Svenstrup, Helle F; Donald, Carol E; Carder, Caroline; Stephenson, Judith M; Morris-Jones, Stephen; Huggett, Jim F; Foy, Carole A

2014-12-01

Molecular diagnostic measurements are currently underpinned by the polymerase chain reaction (PCR). There are also a number of alternative nucleic acid amplification technologies, which unlike PCR, work at a single temperature. These 'isothermal' methods, reportedly offer potential advantages over PCR such as simplicity, speed and resistance to inhibitors and could also be used for quantitative molecular analysis. However there are currently limited mechanisms to evaluate their quantitative performance, which would assist assay development and study comparisons. This study uses a sexually transmitted infection diagnostic model in combination with an adapted metric termed isothermal doubling time (IDT), akin to PCR efficiency, to compare quantitative PCR and quantitative loop-mediated isothermal amplification (qLAMP) assays, and to quantify the impact of matrix interference. The performance metric described here facilitates the comparison of qLAMP assays that could assist assay development and validation activities.

All-optical controlled switching of solitons

NASA Astrophysics Data System (ADS)

Man, Wai Sing

1999-11-01

In this dissertation, we have numerically investigated various method of switching solitons using two different nonlinear optical switching devices, namely the twin core nonlinear directional coupler (TCNLDC) and the nonlinear optical loop mirror (NOLM). In the case of TCNLDC, four different schemes were explored where the polarization of the controlling pulse is either parallel or orthogonal to that of the signal soliton, or the controlling pulse may be launched into either of the input ports or it may have a wavelength different from that of the signal. It has been shown that high switching efficiency and distortionless propagation of the signal pulse through the coupler can only be achieved for the case in which the control pulse is launched into the adjacent port of the directional coupler and that its dispersion has equal magnitude but opposite sign as that of the signal. The effect of varying pulse width, walk-off and timing jitter were also investigated for this particular scheme for signal pulse width of 1 ps wide. In the case of NOLM, a control pulse having central wavelength located at the normal dispersion region is used to switch the soliton. The control pulse width and the NOLM's loop length were varied to obtain the switched soliton with minimum distortion and high switching efficiency. In this analysis, Raman effect is included because the control pulse transfers part of its energy to the co-propagating signal pulse in the optical loop. A compact soliton laser has also been developed for this project and its performance was analyzed experimentally and numerically. In our analysis of this soliton laser, we found that the wavelength of the mode-locked pulse can be tuned by varying the polarization elements in the laser and this is entirely due to the birefringence in the laser cavity. In summary, our works have shown that optical solitons can be switched effectively by TCNLDC and NOLM in the high bit-rate and low switching energy regime. (Abstract shortened by UMI.)

Closed Cycle Magnetohydrodynamic Nuclear Space Power Generation Using Helium/Xenon Working Plasma

NASA Technical Reports Server (NTRS)

Litchford, R. J.; Harada, N.

2005-01-01

A multimegawatt-class nuclear fission powered closed cycle magnetohydrodynamic space power plant using a helium/xenon working gas has been studied, to include a comprehensive system analysis. Total plant efficiency was expected to be 55.2 percent including pre-ionization power. The effects of compressor stage number, regenerator efficiency, and radiation cooler temperature on plant efficiency were investigated. The specific mass of the power generation plant was also examined. System specific mass was estimated to be 3 kg/kWe for a net electrical output power of 1 MWe, 2-3 kg/kWe at 2 MWe, and approx.2 kg/KWe at >3 MWe. Three phases of research and development plan were proposed: (1) Phase I-proof of principle, (2) Phase II-demonstration of power generation, and (3) Phase III-prototypical closed loop test.

A systematic and efficient method to compute multi-loop master integrals

NASA Astrophysics Data System (ADS)

Liu, Xiao; Ma, Yan-Qing; Wang, Chen-Yu

2018-04-01

We propose a novel method to compute multi-loop master integrals by constructing and numerically solving a system of ordinary differential equations, with almost trivial boundary conditions. Thus it can be systematically applied to problems with arbitrary kinematic configurations. Numerical tests show that our method can not only achieve results with high precision, but also be much faster than the only existing systematic method sector decomposition. As a by product, we find a new strategy to compute scalar one-loop integrals without reducing them to master integrals.

Analysis of Loss-of-Offsite-Power Events 1997-2015

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

Johnson, Nancy Ellen; Schroeder, John Alton

2016-07-01

Loss of offsite power (LOOP) can have a major negative impact on a power plant’s ability to achieve and maintain safe shutdown conditions. LOOP event frequencies and times required for subsequent restoration of offsite power are important inputs to plant probabilistic risk assessments. This report presents a statistical and engineering analysis of LOOP frequencies and durations at U.S. commercial nuclear power plants. The data used in this study are based on the operating experience during calendar years 1997 through 2015. LOOP events during critical operation that do not result in a reactor trip, are not included. Frequencies and durations weremore » determined for four event categories: plant-centered, switchyard-centered, grid-related, and weather-related. Emergency diesel generator reliability is also considered (failure to start, failure to load and run, and failure to run more than 1 hour). There is an adverse trend in LOOP durations. The previously reported adverse trend in LOOP frequency was not statistically significant for 2006-2015. Grid-related LOOPs happen predominantly in the summer. Switchyard-centered LOOPs happen predominantly in winter and spring. Plant-centered and weather-related LOOPs do not show statistically significant seasonality. The engineering analysis of LOOP data shows that human errors have been much less frequent since 1997 than in the 1986 -1996 time period.« less

Automatic blocking of nested loops

NASA Technical Reports Server (NTRS)

Schreiber, Robert; Dongarra, Jack J.

1990-01-01

Blocked algorithms have much better properties of data locality and therefore can be much more efficient than ordinary algorithms when a memory hierarchy is involved. On the other hand, they are very difficult to write and to tune for particular machines. The reorganization is considered of nested loops through the use of known program transformations in order to create blocked algorithms automatically. The program transformations used are strip mining, loop interchange, and a variant of loop skewing in which invertible linear transformations (with integer coordinates) of the loop indices are allowed. Some problems are solved concerning the optimal application of these transformations. It is shown, in a very general setting, how to choose a nearly optimal set of transformed indices. It is then shown, in one particular but rather frequently occurring situation, how to choose an optimal set of block sizes.

Rapid and Sensitive Detection of sFAT-1 Transgenic Pigs by Visual Loop-Mediated Isothermal Amplification.

PubMed

Tao, Chenyu; Yang, Yalan; Li, Xunbi; Zheng, Xinmin; Ren, Hongyan; Li, Kui; Zhou, Rong

2016-07-01

Genetically modified (GM) livestock have the potential to contribute to improving the environment and human health, with consumption of fewer resources and reduced waste production. However, the transgene process also poses risks. The safety assessment and control of transgenic animal products have drawn wide attention, and the relevant regulations and technology are being developed. Quick testing technology plays a significant role in on-site and customs sampling. Nowadays, loop-mediated isothermal amplification (LAMP) was widely applied in nucleic acid analysis because of its simplicity, rapidity, high efficiency and specificity. In this study, a specific, sensitive detection system for detecting sFAT-1 transgenic pigs was designed. A set of six primers including two loop primers was designed for the target sequence. The DNA samples were amplified in less than 1 h at the optimized temperature and detecting by both Nephelometer LA-320c and unaided eyes directly adding calcein. The detection limit of sFAT-1 LAMP was as low as 1.26 ng/μL. Furthermore, blind tests of transgenic and non-transgenic DNA samples were all correctly detected. Hence, the results in this study demonstrated that LAMP is a very useful tool for transgenic detection.

An analysis of carrier phase jitter in an MPSK receiver utilizing map estimation. Ph.D. Thesis Semiannual Status Report, Jul. 1993 - Jan. 1994

NASA Technical Reports Server (NTRS)

Osborne, William P.

1994-01-01

The use of 8 and 16 PSK TCM to support satellite communications in an effort to achieve more bandwidth efficiency in a power-limited channel has been proposed. This project addresses the problem of carrier phase jitter in an M-PSK receiver utilizing the high SNR approximation to the maximum aposteriori estimation of carrier phase. In particular, numerical solutions to the 8 and 16 PSK self-noise and phase detector gain in the carrier tracking loop are presented. The effect of changing SNR on the loop noise bandwidth is also discussed. These data are then used to compute variance of phase error as a function of SNR. Simulation and hardware data are used to verify these calculations. The results show that there is a threshold in the variance of phase error versus SNR curves that is a strong function of SNR and a weak function of loop bandwidth. The M-PSK variance thresholds occur at SNR's in the range of practical interest for the use of 8 and 16-PSK TCM. This suggests that phase error variance is an important consideration in the design of these systems.

Molecular dynamics studies of the 3D structure and planar ligand binding of a quadruplex dimer.

PubMed

Li, Ming-Hui; Luo, Quan; Xue, Xiang-Gui; Li, Ze-Sheng

2011-03-01

G-rich sequences can fold into a four-stranded structure called a G-quadruplex, and sequences with short loops are able to aggregate to form stable quadruplex multimers. Few studies have characterized the properties of this variety of quadruplex multimers. Using molecular modeling and molecular dynamics simulations, the present study investigated a dimeric G-quadruplex structure formed from a simple sequence of d(GGGTGGGTGGGTGGGT) (G1), and its interactions with a planar ligand of a perylene derivative (Tel03). A series of analytical methods, including free energy calculations and principal components analysis (PCA), was used. The results show that a dimer structure with stacked parallel monomer structures is maintained well during the entire simulation. Tel03 can bind to the dimer efficiently through end stacking, and the binding mode of the ligand stacked with the 3'-terminal thymine base is most favorable. PCA showed that the dominant motions in the free dimer occur on the loop regions, and the presence of the ligand reduces the flexibility of the loops. Our investigation will assist in understanding the geometric structure of stacked G-quadruplex multimers and may be helpful as a platform for rational drug design.

Adaptive gain, equalization, and wavelength stabilization techniques for silicon photonic microring resonator-based optical receivers

NASA Astrophysics Data System (ADS)

Palermo, Samuel; Chiang, Patrick; Yu, Kunzhi; Bai, Rui; Li, Cheng; Chen, Chin-Hui; Fiorentino, Marco; Beausoleil, Ray; Li, Hao; Shafik, Ayman; Titriku, Alex

2016-03-01

Interconnect architectures based on high-Q silicon photonic microring resonator devices offer a promising solution to address the dramatic increase in datacenter I/O bandwidth demands due to their ability to realize wavelength-division multiplexing (WDM) in a compact and energy efficient manner. However, challenges exist in realizing efficient receivers for these systems due to varying per-channel link budgets, sensitivity requirements, and ring resonance wavelength shifts. This paper reports on adaptive optical receiver design techniques which address these issues and have been demonstrated in two hybrid-integrated prototypes based on microring drop filters and waveguide photodetectors implemented in a 130nm SOI process and high-speed optical front-ends designed in 65nm CMOS. A 10Gb/s powerscalable architecture employs supply voltage scaling of a three inverter-stage transimpedance amplifier (TIA) that is adapted with an eye-monitor control loop to yield the necessary sensitivity for a given channel. As reduction of TIA input-referred noise is more critical at higher data rates, a 25Gb/s design utilizes a large input-stage feedback resistor TIA cascaded with a continuous-time linear equalizer (CTLE) that compensates for the increased input pole. When tested with a waveguide Ge PD with 0.45A/W responsivity, this topology achieves 25Gb/s operation with -8.2dBm sensitivity at a BER=10-12. In order to address microring drop filters sensitivity to fabrication tolerances and thermal variations, efficient wavelength-stabilization control loops are necessary. A peak-power-based monitoring loop which locks the drop filter to the input wavelength, while achieving compatibility with the high-speed TIA offset-correction feedback loop is implemented with a 0.7nm tuning range at 43μW/GHz efficiency.

Mutation of mapped TIA-1/TIAR binding sites in the 3' terminal stem-loop of West Nile virus minus-strand RNA in an infectious clone negatively affects genomic RNA amplification.

PubMed

Emara, Mohamed M; Liu, Hsuan; Davis, William G; Brinton, Margo A

2008-11-01

Previous data showed that the cellular proteins TIA-1 and TIAR bound specifically to the West Nile virus 3' minus-strand stem-loop [WNV3'(-)SL] RNA (37) and colocalized with flavivirus replication complexes in WNV- and dengue virus-infected cells (21). In the present study, the sites on the WNV3'(-)SL RNA required for efficient in vitro T-cell intracellular antigen-related (TIAR) and T-cell intracellular antigen-1 (TIA-1) protein binding were mapped to short AU sequences (UAAUU) located in two internal loops of the WNV3'(-)SL RNA structure. Infectious clone RNAs with all or most of the binding site nucleotides in one of the 3' (-)SL loops deleted or substituted did not produce detectable virus after transfection or subsequent passage. With one exception, deletion/mutation of a single terminal nucleotide in one of the binding sequences had little effect on the efficiency of protein binding or virus production, but mutation of a nucleotide in the middle of a binding sequence reduced both the in vitro protein binding efficiency and virus production. Plaque size, intracellular genomic RNA levels, and virus production progressively decreased with decreasing in vitro TIAR/TIA-1 binding activity, but the translation efficiency of the various mutant RNAs was similar to that of the parental RNA. Several of the mutant RNAs that inefficiently interacted with TIAR/TIA-1 in vitro rapidly reverted in vivo, indicating that they could replicate at a low level and suggesting that an interaction between TIAR/TIA-1 and the viral 3'(-)SL RNA is not required for initial low-level symmetric RNA replication but instead facilitates the subsequent asymmetric amplification of genome RNA from the minus-strand template.

Experimental demonstration of single-mode fiber coupling over relatively strong turbulence with adaptive optics.

PubMed

Chen, Mo; Liu, Chao; Xian, Hao

2015-10-10

High-speed free-space optical communication systems using fiber-optic components can greatly improve the stability of the system and simplify the structure. However, propagation through atmospheric turbulence degrades the spatial coherence of the signal beam and limits the single-mode fiber (SMF) coupling efficiency. In this paper, we analyze the influence of the atmospheric turbulence on the SMF coupling efficiency over various turbulences. The results show that the SMF coupling efficiency drops from 81% without phase distortion to 10% when phase root mean square value equals 0.3λ. The simulations of SMF coupling with adaptive optics (AO) indicate that it is inevitable to compensate the high-order aberrations for SMF coupling over relatively strong turbulence. The SMF coupling efficiency experiments, using an AO system with a 137-element deformable mirror and a Hartmann-Shack wavefront sensor, obtain average coupling efficiency increasing from 1.3% in open loop to 46.1% in closed loop under a relatively strong turbulence, D/r₀=15.1.

Slope efficiency over 30% single-frequency ytterbium-doped fiber laser based on Sagnac loop mirror filter.

PubMed

Yin, Mojuan; Huang, Shenghong; Lu, Baole; Chen, Haowei; Ren, Zhaoyu; Bai, Jintao

2013-09-20

A high-slope-efficiency single-frequency (SF) ytterbium-doped fiber laser, based on a Sagnac loop mirror filter (LMF), was demonstrated. It combined a simple linear cavity with a Sagnac LMF that acted as a narrow-bandwidth filter to select the longitudinal modes. And we introduced a polarization controller to restrain the spatial hole burning effect in the linear cavity. The system could operate at a stable SF oscillating at 1064 nm with the obtained maximum output power of 32 mW. The slope efficiency was found to be primarily dependent on the reflectivity of the fiber Bragg grating. The slope efficiency of multi-longitudinal modes was higher than 45%, and the highest slope efficiency of the single longitudinal mode we achieved was 33.8%. The power stability and spectrum stability were <2% and <0.1%, respectively, and the signal-to-noise ratio measured was around 60 dB.

First-order irreversible thermodynamic approach to a simple energy converter

NASA Astrophysics Data System (ADS)

Arias-Hernandez, L. A.; Angulo-Brown, F.; Paez-Hernandez, R. T.

2008-01-01

Several authors have shown that dissipative thermal cycle models based on finite-time thermodynamics exhibit loop-shaped curves of power output versus efficiency, such as it occurs with actual dissipative thermal engines. Within the context of first-order irreversible thermodynamics (FOIT), in this work we show that for an energy converter consisting of two coupled fluxes it is also possible to find loop-shaped curves of both power output and the so-called ecological function versus efficiency. In a previous work Stucki [J. W. Stucki, Eur. J. Biochem. 109, 269 (1980)] used a FOIT approach to describe the modes of thermodynamic performance of oxidative phosphorylation involved in adenosine triphosphate (ATP) synthesis within mithochondrias. In that work the author did not use the mentioned loop-shaped curves and he proposed that oxidative phosphorylation operates in a steady state at both minimum entropy production and maximum efficiency simultaneously, by means of a conductance matching condition between extreme states of zero and infinite conductances, respectively. In the present work we show that all Stucki’s results about the oxidative phosphorylation energetics can be obtained without the so-called conductance matching condition. On the other hand, we also show that the minimum entropy production state implies both null power output and efficiency and therefore this state is not fulfilled by the oxidative phosphorylation performance. Our results suggest that actual efficiency values of oxidative phosphorylation performance are better described by a mode of operation consisting of the simultaneous maximization of both the so-called ecological function and the efficiency.

DART system analysis.

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

Boggs, Paul T.; Althsuler, Alan; Larzelere, Alex R.

2005-08-01

The Design-through-Analysis Realization Team (DART) is chartered with reducing the time Sandia analysts require to complete the engineering analysis process. The DART system analysis team studied the engineering analysis processes employed by analysts in Centers 9100 and 8700 at Sandia to identify opportunities for reducing overall design-through-analysis process time. The team created and implemented a rigorous analysis methodology based on a generic process flow model parameterized by information obtained from analysts. They also collected data from analysis department managers to quantify the problem type and complexity distribution throughout Sandia's analyst community. They then used this information to develop a communitymore » model, which enables a simple characterization of processes that span the analyst community. The results indicate that equal opportunity for reducing analysis process time is available both by reducing the ''once-through'' time required to complete a process step and by reducing the probability of backward iteration. In addition, reducing the rework fraction (i.e., improving the engineering efficiency of subsequent iterations) offers approximately 40% to 80% of the benefit of reducing the ''once-through'' time or iteration probability, depending upon the process step being considered. Further, the results indicate that geometry manipulation and meshing is the largest portion of an analyst's effort, especially for structural problems, and offers significant opportunity for overall time reduction. Iteration loops initiated late in the process are more costly than others because they increase ''inner loop'' iterations. Identifying and correcting problems as early as possible in the process offers significant opportunity for time savings.« less

Numerical investigation of multichannel laser beam phase locking in turbulent atmosphere

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

Volkov, V A; Volkov, M V; Garanin, S G

2015-12-31

The efficiency of coherent multichannel beam combining under focusing through a turbulent medium on a target in the cases of phase conjugation and target irradiation in the feedback loop is investigated numerically in various approximations. The conditions of efficient focusing of multichannel radiation on the target are found. It is shown that the coherent beam combining with target irradiation in the feedback loop, which does not require a reference beam and wavefront measurements, is as good as the phase conjugation approach in the efficiency of focusing. It is found that the main effect of focusing is provided by properly chosenmore » phase shifts in the channels, whereas taking into account local wavefront tip tilts weakly affects the result. (control of laser radiation parameters)« less

Introduction to Loop Heat Pipes

NASA Technical Reports Server (NTRS)

Ku, Jentung

2015-01-01

This is the presentation file for the short course Introduction to Loop Heat Pipes, to be conducted at the 2015 Thermal Fluids and Analysis Workshop, August 3-7, 2015, Silver Spring, Maryland. This course will discuss operating principles and performance characteristics of a loop heat pipe. Topics include: 1) pressure profiles in the loop; 2) loop operating temperature; 3) operating temperature control; 4) loop startup; 4) loop shutdown; 5) loop transient behaviors; 6) sizing of loop components and determination of fluid inventory; 7) analytical modeling; 8) examples of flight applications; and 9) recent LHP developments.

Acceleration and Storage of Energetic Electrons in Magnetic Loops in the Course of Electric Current Oscillations

NASA Astrophysics Data System (ADS)

Zaitsev, V. V.; Stepanov, A. V.

2017-10-01

A mechanism of electron acceleration and storage of energetic particles in solar and stellar coronal magnetic loops, based on oscillations of the electric current, is considered. The magnetic loop is presented as an electric circuit with the electric current generated by convective motions in the photosphere. Eigenoscillations of the electric current in a loop induce an electric field directed along the loop axis. It is shown that the sudden reductions that occur in the course of type IV continuum and pulsating type III observed in various frequency bands (25 - 180 MHz, 110 - 600 MHz, 0.7 - 3.0 GHz) in solar flares provide evidence for acceleration and storage of the energetic electrons in coronal magnetic loops. We estimate the energization rate and the energy of accelerated electrons and present examples of the storage of energetic electrons in loops in the course of flares on the Sun or on ultracool stars. We also discuss the efficiency of the suggested mechanism as compared with the electron acceleration during the five-minute photospheric oscillations and with the acceleration driven by the magnetic Rayleigh-Taylor instability.

THE INSTABILITY AND NON-EXISTENCE OF MULTI-STRANDED LOOPS WHEN DRIVEN BY TRANSVERSE WAVES

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

Magyar, N.; Van Doorsselaere, T., E-mail: norbert.magyar@wis.kuleuven.be

2016-06-01

In recent years, omni-present transverse waves have been observed in all layers of the solar atmosphere. Coronal loops are often modeled as a collection of individual strands in order to explain their thermal behavior and appearance. We perform three-dimensional (3D) ideal magnetohydrodynamics simulations to study the effect of a continuous small amplitude transverse footpoint driving on the internal structure of a coronal loop composed of strands. The output is also converted into synthetic images, corresponding to the AIA 171 and 193 Å passbands, using FoMo. We show that the multi-stranded loop ceases to exist in the traditional sense of themore » word, because the plasma is efficiently mixed perpendicularly to the magnetic field, with the Kelvin–Helmholtz instability acting as the main mechanism. The final product of our simulation is a mixed loop with density structures on a large range of scales, resembling a power-law. Thus, multi-stranded loops are unstable to driving by transverse waves, and this raises strong doubts on the usability and applicability of coronal loop models consisting of independent strands.« less

Studying DNA looping by single-molecule FRET.

PubMed

Le, Tung T; Kim, Harold D

2014-06-28

Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA.

Studying DNA Looping by Single-Molecule FRET

PubMed Central

Le, Tung T.; Kim, Harold D.

2014-01-01

Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA. PMID:24998459

Isolated and coupled superquadric loop antennas for mobile communications applications

NASA Technical Reports Server (NTRS)

Jensen, Michael A.; Rahmat-Samii, Yahya

1993-01-01

This work provides an investigation of the performance of loop antennas for use in mobile communications applications. The analysis tools developed allow for high flexibility by representing the loop antenna as a superquadric curve, which includes the case of circular, elliptical, and rectangular loops. The antenna may be in an isolated environment, located above an infinite ground plane, or placed near a finite conducting plate or box. In cases where coupled loops are used, the two loops may have arbitrary relative positions and orientations. Several design examples are included to illustrate the versatility of the analysis capabilities. The performance of coupled loops arranged in a diversity scheme is also evaluated, and it is found that high diversity gain can be achieved even when the antennas are closely spaced.

THE ROLE OF KELVIN–HELMHOLTZ INSTABILITY FOR PRODUCING LOOP-TOP HARD X-RAY SOURCES IN SOLAR FLARES

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

Fang, Xia; Yuan, Ding; Xia, Chun

We propose a model for the formation of loop-top hard X-ray (HXR) sources in solar flares through the inverse Compton mechanism, scattering the surrounding soft X-ray (SXR) photons to higher energy HXR photons. We simulate the consequences of a flare-driven energy deposit in the upper chromosphere in the impulsive phase of single loop flares. The consequent chromosphere evaporation flows from both footpoints reach speeds up to hundreds of kilometers per second, and we demonstrate how this triggers Kelvin–Helmholtz instability (KHI) in the loop top, under mildly asymmetric conditions, or more toward the loop flank for strongly asymmetric cases. The KHImore » vortices further fragment the magnetic topology into multiple magnetic islands and current sheets, and the hot plasma within leads to a bright loop-top SXR source region. We argue that the magnetohydrodynamic turbulence that appears at the loop apex could be an efficient accelerator of non-thermal particles, which the island structures can trap at the loop-top. These accelerated non-thermal particles can upscatter the surrounding thermal SXR photons emitted by the extremely hot evaporated plasma to HXR photons.« less

Power impact of loop buffer schemes for biomedical wireless sensor nodes.

PubMed

Artes, Antonio; Ayala, Jose L; Catthoor, Francky

2012-11-06

Instruction memory organisations are pointed out as one of the major sources of energy consumption in embedded systems. As these systems are characterised by restrictive resources and a low-energy budget, any enhancement in this component allows not only to decrease the energy consumption but also to have a better distribution of the energy budget throughout the system. Loop buffering is an effective scheme to reduce energy consumption in instruction memory organisations. In this paper, the loop buffer concept is applied in real-life embedded applications that are widely used in biomedical Wireless Sensor Nodes, to show which scheme of loop buffer is more suitable for applications with certain behaviour. Post-layout simulations demonstrate that a trade-off exists between the complexity of the loop buffer architecture and the energy savings of utilising it. Therefore, the use of loop buffer architectures in order to optimise the instruction memory organisation from the energy efficiency point of view should be evaluated carefully, taking into account two factors: (1) the percentage of the execution time of the application that is related to the execution of the loops, and (2) the distribution of the execution time percentage over each one of the loops that form the application.

Energetics analysis of interstitial loops in single-phase concentrated solid-solution alloys

NASA Astrophysics Data System (ADS)

Wang, Xin-Xin; Niu, Liang-Liang; Wang, Shaoqing

2018-04-01

Systematic energetics analysis on the shape preference, relative stability and radiation-induced segregation of interstitial loops in nickel-containing single-phase concentrated solid-solution alloys have been conducted using atomistic simulations. It is shown that the perfect loops prefer rhombus shape for its low potential energy, while the Frank faulted loops favor ellipse for its low potential energy and the possible large configurational entropy. The decrease of stacking fault energy with increasing compositional complexity provides the energetic driving force for the formation of faulted loops, which, in conjunction with the kinetic factors, explains the experimental observation that the fraction of faulted loops rises with increasing compositional complexity. Notably, the kinetics is primarily responsible for the absence of faulted loops in nickel-cobalt with a very low stacking fault energy. We further demonstrate that the simultaneous nickel enrichment and iron/chromium depletion on interstitial loops can be fully accounted for by their energetics.

Stepwise Loop Insertion Strategy for Active Site Remodeling to Generate Novel Enzyme Functions.

PubMed

Hoque, Md Anarul; Zhang, Yong; Chen, Liuqing; Yang, Guangyu; Khatun, Mst Afroza; Chen, Haifeng; Hao, Liu; Feng, Yan

2017-05-19

The remodeling of active sites to generate novel biocatalysts is an attractive and challenging task. We developed a stepwise loop insertion strategy (StLois), in which randomized residue pairs are inserted into active site loops. The phosphotriesterase-like lactonase from Geobacillus kaustophilus (GkaP-PLL) was used to investigate StLois's potential for changing enzyme function. By inserting six residues into active site loop 7, the best variant ML7-B6 demonstrated a 16-fold further increase in catalytic efficiency toward ethyl-paraoxon compared with its initial template, that is a 609-fold higher, >10 7 fold substrate specificity shift relative to that of wild-type lactonase. The remodeled variants displayed 760-fold greater organophosphate hydrolysis activity toward the organophosphates parathion, diazinon, and chlorpyrifos. Structure and docking computations support the source of notably inverted enzyme specificity. Considering the fundamental importance of active site loops, the strategy has potential for the rapid generation of novel enzyme functions by loop remodeling.

Asymmetric dual-loop feedback to suppress spurious tones and reduce timing jitter in self-mode-locked quantum-dash lasers emitting at 155 μm

NASA Astrophysics Data System (ADS)

Asghar, Haroon; McInerney, John G.

2017-09-01

We demonstrate an asymmetric dual-loop feedback scheme to suppress external cavity side-modes induced in self-mode-locked quantum-dash lasers with conventional single and dual-loop feedback. In this letter, we achieved optimal suppression of spurious tones by optimizing the length of second delay time. We observed that asymmetric dual-loop feedback, with large (~8x) disparity in cavity lengths, eliminates all external-cavity side-modes and produces flat RF spectra close to the main peak with low timing jitter compared to single-loop feedback. Significant reduction in RF linewidth and reduced timing jitter was also observed as a function of increased second feedback delay time. The experimental results based on this feedback configuration validate predictions of recently published numerical simulations. This interesting asymmetric dual-loop feedback scheme provides simplest, efficient and cost effective stabilization of side-band free optoelectronic oscillators based on mode-locked lasers.

Navigating around the algebraic jungle of QCD: efficient evaluation of loop helicity amplitudes

NASA Astrophysics Data System (ADS)

Lam, C. S.

1993-05-01

A method is developed whereby spinor helicity techniques can be used to simlify the calculation of loop amplitudes. This is achieved by using the Feynman-parameter representation where the offending off-shell loop momenta do not appear. Other shortcuts motivated by the Bern-Kosower one-loop string calculations can be incorporated into the formalism. This includes color reorganization into Chan-Paton factors and the use of background Feynman gauge. This method is applicable to any Feynman diagram with any number of loops as long as the external masses can be ignored. In order to minimize the very considerable algebra encountered in non-abelian gauge theories, graphical methods are developed for most of the calculations. This enables the large number of terms encountered to be organized implicitly in the Feynman diagram without the necessity of writing down any of them algebraically. A one-loop four-gluon amplitude in a particular helicity configuration is computed explicitly to illustrate the method.

Recovery Act: Cedarville School District Retrofit of Heating and Cooling Systems with Geothermal Heat Pumps and Ground Source Water Loops

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

Jarrell, Mark

Cedarville School District retrofitted the heating and cooling systems in three campus areas (High School, Middle School, and Upper Elementary School) with geothermal heat pumps and ground source water loops, as a demonstration project for the effective implementation of geothermal heat pump systems and other energy efficiency and air quality improvements.

Rapid Damping of the Oscillations of Coronal Loops with an Azimuthal Magnetic Field

NASA Astrophysics Data System (ADS)

Mikhalyaev, B. B.

2005-06-01

We consider the MHD oscillations of an inhomogeneous coronal loop that consists of a dense cord surrounded by a shell. The magnetic field is longitudinal in the cord and has only an azimuthal component in the shell. The parameters of the loop are chosen to be such that there are no resonances; i.e., the resonance points are cut off. This choice is dictated by the formulated problem of considering the influence of the radiation of MHD waves into the surrounding space on the loop oscillations, thereby ruling out the possibility of resonant energy absorption. The wave radiation efficiency is high and allows low oscillation Q-factors, which are equal in order of magnitude to their observed values, to be obtained.

Hardware platforms for MEMS gyroscope tuning based on evolutionary computation using open-loop and closed -loop frequency response

NASA Technical Reports Server (NTRS)

Keymeulen, Didier; Ferguson, Michael I.; Fink, Wolfgang; Oks, Boris; Peay, Chris; Terrile, Richard; Cheng, Yen; Kim, Dennis; MacDonald, Eric; Foor, David

2005-01-01

We propose a tuning method for MEMS gyroscopes based on evolutionary computation to efficiently increase the sensitivity of MEMS gyroscopes through tuning. The tuning method was tested for the second generation JPL/Boeing Post-resonator MEMS gyroscope using the measurement of the frequency response of the MEMS device in open-loop operation. We also report on the development of a hardware platform for integrated tuning and closed loop operation of MEMS gyroscopes. The control of this device is implemented through a digital design on a Field Programmable Gate Array (FPGA). The hardware platform easily transitions to an embedded solution that allows for the miniaturization of the system to a single chip.

Substructure coupling in the frequency domain

NASA Technical Reports Server (NTRS)

1985-01-01

Frequency domain analysis was found to be a suitable method for determining the transient response of systems subjected to a wide variety of loads. However, since a large number of calculations are performed within the discrete frequency loop, the method loses it computational efficiency if the loads must be represented by a large number of discrete frequencies. It was also discovered that substructure coupling in the frequency domain work particularly well for analyzing structural system with a small number of interface and loaded degrees of freedom. It was discovered that substructure coupling in the frequency domain can lead to an efficient method of obtaining natural frequencies of undamped structures. It was also found that the damped natural frequencies of a system may be determined using frequency domain techniques.

γ5 in the four-dimensional helicity scheme

NASA Astrophysics Data System (ADS)

Gnendiger, C.; Signer, A.

2018-05-01

We investigate the regularization-scheme dependent treatment of γ5 in the framework of dimensional regularization, mainly focusing on the four-dimensional helicity scheme (fdh). Evaluating distinctive examples, we find that for one-loop calculations, the recently proposed four-dimensional formulation (fdf) of the fdh scheme constitutes a viable and efficient alternative compared to more traditional approaches. In addition, we extend the considerations to the two-loop level and compute the pseudoscalar form factors of quarks and gluons in fdh. We provide the necessary operator renormalization and discuss at a practical level how the complexity of intermediate calculational steps can be reduced in an efficient way.

Energy Efficient Engine: Control system preliminary definition report

NASA Technical Reports Server (NTRS)

Howe, David C.

1986-01-01

The object of the Control Preliminary Definition Program was to define a preliminary control system concept as a part of the Energy Efficient Engine program. The program was limited to a conceptual definition of a full authority digital electronic control system. System requirements were determined and a control system was conceptually defined to these requirements. Areas requiring technological development were identified and a plan was established for implementing the identified technological features, including a control technology demonstration. A significant element of this program was a study of the potential benefits of closed-loop active clearance control, along with laboratory tests of candidate clearance sensor elements for a closed loop system.

Mutational analysis of the active site flap (20s loop) of mandelate racemase.

PubMed

Bourque, Jennifer R; Bearne, Stephen L

2008-01-15

Mandelate racemase from Pseudomonas putida catalyzes the Mg2+-dependent 1,1-proton transfer that interconverts the enantiomers of mandelate. Residues of the 20s and 50s loops determine, in part, the topology and polarity of the active site and hence the substrate specificity. Previously, we proposed that, during racemization, the phenyl ring of mandelate moves between an S-pocket comprised of residues from the 50s loop and an R-pocket comprised of residues from the 20s loop [Siddiqi, F., Bourque, J. R., Jiang, H., Gardner, M., St. Maurice, M., Blouin, C., and Bearne, S. L. (2005) Biochemistry 44, 9013-9021]. The 20s loop constitutes a mobile beta-meander flap that covers the active site cavity shielding it from solvent and controlling entry and egress of ligands. To understand the role of the 20s loop in catalysis and substrate specificity, we constructed a series of mutants (V22A, V22I, V22F, T24S, A25V, V26A, V26L, V26F, V29A, V29L, V29F, V26A/V29L, and V22I/V29L) in which the sizes of hydrophobic side chains of the loop residues were varied. Catalytic efficiencies (kcat/Km) for all mutants were reduced between 6- and 40-fold with the exception of those of V22I, V26A, V29L, and V22I/V29L which had near wild-type efficiencies with mandelate. Thr 24 and Ala 25, located at the tip of the 20s loop, were particularly sensitive to minor alterations in the size of their hydrophobic side chains; however, most mutations were tolerated quite well, suggesting that flap mobility could compensate for increases in the steric bulk of hydrophobic side chains. With the exception of V29L, with mandelate as the substrate, and V22F and V26A/V29L, with 2-naphthylglycolate (2-NG) as the substrate, the values of kcat and Km were not altered in a manner consistent with steric obstruction of the R-pocket, perhaps due to flap mobility compensating for the increased size of the hydrophobic side chains. Surprisingly, V22I and V29L catalyzed the racemization of the bulkier substrate 2-NG with kcat/Km values approximately 2-fold greater than those observed for wild-type mandelate racemase. Although minor changes in substrate specificity were achieved through alterations of the active site flap of mandelate racemase, our results suggest that hydrophobic residues that reside on a flexible flap and define the topology of an active site through their van der Waals contacts with the substrate are quite tolerant of a variety of steric substitutions.

Analysis of a first order phase locked loop in the presence of Gaussian noise

NASA Technical Reports Server (NTRS)

Blasche, P. R.

1977-01-01

A first-order digital phase locked loop is analyzed by application of a Markov chain model. Steady state loop error probabilities, phase standard deviation, and mean loop transient times are determined for various input signal to noise ratios. Results for direct loop simulation are presented for comparison.

Relative stability of the open and closed conformations of the active site loop of streptavidin

NASA Astrophysics Data System (ADS)

Ignacio J., General; Meirovitch, Hagai

2011-01-01

The eight-residue surface loop, 45-52 (Ser, Ala, Val, Gly, Asn, Ala, Glu, Ser), of the homotetrameric protein streptavidin has a "closed" conformation in the streptavidin-biotin complex, where the corresponding binding affinity is one of the strongest found in nature (ΔG ˜ -18 kcal/mol). However, in most of the crystal structures of apo (unbound) streptavidin, the loop conformation is "open" and typically exhibits partial disorder and high B-factors. Thus, it is plausible to assume that the loop structure is changed from open to closed upon binding of biotin, and the corresponding difference in free energy, ΔF = Fopen - Fclosed in the unbound protein, should therefore be considered in the total absolute free energy of binding. ΔF (which has generally been neglected) is calculated here using our "hypothetical scanning molecular-dynamics" (HSMD) method. We use a protein model in which only the atoms closest to the loop are considered (the "template") and they are fixed in the x-ray coordinates of the free protein; the x-ray conformation of the closed loop is attached to the same (unbound) template and both systems are capped with the same sphere of TIP3P water. Using the force field of the assisted model building with energy refinement (AMBER), we carry out two separate MD simulations (at temperature T = 300 K), starting from the open and closed conformations, where only the atoms of the loop and water are allowed to move (the template-water and template-loop interactions are considered). The absolute Fopen and Fclosed (of loop + water) are calculated from these trajectories, where the loop and water contributions are obtained by HSMD and a thermodynamic integration (TI) process, respectively. The combined HSMD-TI procedure leads to total (loop + water) ΔF = -27.1 ± 2.0 kcal/mol, where the entropy TΔS constitutes 34% of ΔF, meaning that the effect of S is significant and should not be ignored. Also, ΔS is positive, in accord with the high flexibility of the open loop observed in crystal structures, while the energy ΔE is unexpectedly negative, thus also adding to the stability of the open loop. The loop and the 250 capped water molecules are the largest system studied thus far, which constitutes a test for the efficiency of HSMD-TI; this efficiency and technical issues related to the implementation of the method are also discussed. Finally, the result for ΔF is a prediction that will be considered in the calculation of the absolute free energy of binding of biotin to streptavidin, which constitutes our next project.

Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 2: Data

NASA Technical Reports Server (NTRS)

Waszak, M. R.; Schmidt, D. K.

1985-01-01

Two analysis methods are applied to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop modal analysis technique. This method considers the effect of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Both analyses indicated that dynamic aeroelastic effects caused a degradation in vehicle tracking performance, based on the evaluation of some simulation results. Volume 2 consists of the presentation of the state variable models of the flexible aircraft configurations used in the analysis applications mode shape plots for the structural modes, numerical results from the modal analysis frequency response plots from the pilot in the loop analysis and a listing of the modal analysis computer program.

Restriction enzyme cutting site distribution regularity for DNA looping technology.

PubMed

Shang, Ying; Zhang, Nan; Zhu, Pengyu; Luo, Yunbo; Huang, Kunlun; Tian, Wenying; Xu, Wentao

2014-01-25

The restriction enzyme cutting site distribution regularity and looping conditions were studied systematically. We obtained the restriction enzyme cutting site distributions of 13 commonly used restriction enzymes in 5 model organism genomes through two novel self-compiled software programs. All of the average distances between two adjacent restriction sites fell sharply with increasing statistic intervals, and most fragments were 0-499 bp. A shorter DNA fragment resulted in a lower looping rate, which was also directly proportional to the DNA concentration. When the length was more than 500 bp, the concentration did not affect the looping rate. Therefore, the best known fragment length was longer than 500 bp, and did not contain the restriction enzyme cutting sites which would be used for digestion. In order to make the looping efficiencies reach nearly 100%, 4-5 single cohesive end systems were recommended to digest the genome separately. Copyright © 2013 Elsevier B.V. All rights reserved.

Comparison between solar utilization of a closed microalgae-based bio-loop and that of a stand-alone photovoltaic system.

PubMed

Jin, Qiang; Chen, Lei; Li, Aimin; Liu, Fuqiang; Long, Chao; Shan, Aidang; Borthwick, Alistair G L

2015-05-01

This study compared the solar energy utilization of a closed microalgae-based bio-loop for energy efficient production of biogas with fertilizer recovery against that of a stand-alone photovoltaic (PV) system. The comparison was made from the perspective of broad life cycle assessment, simultaneously taking exergy to be the functional unit. The results indicated that the bio-loop was more environmentally competitive than an equivalent stand-alone PV system, but had higher economic cost due to high energy consumption during the operational phase. To fix the problem, a patented, interior pressurization scheduling method was used to operate the bio-loop, with microalgae and aerobic bacterial placed together in the same reactor. As a result, the overall environmental impact and total investment were respectively reduced by more than 75% and 84%, a vast improvement on the bio-loop. Copyright © 2014 Elsevier Ltd. All rights reserved.

Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements

PubMed Central

PENEDO, J. CARLOS; WILSON, TIMOTHY J.; JAYASENA, SUMEDHA D.; KHVOROVA, ANASTASIA; LILLEY, DAVID M.J.

2004-01-01

It has been shown that the activity of the hammerhead ribozyme at μM magnesium ion concentrations is markedly increased by the inclusion of loops in helices I and II. We have studied the effect of such loops on the magnesium ion-induced folding of the ribozyme, using fluorescence resonance energy transfer. We find that with the loops in place, folding into the active conformation occurs in a single step, in the μM range of magnesium ion concentration. Disruption of the loop–loop interaction leads to a reversion to two-step folding, with the second stage requiring mM concentrations of magnesium ion. Sodium ions also promote the folding of the natural form of the ribozyme at high concentrations, but the folding occurs as a two-stage process. The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions. PMID:15100442

Numerical analysis of radial inward flow turbine for CO2 based closed loop Brayton cycle

NASA Astrophysics Data System (ADS)

Kisan, Jadhav Amit; Govardhan, M.

2017-06-01

Last few decades have witnessed a phenomenal growth in the demand for power, which has driven the suppliers to find new sources of energy and increase the efficiency of power generation process. Power generation cycles are either steam based Rankine cycle or closed loop Brayton cycles providing an efficiency of 30 to 40%. An upcoming technology in this regard is the CO2 based Brayton cycle operating near the critical region which has applications in vast areas. Power generation of CO2 based Brayton cycle can vary from few kilowatts for waste heat recovery to hundreds of megawatts in sodium cooled fast reactors. A CO2 based Brayton cycle is being studied for power generation especially in mid-sized concentrated solar power plants by numerous research groups around the world. One of the main components of such a setting is its turbine. Simulating the flow conditions inside the turbine becomes very crucial in order to accurately predict the performance of the system. The flow inside radial inflow turbine is studied at various inlet temperatures and mass flow rates in order to predict the behavior of the turbine under various boundary conditions. The performance investigation of the turbine system is done on the basis of parameters such as total efficiency, pressure ratio, and power coefficient. Effect of different inlet stagnation temperature and exit mass flow rates on these parameters is also studied. Results obtained are encouraging for the use of CO2 as working fluid in Brayton cycle.

Virtual Induction Loops Based on Cooperative Vehicular Communications

PubMed Central

Gramaglia, Marco; Bernardos, Carlos J.; Calderon, Maria

2013-01-01

Induction loop detectors have become the most utilized sensors in traffic management systems. The gathered traffic data is used to improve traffic efficiency (i.e., warning users about congested areas or planning new infrastructures). Despite their usefulness, their deployment and maintenance costs are expensive. Vehicular networks are an emerging technology that can support novel strategies for ubiquitous and more cost-effective traffic data gathering. In this article, we propose and evaluate VIL (Virtual Induction Loop), a simple and lightweight traffic monitoring system based on cooperative vehicular communications. The proposed solution has been experimentally evaluated through simulation using real vehicular traces. PMID:23348033

Intelligent flight control systems

NASA Technical Reports Server (NTRS)

Stengel, Robert F.

1993-01-01

The capabilities of flight control systems can be enhanced by designing them to emulate functions of natural intelligence. Intelligent control functions fall in three categories. Declarative actions involve decision-making, providing models for system monitoring, goal planning, and system/scenario identification. Procedural actions concern skilled behavior and have parallels in guidance, navigation, and adaptation. Reflexive actions are spontaneous, inner-loop responses for control and estimation. Intelligent flight control systems learn knowledge of the aircraft and its mission and adapt to changes in the flight environment. Cognitive models form an efficient basis for integrating 'outer-loop/inner-loop' control functions and for developing robust parallel-processing algorithms.

Closed-loop, pilot/vehicle analysis of the approach and landing task

NASA Technical Reports Server (NTRS)

Anderson, M. R.; Schmidt, D. K.

1986-01-01

In the case of approach and landing, it is universally accepted that the pilot uses more than one vehicle response, or output, to close his control loops. Therefore, to model this task, a multi-loop analysis technique is required. The analysis problem has been in obtaining reasonable analytic estimates of the describing functions representing the pilot's loop compensation. Once these pilot describing functions are obtained, appropriate performance and workload metrics must then be developed for the landing task. The optimal control approach provides a powerful technique for obtaining the necessary describing functions, once the appropriate task objective is defined in terms of a quadratic objective function. An approach is presented through the use of a simple, reasonable objective function and model-based metrics to evaluate loop performance and pilot workload. The results of an analysis of the LAHOS (Landing and Approach of Higher Order Systems) study performed by R.E. Smith is also presented.

Design and Development of a Regenerative Blower for EVA Suit Ventilation

NASA Technical Reports Server (NTRS)

Izenson, Michael G.; Chen, Weibo; Hill, Roger W.; Phillips, Scott D.; Paul, Heather L.

2011-01-01

Ventilation subsystems in future space suits require a dedicated ventilation fan. The unique requirements for the ventilation fan - including stringent safety requirements and the ability to increase output to operate in buddy mode - combine to make a regenerative blower an attractive choice. This paper describes progress in the design, development, and testing of a regenerative blower designed to meet requirements for ventilation subsystems in future space suits. We have developed analysis methods for the blower s complex, internal flows and identified impeller geometries that enable significant improvements in blower efficiency. We verified these predictions by test, measuring aerodynamic efficiencies of 45% at operating conditions that correspond to the ventilation fan s design point. We have developed a compact motor/controller to drive the blower efficiently at low rotating speed (4500 rpm). Finally, we have assembled a low-pressure oxygen test loop to demonstrate the blower s reliability under prototypical conditions.

Organic Solar Cells beyond One Pair of Donor-Acceptor: Ternary Blends and More.

PubMed

Yang, Liqiang; Yan, Liang; You, Wei

2013-06-06

Ternary solar cells enjoy both an increased light absorption width, and an easy fabrication process associated with their simple structures. Significant progress has been made for such solar cells with demonstrated efficiencies over 7%; however, their fundamental working principles are still under investigation. This Perspective is intended to offer our insights on the three major governing mechanisms in these intriguing ternary solar cells: charge transfer, energy transfer, and parallel-linkage. Through careful analysis of exemplary cases, we summarize the advantages and limitations of these three major mechanisms and suggest future research directions. For example, incorporating additional singlet fission or upconversion materials into the energy transfer dominant ternary solar cells has the potential to break the theoretical efficiency limit in single junction organic solar cells. Clearly, a feedback loop between fundamental understanding and materials selection is in urgent need to accelerate the efficiency improvement of these ternary solar cells.

Finite element generation of arbitrary 3-D fracture networks for flow analysis in complicated discrete fracture networks

NASA Astrophysics Data System (ADS)

Zhang, Qi-Hua

2015-10-01

Finite element generation of complicated fracture networks is the core issue and source of technical difficulty in three-dimensional (3-D) discrete fracture network (DFN) flow models. Due to the randomness and uncertainty in the configuration of a DFN, the intersection lines (traces) are arbitrarily distributed in each face (fracture and other surfaces). Hence, subdivision of the fractures is an issue relating to subdivision of two-dimensional (2-D) domains with arbitrarily-distributed constraints. When the DFN configuration is very complicated, the well-known approaches (e.g. Voronoi Delaunay-based methods and advancing-front techniques) cannot operate properly. This paper proposes an algorithm to implement end-to-end connection between traces to subdivide 2-D domains into closed loops. The compositions of the vertices in the common edges between adjacent loops (which may belong to a single fracture or two connected fractures) are thus ensured to be topologically identical. The paper then proposes an approach for triangulating arbitrary loops which does not add any nodes to ensure consistency of the meshes at the common edges. In addition, several techniques relating to tolerance control and improving code robustness are discussed. Finally, the equivalent permeability of the rock mass is calculated for some very complicated DFNs (the DFN may contain 1272 fractures, 633 connected fractures, and 16,270 closed loops). The results are compared with other approaches to demonstrate the veracity and efficiency of the approach proposed in this paper.

The use of real-time, hardware-in-the-loop simulation in the design and development of the new Hughes HS601 spacecraft attitude control system

NASA Technical Reports Server (NTRS)

Slafer, Loren I.

1989-01-01

Realtime simulation and hardware-in-the-loop testing is being used extensively in all phases of the design, development, and testing of the attitude control system (ACS) for the new Hughes HS601 satellite bus. Realtime, hardware-in-the-loop simulation, integrated with traditional analysis and pure simulation activities is shown to provide a highly efficient and productive overall development program. Implementation of high fidelity simulations of the satellite dynamics and control system algorithms, capable of real-time execution (using applied Dynamics International's System 100), provides a tool which is capable of being integrated with the critical flight microprocessor to create a mixed simulation test (MST). The MST creates a highly accurate, detailed simulated on-orbit test environment, capable of open and closed loop ACS testing, in which the ACS design can be validated. The MST is shown to provide a valuable extension of traditional test methods. A description of the MST configuration is presented, including the spacecraft dynamics simulation model, sensor and actuator emulators, and the test support system. Overall system performance parameters are presented. MST applications are discussed; supporting ACS design, developing on-orbit system performance predictions, flight software development and qualification testing (augmenting the traditional software-based testing), mission planning, and a cost-effective subsystem-level acceptance test. The MST is shown to provide an ideal tool in which the ACS designer can fly the spacecraft on the ground.

Quantum efficiency measurement of the Transiting Exoplanet Survey Satellite (TESS) CCD detectors

NASA Astrophysics Data System (ADS)

Krishnamurthy, A.; Villasenor, J.; Thayer, C.; Kissel, S.; Ricker, G.; Seager, S.; Lyle, R.; Deline, A.; Morgan, E.; Sauerwein, T.; Vanderspek, R.

2016-07-01

Very precise on-ground characterization and calibration of TESS CCD detectors will significantly assist in the analysis of the science data from the mission. An accurate optical test bench with very high photometric stability has been developed to perform precise measurements of the absolute quantum efficiency. The setup consists of a vacuum dewar with a single MIT Lincoln Lab CCID-80 device mounted on a cold plate with the calibrated reference photodiode mounted next to the CCD. A very stable laser-driven light source is integrated with a closed-loop intensity stabilization unit to control variations of the light source down to a few parts-per-million when averaged over 60 s. Light from the stabilization unit enters a 20 inch integrating sphere. The output light from the sphere produces near-uniform illumination on the cold CCD and on the calibrated reference photodiode inside the dewar. The ratio of the CCD and photodiode signals provides the absolute quantum efficiency measurement. The design, key features, error analysis, and results from the test campaign are presented.

The effects of recycling loops in food waste management in Japan: based on the environmental and economic evaluation of food recycling.

PubMed

Takata, Miki; Fukushima, Kazuyo; Kino-Kimata, Noriko; Nagao, Norio; Niwa, Chiaki; Toda, Tatsuki

2012-08-15

In Japan, a revised Food Recycling Law went into effect in 2007 to promote a "recycling loop" that requires food industries to purchase farm products that are grown using food waste-derived compost/animal feed. To realize and expand food recycling, it is necessary to evaluate how the recycling facilities work in the recycling loop. The purpose of this study is to assess the environmental and economic efficiency of the food recycling facilities that are involved in the recycling loop, which are also known as looped facilities. The global warming potential and running cost of five looped facilities were evaluated by LCA (life cycle assessment) and LCC (life cycle cost) approaches: machine integrated compost, windrow compost, liquid feed, dry feed, and bio-gasification. The LCA results showed low total GHG (greenhouse gas) emissions of -126 and -49 kg-CO(2)/t-waste, respectively, for dry feed and bio-gasification facilities, due to a high substitution effect. The LCC study showed a low running cost for composting facilities of -15,648 and -18,955 yen/t-waste, respectively, due to high revenue from the food waste collection. It was found that the mandatory reporting of food waste emitters to the government increased collection fees; however, the collection fee in animal feed facilities was relatively low because food waste was collected at a low price or nutritious food waste was purchased to produce quality feed. In the characterisation survey of various treatment methods, the composting facilities showed a relatively low environmental impact and a high economic efficiency. Animal feed facilities had a wide distribution of the total GHG emissions, depending on both the energy usage during the drying process and the substitution effect, which were related to the water content of the food waste and the number of recycled products. In comparison with incineration, the majority of the food recycling facilities showed low GHG emissions and economic effectiveness. This paper also reported on the effects of recycling loops by comparing looped and non-looped animal feed facilities, and confirmed that the looped facilities were economically effective, due to an increased amount of food waste collection. Copyright © 2012 Elsevier B.V. All rights reserved.

An analysis by metabolic labelling of the encephalomyocarditis virus ribosomal frameshifting efficiency and stimulators.

PubMed

Ling, Roger; Firth, Andrew E

2017-08-01

Programmed -1 ribosomal frameshifting is a mechanism of gene expression whereby specific signals within messenger RNAs direct a proportion of ribosomes to shift -1 nt and continue translating in the new reading frame. Such frameshifting normally depends on an RNA structure stimulator 3'-adjacent to a 'slippery' heptanucleotide shift site sequence. Recently we identified an unusual frameshifting mechanism in encephalomyocarditis virus, where the stimulator involves a trans-acting virus protein. Thus, in contrast to other examples of -1 frameshifting, the efficiency of frameshifting in encephalomyocarditis virus is best studied in the context of virus infection. Here we use metabolic labelling to analyse the frameshifting efficiency of wild-type and mutant viruses. Confirming previous results, frameshifting depends on a G_GUU_UUU shift site sequence and a 3'-adjacent stem-loop structure, but is not appreciably affected by the 'StopGo' sequence present ~30 nt upstream. At late timepoints, frameshifting was estimated to be 46-76 % efficient.

[An implantable micro-device using wireless power transmission for measuring aortic aneurysm sac pressure].

PubMed

Guo, Xudong; Ge, Bin; Wang, Wenxing

2013-08-01

In order to detect endoleaks after endovascular aneurysm repair (EVAR), we developed an implantable micro-device based on wireless power transmission to measure aortic aneurysm sac pressure. The implantable micro-device is composed of a miniature wireless pressure sensor, an energy transmitting coil, a data recorder and a data processing platform. Power transmission without interconnecting wires is performed by a transmitting coil and a receiving coil. The coupling efficiency of wireless power transmission depends on the coupling coefficient between the transmitting coil and the receiving coil. With theoretical analysis and experimental study, we optimized the geometry of the receiving coil to increase the coupling coefficient. In order to keep efficiency balance and satisfy the maximizing conditions, we designed a closed loop power transmission circuit, including a receiving voltage feedback module based on wireless communication. The closed loop improved the stability and reliability of transmission energy. The prototype of the micro-device has been developed and the experiment has been performed. The experiments showed that the micro-device was feasible and valid. For normal operation, the distance between the transmitting coil and the receiving coil is smaller than 8cm. Besides, the distance between the micro-device and the data recorder is within 50cm.

Closed-loop spontaneous baroreflex transfer function is inappropriate for system identification of neural arc but partly accurate for peripheral arc: predictability analysis

PubMed Central

Kamiya, Atsunori; Kawada, Toru; Shimizu, Shuji; Sugimachi, Masaru

2011-01-01

Abstract Although the dynamic characteristics of the baroreflex system have been described by baroreflex transfer functions obtained from open-loop analysis, the predictability of time-series output dynamics from input signals, which should confirm the accuracy of system identification, remains to be elucidated. Moreover, despite theoretical concerns over closed-loop system identification, the accuracy and the predictability of the closed-loop spontaneous baroreflex transfer function have not been evaluated compared with the open-loop transfer function. Using urethane and α-chloralose anaesthetized, vagotomized and aortic-denervated rabbits (n = 10), we identified open-loop baroreflex transfer functions by recording renal sympathetic nerve activity (SNA) while varying the vascularly isolated intracarotid sinus pressure (CSP) according to a binary random (white-noise) sequence (operating pressure ± 20 mmHg), and using a simplified equation to calculate closed-loop-spontaneous baroreflex transfer function while matching CSP with systemic arterial pressure (AP). Our results showed that the open-loop baroreflex transfer functions for the neural and peripheral arcs predicted the time-series SNA and AP outputs from measured CSP and SNA inputs, with r2 of 0.8 ± 0.1 and 0.8 ± 0.1, respectively. In contrast, the closed-loop-spontaneous baroreflex transfer function for the neural arc was markedly different from the open-loop transfer function (enhanced gain increase and a phase lead), and did not predict the time-series SNA dynamics (r2; 0.1 ± 0.1). However, the closed-loop-spontaneous baroreflex transfer function of the peripheral arc partially matched the open-loop transfer function in gain and phase functions, and had limited but reasonable predictability of the time-series AP dynamics (r2, 0.7 ± 0.1). A numerical simulation suggested that a noise predominantly in the neural arc under resting conditions might be a possible mechanism responsible for our findings. Furthermore, the predictabilities of the neural arc transfer functions obtained in open-loop and closed-loop conditions were validated by closed-loop pharmacological (phenylephrine and nitroprusside infusions) pressure interventions. Time-series SNA responses to drug-induced AP changes predicted by the open-loop transfer function matched closely the measured responses (r2, 0.9 ± 0.1), whereas SNA responses predicted by closed-loop-spontaneous transfer function deviated greatly and were the inverse of measured responses (r, −0.8 ± 0.2). These results indicate that although the spontaneous baroreflex transfer function obtained by closed-loop analysis has been believed to represent the neural arc function, it is inappropriate for system identification of the neural arc but is essentially appropriate for the peripheral arc under resting conditions, when compared with open-loop analysis. PMID:21486839

An efficient cooling loop for connecting cryocooler to a helium reservoir

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

Taylor, C.E.; Abbott, C.S.R.; Leitner, D.

2003-09-21

The magnet system of the VENUS ECR Ion Source at LBNL has two 1.5-watt cryocoolers suspended in the cryostat vacuum. Helium vapor from the liquid reservoir is admitted to a finned condenser bolted to the cryocooler 2nd stage and returns as liquid via gravity. Small-diameter flexible tubes allow the cryocoolers to be located remotely from the reservoir. With 3.1 watts load, the helium reservoir is maintained at 4.35 K, 0.05K above the cryocooler temperature. Design, analysis, and performance are presented.

Isotope Brayton electric power system for the 500 to 2500 watt range

NASA Technical Reports Server (NTRS)

Macosko, R. P.; Barna, G. J.; Block, H. B.; Ingle, B. D.

1972-01-01

An extensive study was conducted at the Lewis Research Center to evaluate an isotope Brayton electric power system for use in the 500 to 2500 W power range. Overall system simplicity was emphasized in order to reduce parasitic power losses and improve system reliability. Detailed parametric cycle analysis, conceptual component designs, and evaluation of system packaging were included. A single-loop system (gas) with six major components including one rotating unit was selected. Calculated net system efficiency varies from 23 to 28 percent over the power range.

Smooth and rapid microwave synthesis of MIL-53(Fe) including superparamagnetic γ-Fe2O3 nanoparticles

NASA Astrophysics Data System (ADS)

Wengert, Simon; Albrecht, Joachim; Ruoss, Stephen; Stahl, Claudia; Schütz, Gisela; Schäfer, Ronald

2017-12-01

MIL-53(Fe) linked to superparamagnetic γ-Fe2O3 nanoparticles was created using time-efficient microwave synthesis. Intermediates as well as the final product have been characterized by Dynamic Light Scattering (DLS), Infrared Spectroscopy (FTIR) and Thermal Gravimetric Analysis (TGA). It is found that this route allows the production of Fe nanoparticles with typical sizes of about 80 nm that are embedded inside the metal-organic structures. Detailed magnetization measurements using SQUID magnetometry revealed a nearly reversible magnetization loop indicating essentially superparamagnetic behavior.

Vortex spin-torque oscillator stabilized by phase locked loop using integrated circuits

NASA Astrophysics Data System (ADS)

Kreissig, Martin; Lebrun, R.; Protze, F.; Merazzo-Jaimes, K.; Hem, J.; Vila, L.; Ferreira, R.; Cyrille, M.-C.; Ellinger, F.; Cros, V.; Ebels, U.; Bortolotti, P.

2017-05-01

Spin-torque nano-oscillators (STO) are candidates for the next technological implementation of spintronic devices in commercial electronic systems. For use in microwave applications, improving the noise figures by efficient control of their phase dynamics is a mandatory requirement. In order to achieve this, we developed a compact phase locked loop (PLL) based on custom integrated circuits (ICs) and demonstrate that it represents an efficient way to reduce the phase noise level of a vortex based STO. The advantage of our approach to phase stabilize STOs is that our compact system is highly reconfigurable e.g. in terms of the frequency divider ratio N, RF gain and loop gain. This makes it robust against device to device variations and at the same time compatible with a large range of STOs. Moreover, by taking advantage of the natural highly non-isochronous nature of the STO, the STO frequency can be easily controlled by e.g. changing the divider ratio N.

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

Imani, Mohammadreza F., E-mail: mohamad.imani@gmail.com; Grbic, Anthony

One of the obstacles preventing wireless power transfer from becoming ubiquitous is their leakage of power: high-amplitude electromagnetic fields that can interfere with other electronic devices, increase health concerns, or hinder power metering. In this paper, we present near-field plates (NFPs) as a novel method to tailor the electromagnetic fields generated by a wireless power transfer system while maintaining high efficiency. NFPs are modulated arrays or surfaces designed to form prescribed near-field patterns. The NFP proposed in this paper consists of an array of loaded loops that are designed to confine the electromagnetic fields of a resonant transmitting loop tomore » the desired direction (receiving loop) while suppressing fields in other directions. The step-by-step design procedure for this device is outlined. Two NFPs are designed and examined in full-wave simulation. Their performance is shown to be in close agreement with the design predictions, thereby verifying the proposed design and operation. A NFP is also fabricated and experimentally shown to form a unidirectional wireless power transfer link with high efficiency.« less

Neutron activation analysis system

DOEpatents

Taylor, M.C.; Rhodes, J.R.

1973-12-25

A neutron activation analysis system for monitoring a generally fluid media, such as slurries, solutions, and fluidized powders, including two separate conduit loops for circulating fluid samples within the range of radiation sources and detectors is described. Associated with the first loop is a neutron source that emits s high flux of slow and thermal neutrons. The second loop employs a fast neutron source, the flux from which is substantially free of thermal neutrons. Adjacent to both loops are gamma counters for spectrographic determination of the fluid constituents. Other gsmma sources and detectors are arranged across a portion of each loop for deterMining the fluid density. (Official Gazette)

Structure and Dynamics Analysis on Plexin-B1 Rho GTPase Binding Domain as a Monomer and Dimer

PubMed Central

2015-01-01

Plexin-B1 is a single-pass transmembrane receptor. Its Rho GTPase binding domain (RBD) can associate with small Rho GTPases and can also self-bind to form a dimer. In total, more than 400 ns of NAMD molecular dynamics simulations were performed on RBD monomer and dimer. Different analysis methods, such as root mean squared fluctuation (RMSF), order parameters (S2), dihedral angle correlation, transfer entropy, principal component analysis, and dynamical network analysis, were carried out to characterize the motions seen in the trajectories. RMSF results show that after binding, the L4 loop becomes more rigid, but the L2 loop and a number of residues in other regions become slightly more flexible. Calculating order parameters (S2) for CH, NH, and CO bonds on both backbone and side chain shows that the L4 loop becomes essentially rigid after binding, but part of the L1 loop becomes slightly more flexible. Backbone dihedral angle cross-correlation results show that loop regions such as the L1 loop including residues Q25 and G26, the L2 loop including residue R61, and the L4 loop including residues L89–R91, are highly correlated compared to other regions in the monomer form. Analysis of the correlated motions at these residues, such as Q25 and R61, indicate two signal pathways. Transfer entropy calculations on the RBD monomer and dimer forms suggest that the binding process should be driven by the L4 loop and C-terminal. However, after binding, the L4 loop functions as the motion responder. The signal pathways in RBD were predicted based on a dynamical network analysis method using the pathways predicted from the dihedral angle cross-correlation calculations as input. It is found that the shortest pathways predicted from both inputs can overlap, but signal pathway 2 (from F90 to R61) is more dominant and overlaps all of the routes of pathway 1 (from F90 to P111). This project confirms the allosteric mechanism in signal transmission inside the RBD network, which was in part proposed in the previous experimental study. PMID:24901636

To BG or not to BG: Background Subtraction for EIT Coronal Loops

NASA Astrophysics Data System (ADS)

Beene, J. E.; Schmelz, J. T.

2003-05-01

One of the few observational tests for various coronal heating models is to determine the temperature profile along coronal loops. Since loops are such an abundant coronal feature, this method originally seemed quite promising - that the coronal heating problem might actually be solved by determining the temperature as a function of arc length and comparing these observations with predictions made by different models. But there are many instruments currently available to study loops, as well as various techniques used to determine their temperature characteristics. Consequently, there are many different, mostly conflicting temperature results. We chose data for ten coronal loops observed with the Extreme ultraviolet Imaging Telescope (EIT), and chose specific pixels along each loop, as well as corresponding nearby background pixels where the loop emission was not present. Temperature analysis from the 171-to-195 and 195-to-284 angstrom image ratios was then performed on three forms of the data: the original data alone, the original data with a uniform background subtraction, and the original data with a pixel-by-pixel background subtraction. The original results show loops of constant temperature, as other authors have found before us, but the 171-to-195 and 195-to-284 results are significantly different. Background subtraction does not change the constant-temperature result or the value of the temperature itself. This does not mean that loops are isothermal, however, because the background pixels, which are not part of any contiguous structure, also produce a constant-temperature result with the same value as the loop pixels. These results indicate that EIT temperature analysis should not be trusted, and the isothermal loops that result from EIT (and TRACE) analysis may be an artifact of the analysis process. Solar physics research at the University of Memphis is supported by NASA grants NAG5-9783 and NAG5-12096.

Behaviour of fractional loop delay zero crossing digital phase locked loop (FR-ZCDPLL)

NASA Astrophysics Data System (ADS)

Nasir, Qassim

2018-01-01

This article analyses the performance of the first-order zero crossing digital phase locked loops (FR-ZCDPLL) when fractional loop delay is added to loop. The non-linear dynamics of the loop is presented, analysed and examined through bifurcation behaviour. Numerical simulation of the loop is conducted to proof the mathematical analysis of the loop operation. The results of the loop simulation show that the proposed FR-ZCDPLL has enhanced the performance compared to the conventional zero crossing DPLL in terms of wider lock range, captured range and stable operation region. In addition, extensive experimental simulation was conducted to find the optimum loop parameters for different loop environmental conditions. The addition of the fractional loop delay network in the conventional loop also reduces the phase jitter and its variance especially when the signal-to-noise ratio is low.

Power Impact of Loop Buffer Schemes for Biomedical Wireless Sensor Nodes

PubMed Central

Artes, Antonio; Ayala, Jose L.; Catthoor, Francky

2012-01-01

Instruction memory organisations are pointed out as one of the major sources of energy consumption in embedded systems. As these systems are characterised by restrictive resources and a low-energy budget, any enhancement in this component allows not only to decrease the energy consumption but also to have a better distribution of the energy budget throughout the system. Loop buffering is an effective scheme to reduce energy consumption in instruction memory organisations. In this paper, the loop buffer concept is applied in real-life embedded applications that are widely used in biomedical Wireless Sensor Nodes, to show which scheme of loop buffer is more suitable for applications with certain behaviour. Post-layout simulations demonstrate that a trade-off exists between the complexity of the loop buffer architecture and the energy savings of utilising it. Therefore, the use of loop buffer architectures in order to optimise the instruction memory organisation from the energy efficiency point of view should be evaluated carefully, taking into account two factors: (1) the percentage of the execution time of the application that is related to the execution of the loops, and (2) the distribution of the execution time percentage over each one of the loops that form the application. PMID:23202202

Shielded dual-loop resonator for arterial spin labeling at the neck.

PubMed

Hetzer, Stefan; Mildner, Toralf; Driesel, Wolfgang; Weder, Manfred; Möller, Harald E

2009-06-01

To construct a dual-loop coil for continuous arterial spin labeling (CASL) at the human neck and characterize it using computer simulations and magnetic resonance experiments. The labeling coil was designed as a perpendicular pair of shielded-loop resonators made from coaxial cable to obtain balanced circular loops with minimal electrical interaction with the lossy tissue. Three different excitation modes depending on the phase shift, Deltapsi, of the currents driving the two circular loops were investigated including a "Maxwell mode" (Deltapsi = 0 degrees ; ie, opposite current directions in both loops), a "quadrature mode" (Deltapsi = 90 degrees ), and a "Helmholtz mode" (Deltapsi = 180 degrees ; ie, identical current directions in both loops). Simulations of the radiofrequency field distribution indicated a high inversion efficiency at the locations of the carotid and vertebral arteries. With a 7-mm-thick polypropylene insulation, a sufficient distance from tissue was achieved to guarantee robust performance at a local specific absorption rate (SAR) well below legal safety limits. Application in healthy volunteers at 3 T yielded quantitative maps of gray matter perfusion with low intersubject variability. The coil permits robust labeling with low SAR and minimal sensitivity to different loading conditions.

Influence of cross-sectional ratio of down comer to riser on the efficiency of liquid circulation in loop air lift bubble column

NASA Astrophysics Data System (ADS)

Yamamoto, Tatsumi; Kawasaki, Hiroyuki; Mori, Hidetoshi

2017-11-01

Loop type bubble columns have good performance of liquid circulation and mass transfer by airlift effect, where the liquid circulation time is an important measurable characteristic parameter. This parameter is affected by the column construction, the aspect ratio of the column, the cross-sectional area ratio of down comer to riser (R), and the superficial gas velocity in the riser (UGR). In this work, the mean gas holdup and the liquid circulation time (TC) have been measured in four types of loop airlift type bubble column: concentric tube internal loop airlift type, rectangular internal loop airlift type, external loop airlift type, external loop airlift with separator. Air and tap water were used as gas and liquid phase, respectively. The results have demonstrated that the mean gas holdup in riser increases in proportion to UGR, and that it in downcomer changes according to the geometric parameters of each bubble column. TC has been found to conform to an empirical equation which depends on UGR and the length of draft tube or division plate in the region of 0.33 < R < 1.

RCD+: Fast loop modeling server.

PubMed

López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang; Chacón, Pablo

2016-07-08

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Search for Directed Networks by Different Random Walk Strategies

NASA Astrophysics Data System (ADS)

Zhu, Zi-Qi; Jin, Xiao-Ling; Huang, Zhi-Long

2012-03-01

A comparative study is carried out on the efficiency of five different random walk strategies searching on directed networks constructed based on several typical complex networks. Due to the difference in search efficiency of the strategies rooted in network clustering, the clustering coefficient in a random walker's eye on directed networks is defined and computed to be half of the corresponding undirected networks. The search processes are performed on the directed networks based on Erdös—Rényi model, Watts—Strogatz model, Barabási—Albert model and clustered scale-free network model. It is found that self-avoiding random walk strategy is the best search strategy for such directed networks. Compared to unrestricted random walk strategy, path-iteration-avoiding random walks can also make the search process much more efficient. However, no-triangle-loop and no-quadrangle-loop random walks do not improve the search efficiency as expected, which is different from those on undirected networks since the clustering coefficient of directed networks are smaller than that of undirected networks.

An efficient algorithm to compute marginal posterior genotype probabilities for every member of a pedigree with loops

PubMed Central

2009-01-01

Background Marginal posterior genotype probabilities need to be computed for genetic analyses such as geneticcounseling in humans and selective breeding in animal and plant species. Methods In this paper, we describe a peeling based, deterministic, exact algorithm to compute efficiently genotype probabilities for every member of a pedigree with loops without recourse to junction-tree methods from graph theory. The efficiency in computing the likelihood by peeling comes from storing intermediate results in multidimensional tables called cutsets. Computing marginal genotype probabilities for individual i requires recomputing the likelihood for each of the possible genotypes of individual i. This can be done efficiently by storing intermediate results in two types of cutsets called anterior and posterior cutsets and reusing these intermediate results to compute the likelihood. Examples A small example is used to illustrate the theoretical concepts discussed in this paper, and marginal genotype probabilities are computed at a monogenic disease locus for every member in a real cattle pedigree. PMID:19958551

Closed-loop analysis and control of a non-inverting buck-boost converter

NASA Astrophysics Data System (ADS)

Chen, Zengshi; Hu, Jiangang; Gao, Wenzhong

2010-11-01

In this article, a cascade controller is designed and analysed for a non-inverting buck-boost converter. The fast inner current loop uses sliding mode control. The slow outer voltage loop uses the proportional-integral (PI) control. Stability analysis and selection of PI gains are based on the nonlinear closed-loop error dynamics incorporating both the inner and outer loop controllers. The closed-loop system is proven to have a nonminimum phase structure. The voltage transient due to step changes of input voltage or resistance is predictable. The operating range of the reference voltage is discussed. The controller is validated by a simulation circuit. The simulation results show that the reference output voltage is well-tracked under system uncertainties or disturbances, confirming the validity of the proposed controller.

Extending the Universal One-Loop Effective Action: heavy-light coefficients

DOE PAGES

Ellis, Sebastian A. R.; Quevillon, Jérémie; You, Tevong; ...

2017-08-16

The Universal One-Loop Effective Action (UOLEA) is a general expression for the effective action obtained by evaluating in a model-independent way the one-loop expansion of a functional path integral. It can also be used to match UV theories to their low-energy EFTs more efficiently by avoiding redundant steps in the application of functional methods, simplifying the process of obtaining Wilson coefficients of operators up to dimension six. In addition to loops involving only heavy fields, matching may require the inclusion of loops containing both heavy and light particles. Here we use the recently-developed covariant diagram technique to extend the UOLEAmore » to include heavy-light terms which retain the same universal structure as the previously-derived heavy-only terms. As an example of its application, we integrate out a heavy singlet scalar with a linear coupling to a light doublet Higgs. The extension presented here is a first step towards completing the UOLEA to incorporate all possible structures encountered in a covariant derivative expansion of the one-loop path integral.« less

Extending the Universal One-Loop Effective Action: heavy-light coefficients

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

Ellis, Sebastian A. R.; Quevillon, Jérémie; You, Tevong

The Universal One-Loop Effective Action (UOLEA) is a general expression for the effective action obtained by evaluating in a model-independent way the one-loop expansion of a functional path integral. It can also be used to match UV theories to their low-energy EFTs more efficiently by avoiding redundant steps in the application of functional methods, simplifying the process of obtaining Wilson coefficients of operators up to dimension six. In addition to loops involving only heavy fields, matching may require the inclusion of loops containing both heavy and light particles. Here we use the recently-developed covariant diagram technique to extend the UOLEAmore » to include heavy-light terms which retain the same universal structure as the previously-derived heavy-only terms. As an example of its application, we integrate out a heavy singlet scalar with a linear coupling to a light doublet Higgs. The extension presented here is a first step towards completing the UOLEA to incorporate all possible structures encountered in a covariant derivative expansion of the one-loop path integral.« less

Efficient numerical evaluation of Feynman integrals

NASA Astrophysics Data System (ADS)

Li, Zhao; Wang, Jian; Yan, Qi-Shu; Zhao, Xiaoran

2016-03-01

Feynman loop integrals are a key ingredient for the calculation of higher order radiation effects, and are responsible for reliable and accurate theoretical prediction. We improve the efficiency of numerical integration in sector decomposition by implementing a quasi-Monte Carlo method associated with the CUDA/GPU technique. For demonstration we present the results of several Feynman integrals up to two loops in both Euclidean and physical kinematic regions in comparison with those obtained from FIESTA3. It is shown that both planar and non-planar two-loop master integrals in the physical kinematic region can be evaluated in less than half a minute with accuracy, which makes the direct numerical approach viable for precise investigation of higher order effects in multi-loop processes, e.g. the next-to-leading order QCD effect in Higgs pair production via gluon fusion with a finite top quark mass. Supported by the Natural Science Foundation of China (11305179 11475180), Youth Innovation Promotion Association, CAS, IHEP Innovation (Y4545170Y2), State Key Lab for Electronics and Particle Detectors, Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Y4KF061CJ1), Cluster of Excellence Precision Physics, Fundamental Interactions and Structure of Matter (PRISMA-EXC 1098)

Energy-Looping Nanoparticles: Harnessing Excited-State Absorption for Deep-Tissue Imaging.

PubMed

Levy, Elizabeth S; Tajon, Cheryl A; Bischof, Thomas S; Iafrati, Jillian; Fernandez-Bravo, Angel; Garfield, David J; Chamanzar, Maysamreza; Maharbiz, Michel M; Sohal, Vikaas S; Schuck, P James; Cohen, Bruce E; Chan, Emory M

2016-09-27

Near infrared (NIR) microscopy enables noninvasive imaging in tissue, particularly in the NIR-II spectral range (1000-1400 nm) where attenuation due to tissue scattering and absorption is minimized. Lanthanide-doped upconverting nanocrystals are promising deep-tissue imaging probes due to their photostable emission in the visible and NIR, but these materials are not efficiently excited at NIR-II wavelengths due to the dearth of lanthanide ground-state absorption transitions in this window. Here, we develop a class of lanthanide-doped imaging probes that harness an energy-looping mechanism that facilitates excitation at NIR-II wavelengths, such as 1064 nm, that are resonant with excited-state absorption transitions but not ground-state absorption. Using computational methods and combinatorial screening, we have identified Tm(3+)-doped NaYF4 nanoparticles as efficient looping systems that emit at 800 nm under continuous-wave excitation at 1064 nm. Using this benign excitation with standard confocal microscopy, energy-looping nanoparticles (ELNPs) are imaged in cultured mammalian cells and through brain tissue without autofluorescence. The 1 mm imaging depths and 2 μm feature sizes are comparable to those demonstrated by state-of-the-art multiphoton techniques, illustrating that ELNPs are a promising class of NIR probes for high-fidelity visualization in cells and tissue.

Direct Observation of Sink-Dependent Defect Evolution in Nanocrystalline Iron under Irradiation

DOE PAGES

El Atwani, Osman; Nathaniel, James; Leff, Asher C.; ...

2017-05-12

Crystal defects generated during irradiation can result in severe changes in morphology and an overall degradation of mechanical properties in a given material. Nanomaterials have been proposed as radiation damage tolerant materials, due to the hypothesis that defect density decreases with grain size refinement due to the increase in grain boundary surface area. The lower defect density should arise from grain boundary-point defect absorption and enhancement of interstitial-vacancy annihilation. In this study, low energy helium ion irradiation on free-standing iron thin films were performed at 573 K. Interstitial loops of a 0 /2 [111] Burgers vector were directly observed asmore » a result of the displacement damage. Loop density trends with grain size demonstrated an increase in the nanocrystalline (<100 nm) regime, but scattered behavior in the transition from the nanocrystalline to the ultra-fine regime (100–500 nm). To examine the validity of such trends, loop density and area for different grains at various irradiation doses were compared and revealed efficient defect absorption in the nanocrystalline grain size regime, but loop coalescence in the ultra-fine grain size regime. Lastly, a relationship between the denuded zone formation, a measure of grain boundary absorption efficiency, grain size, grain boundary type and misorientation angle is determined.« less

Direct Observation of Sink-Dependent Defect Evolution in Nanocrystalline Iron under Irradiation

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

El Atwani, Osman; Nathaniel, James; Leff, Asher C.

Crystal defects generated during irradiation can result in severe changes in morphology and an overall degradation of mechanical properties in a given material. Nanomaterials have been proposed as radiation damage tolerant materials, due to the hypothesis that defect density decreases with grain size refinement due to the increase in grain boundary surface area. The lower defect density should arise from grain boundary-point defect absorption and enhancement of interstitial-vacancy annihilation. In this study, low energy helium ion irradiation on free-standing iron thin films were performed at 573 K. Interstitial loops of a 0 /2 [111] Burgers vector were directly observed asmore » a result of the displacement damage. Loop density trends with grain size demonstrated an increase in the nanocrystalline (<100 nm) regime, but scattered behavior in the transition from the nanocrystalline to the ultra-fine regime (100–500 nm). To examine the validity of such trends, loop density and area for different grains at various irradiation doses were compared and revealed efficient defect absorption in the nanocrystalline grain size regime, but loop coalescence in the ultra-fine grain size regime. Lastly, a relationship between the denuded zone formation, a measure of grain boundary absorption efficiency, grain size, grain boundary type and misorientation angle is determined.« less

[Feasibility of treatment of landfill leachates by external loop three phase fluidized bed-constructed wetland system].

PubMed

Zhang, Jin-Sheng; Yuan, Xing-Zhong; Zeng, Guang-Ming; Dong, Bei-Bei; Liang, Yun-Shan

2009-11-01

In this study, the system composed with the external loop fluidized bed reactor and constructed wetland was used to treat the landfill leachate. The change of water quality for the landfill leachate treated by this system was investigated. The experimental results indicated that the COD and NH4(+) -N of the influent reduced from 4000 mg x L(-1) and 300 mg x L(-1) to 1 500 mg x L(-1) and 150 mg x L(-1) after the external loop three phase fluidized bed reactor and steady at 200 mg x L(-1) and 10 mg x L(-1) behind treated by the constructed wetland. The heavy metals of Cd, Zn, Pb were also reduced for treatment by external loop three phase fluidized bed reactor. They were steady at 0.01 mg x L(-1), 0.5 mg x L(-1), 0.1 mg x L(-1) from 0.12 mg x L(-1), 3.0 mg x L(-1), 1.4 mg x L(-1) because of the constructed wetland. We also compared the different plants for the efficiency, the results showed that whatever plants, there was little effects on the efficiency of the COD and NH4(+) -N, but the effect of heavy metal was markedness.

Towards a Certified Lightweight Array Bound Checker for Java Bytecode

NASA Technical Reports Server (NTRS)

Pichardie, David

2009-01-01

Dynamic array bound checks are crucial elements for the security of a Java Virtual Machines. These dynamic checks are however expensive and several static analysis techniques have been proposed to eliminate explicit bounds checks. Such analyses require advanced numerical and symbolic manipulations that 1) penalize bytecode loading or dynamic compilation, 2) complexify the trusted computing base. Following the Foundational Proof Carrying Code methodology, our goal is to provide a lightweight bytecode verifier for eliminating array bound checks that is both efficient and trustable. In this work, we define a generic relational program analysis for an imperative, stackoriented byte code language with procedures, arrays and global variables and instantiate it with a relational abstract domain as polyhedra. The analysis has automatic inference of loop invariants and method pre-/post-conditions, and efficient checking of analysis results by a simple checker. Invariants, which can be large, can be specialized for proving a safety policy using an automatic pruning technique which reduces their size. The result of the analysis can be checked efficiently by annotating the program with parts of the invariant together with certificates of polyhedral inclusions. The resulting checker is sufficiently simple to be entirely certified within the Coq proof assistant for a simple fragment of the Java bytecode language. During the talk, we will also report on our ongoing effort to scale this approach for the full sequential JVM.

Renormalization scheme dependence of high-order perturbative QCD predictions

NASA Astrophysics Data System (ADS)

Ma, Yang; Wu, Xing-Gang

2018-02-01

Conventionally, one adopts typical momentum flow of a physical observable as the renormalization scale for its perturbative QCD (pQCD) approximant. This simple treatment leads to renormalization scheme-and-scale ambiguities due to the renormalization scheme and scale dependence of the strong coupling and the perturbative coefficients do not exactly cancel at any fixed order. It is believed that those ambiguities will be softened by including more higher-order terms. In the paper, to show how the renormalization scheme dependence changes when more loop terms have been included, we discuss the sensitivity of pQCD prediction on the scheme parameters by using the scheme-dependent {βm ≥2}-terms. We adopt two four-loop examples, e+e-→hadrons and τ decays into hadrons, for detailed analysis. Our results show that under the conventional scale setting, by including more-and-more loop terms, the scheme dependence of the pQCD prediction cannot be reduced as efficiently as that of the scale dependence. Thus a proper scale-setting approach should be important to reduce the scheme dependence. We observe that the principle of minimum sensitivity could be such a scale-setting approach, which provides a practical way to achieve optimal scheme and scale by requiring the pQCD approximate be independent to the "unphysical" theoretical conventions.

Recycling Pricing and Coordination of WEEE Dual-Channel Closed-Loop Supply Chain Considering Consumers' Bargaining.

PubMed

Zhu, Xiaodong; Wang, Jing; Tang, Juan

2017-12-15

Environmentally friendly handling and efficient recycling of waste electrical on Waste Electrical and Electronic Equipment (WEEE) have grown to be a global social problem. As holders of WEEE, consumers have a significant effect on the recycling process. A consideration of and attention to the influence of consumer behavior in the recycling process can help achieve more effective recycling of WEEE. In this paper, we built a dual-channel closed-loop supply chain model composed of manufacturers, retailers, and network recycling platforms. Based on the influence of customer bargaining behavior, we studied several different scenarios of centralized decision-making, decentralized decision-making, and contract coordination, using the Stackelberg game theory. The results show that retailers and network recycling platforms will reduce the direct recovery prices to maintain their own profit when considering the impact of consumer bargaining behavior, while remanufacturers will improve the transfer payment price for surrendering part of the profit under revenue and the expense sharing contract. Using this contract, we can achieve supply chain coordination and eliminate the effect of consumer bargaining behavior on supply chain performance. It can be viewed from the parameter sensitivity analysis that when we select the appropriate sharing coefficient, the closed-loop supply chain can achieve the same system performance under a centralized decision.

Recycling Pricing and Coordination of WEEE Dual-Channel Closed-Loop Supply Chain Considering Consumers’ Bargaining

PubMed Central

Zhu, Xiaodong; Wang, Jing; Tang, Juan

2017-01-01

Environmentally friendly handling and efficient recycling of waste electrical on Waste Electrical and Electronic Equipment (WEEE) have grown to be a global social problem. As holders of WEEE, consumers have a significant effect on the recycling process. A consideration of and attention to the influence of consumer behavior in the recycling process can help achieve more effective recycling of WEEE. In this paper, we built a dual-channel closed-loop supply chain model composed of manufacturers, retailers, and network recycling platforms. Based on the influence of customer bargaining behavior, we studied several different scenarios of centralized decision-making, decentralized decision-making, and contract coordination, using the Stackelberg game theory. The results show that retailers and network recycling platforms will reduce the direct recovery prices to maintain their own profit when considering the impact of consumer bargaining behavior, while remanufacturers will improve the transfer payment price for surrendering part of the profit under revenue and the expense sharing contract. Using this contract, we can achieve supply chain coordination and eliminate the effect of consumer bargaining behavior on supply chain performance. It can be viewed from the parameter sensitivity analysis that when we select the appropriate sharing coefficient, the closed-loop supply chain can achieve the same system performance under a centralized decision. PMID:29244778

Optimal Dynamic Detection of Explosives (ODD-EX)

DTIC Science & Technology

2011-12-29

2. Control of nitromethane photoionization efficiency with shaped femtosecond pulses, J. Roslund, O. Shir, A. Dogariu, R. Miles, H. Rabitz, J. Chem...feedback loop. 2. Control of nitromethane photoionization efficiency with shaped femtosecond pulses, J. Roslund, O. Shir, A. Dogariu, R. Miles, H. Rabitz...resonances that allow a significant increase in the photoionization efficiency of nitromethane with shaped near-infrared femtosecond pulses. The

LOOPREF: A Fluid Code for the Simulation of Coronal Loops

NASA Technical Reports Server (NTRS)

deFainchtein, Rosalinda; Antiochos, Spiro; Spicer, Daniel

1998-01-01

This report documents the code LOOPREF. LOOPREF is a semi-one dimensional finite element code that is especially well suited to simulate coronal-loop phenomena. It has a full implementation of adaptive mesh refinement (AMR), which is crucial for this type of simulation. The AMR routines are an improved version of AMR1D. LOOPREF's versatility makes is suitable to simulate a wide variety of problems. In addition to efficiently providing very high resolution in rapidly changing regions of the domain, it is equipped to treat loops of variable cross section, any non-linear form of heat conduction, shocks, gravitational effects, and radiative loss.

The structure of the L3 loop from the hepatitis delta virus ribozyme: a syn cytidine.

PubMed Central

Lynch, S R; Tinoco, I

1998-01-01

The structure of the L3 central hairpin loop isolated from the antigenomic sequence of the hepatitis delta virus ribozyme with the P2 and P3 stems from the ribozyme stacked on top of the loop has been determined by NMR spectroscopy. The 26 nt stem-loop structure contains nine base pairs and a 7 nt loop (5'-UCCUCGC-3'). This hairpin loop is critical for efficient catalysis in the intact ribozyme. The structure was determined using homonuclear and heteronuclear NMR techniques on non-labeled and15N-labeled RNA oligonucleotides. The overall root mean square deviation for the structure was 1.15 A (+/- 0.28 A) for the loop and the closing C.G base pair and 0.90 A (+/- 0.18 A) for the loop and the closing C.G base pair but without the lone purine in the loop, which is not well defined in the structure. The structure indicates a U.C base pair between the nucleotides on the 5'- and 3'-ends of the loop. This base pair is formed with a single hydrogen bond involving the cytosine exocyclic amino proton and the carbonyl O4 of the uracil. The most unexpected finding in the loop is a syn cytidine. While not unprecedented, syn pyrimidines are highly unusual. This one can be confidently established by intranucleotide distances between the ribose and the base determined by NMR spectroscopy. A similar study of the structure of this loop showed a somewhat different three-dimensional structure. A discussion of differences in the two structures, as well as possible sites of interaction with the cleavage site, will be presented. PMID:9461457

Microbial and sponge loops modify fish production in phase-shifting coral reefs.

PubMed

Silveira, Cynthia B; Silva-Lima, Arthur W; Francini-Filho, Ronaldo B; Marques, Jomar S M; Almeida, Marcelo G; Thompson, Cristiane C; Rezende, Carlos E; Paranhos, Rodolfo; Moura, Rodrigo L; Salomon, Paulo S; Thompson, Fabiano L

2015-10-01

Shifts from coral to algae dominance of corals reefs have been correlated to fish biomass loss and increased microbial metabolism. Here we investigated reef benthic and planktonic primary production, benthic dissolved organic carbon (DOC) release and bacterial growth efficiency in the Abrolhos Bank, South Atlantic. Benthic DOC release rates are higher while water column bacterial growth efficiency is lower at impacted reefs. A trophic model based on the benthic and planktonic primary production was able to predict the observed relative fish biomass in healthy reefs. In contrast, in impacted reefs, the observed omnivorous fish biomass is higher, while that of the herbivorous/coralivorous fish is lower than predicted by the primary production-based model. Incorporating recycling of benthic-derived carbon in the model through microbial and sponge loops explains the difference and predicts the relative fish biomass in both reef types. Increased benthic carbon release rates and bacterial carbon metabolism, but decreased bacterial growth efficiency could lead to carbon losses through respiration and account for the uncoupling of benthic and fish production in phase-shifting reefs. Carbon recycling by microbial and sponge loops seems to promote an increase of small-bodied fish productivity in phase-shifting coral reefs. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

A method for paraplegic upper-body posture estimation during standing: a pilot study for rehabilitation purposes.

PubMed

Pages, Gaël; Ramdani, Nacim; Fraisse, Philippe; Guiraud, David

2009-06-01

This paper presents a contribution for restoring standing in paraplegia while using functional electrical stimulation (FES). Movement generation induced by FES remains mostly open looped and stimulus intensities are tuned empirically. To design an efficient closed-loop control, a preliminary study has been carried out to investigate the relationship between body posture and voluntary upper body movements. A methodology is proposed to estimate body posture in the sagittal plane using force measurements exerted on supporting handles during standing. This is done by setting up constraints related to the geometric equations of a two-dimensional closed chain model and the hand-handle interactions. All measured quantities are subject to an uncertainty assumed unknown but bounded. The set membership estimation problem is solved via interval analysis. Guaranteed uncertainty bounds are computed for the estimated postures. In order to test the feasibility of our methodology, experiments were carried out with complete spinal cord injured patients.

Sequence and structure determinants of Drosophila Hsp70 mRNA translation: 5'UTR secondary structure specifically inhibits heat shock protein mRNA translation.

PubMed Central

Hess, M A; Duncan, R F

1996-01-01

Preferential translation of Drosophila heat shock protein 70 (Hsp70) mRNA requires only the 5'-untranslated region (5'-UTR). The sequence of this region suggests that it has relatively little secondary structure, which may facilitate efficient protein synthesis initiation. To determine whether minimal 5'-UTR secondary structure is required for preferential translation during heat shock, the effect of introducing stem-loops into the Hsp70 mRNA 5'-UTR was measured. Stem-loops of -11 kcal/mol abolished translation during heat shock, but did not reduce translation in non-heat shocked cells. A -22 kcal/mol stem-loop was required to comparably inhibit translation during growth at normal temperatures. To investigate whether specific sequence elements are also required for efficient preferential translation, deletion and mutation analyses were conducted in a truncated Hsp70 5'-UTR containing only the cap-proximal and AUG-proximal segments. Linker-scanner mutations in the cap-proximal segment (+1 to +37) did not impair translation. Re-ordering the segments reduced mRNA translational efficiency by 50%. Deleting the AUG-proximal segment severely inhibited translation. A 5-extension of the full-length leader specifically impaired heat shock translation. These results indicate that heat shock reduces the capacity to unwind 5-UTR secondary structure, allowing only mRNAs with minimal 5'-UTR secondary structure to be efficiently translated. A function for specific sequences is also suggested. PMID:8710519

Approximate inference on planar graphs using loop calculus and belief progagation

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

Chertkov, Michael; Gomez, Vicenc; Kappen, Hilbert

We introduce novel results for approximate inference on planar graphical models using the loop calculus framework. The loop calculus (Chertkov and Chernyak, 2006b) allows to express the exact partition function Z of a graphical model as a finite sum of terms that can be evaluated once the belief propagation (BP) solution is known. In general, full summation over all correction terms is intractable. We develop an algorithm for the approach presented in Chertkov et al. (2008) which represents an efficient truncation scheme on planar graphs and a new representation of the series in terms of Pfaffians of matrices. We analyzemore » in detail both the loop series and the Pfaffian series for models with binary variables and pairwise interactions, and show that the first term of the Pfaffian series can provide very accurate approximations. The algorithm outperforms previous truncation schemes of the loop series and is competitive with other state-of-the-art methods for approximate inference.« less

A loop resonator for slice-selective in vivo EPR imaging in rats

PubMed Central

Hirata, Hiroshi; He, Guanglong; Deng, Yuanmu; Salikhov, Ildar; Petryakov, Sergey; Zweier, Jay L.

2008-01-01

A loop resonator was developed for 300-MHz continuous-wave electron paramagnetic resonance (CW-EPR) spectroscopy and imaging in live rats. A single-turn loop (55 mm in diameter) was used to provide sufficient space for the rat body. Efficiency for generating a radiofrequency magnetic field of 38 µT/W1/2 was achieved at the center of the loop. For the resonator itself, an unloaded quality factor of 430 was obtained. When a 350 g rat was placed in the resonator at the level of the lower abdomen, the quality factor decreased to 18. The sensitive volume in the loop was visualized with a bottle filled with an aqueous solution of the nitroxide spin probe 3-carbamoyl-2,2,5,5-tetramethyl-3-pyrrolin-1-yloxy (3-CP). The resonator was shown to enable EPR imaging in live rats. Imaging was performed for 3-CP that had been infused intravenously into the rat and its distribution was visualized within the lower abdomen. PMID:18006343

Resection with laser and high frequency cutting loop in tracheo-bronchial diseases.

PubMed

Illum, P

1989-04-01

A total of 23 patients have been treated endoscopically during the last three and a half years for a variety of diseases in the tracheo-bronchial tree; nine had a tracheal stenosis. Thirteen patients have been treated by resection with a high frequency cutting loop, eleven with a CO2-laser and one with an argon laser. A total of 44 treatments have been performed. Half of the treatments were given because of various malignant diseases. The results of the treatment of this very mixed group of patients were, as a whole, satisfactory with both CO2-laser and cutting loop. A more precise technique can be applied with the CO2-laser than the cutting loop, though the latter is the more efficient and easy to work with. Care must be taken with the loop because of its greater cutting depth. The argon laser has only limited use in the treatment of diseases in the trachea.

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Fernandez-Carmona, Juan; Condom, Roger; Cabrol-Bass, Daniel

2004-12-01

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

Thermodynamics-hydration relationships within loops that affect G-quadruplexes under molecular crowding conditions.

PubMed

Fujimoto, Takeshi; Nakano, Shu-ichi; Sugimoto, Naoki; Miyoshi, Daisuke

2013-01-31

We systematically investigated the effects of loop length on the conformation, thermodynamic stability, and hydration of DNA G-quadruplexes under dilute and molecular crowding conditions in the presence of Na(+). Structural analysis showed that molecular crowding induced conformational switches of oligonucleotides with the longer guanine stretch and the shorter thymine loop. Thermodynamic parameters further demonstrated that the thermodynamic stability of G-quadruplexes increased by increasing the loop length from two to four, whereas it decreased by increasing the loop length from four to six. Interestingly, we found by osmotic pressure analysis that the number of water molecules released from the G-quadruplex decreased with increasing thermodynamic stability. We assumed that base-stacking interactions within the loops not only stabilized the whole G-quadruplex structure but also created hydration sites by accumulating nucleotide functional groups. The molecular crowding effects on the stability of G-quadruplexes composed of abasic sites, which reduce the stacking interactions at the loops, further demonstrated that G-quadruplexes with fewer stacking interactions within the loops released a larger number of water molecules upon folding. These results showed that the stacking interactions within the loops determined the thermodynamic stability and hydration of the whole G-quadruplex.

Analysis of the bacterial luciferase mobile loop by replica-exchange molecular dynamics.

PubMed

Campbell, Zachary T; Baldwin, Thomas O; Miyashita, Osamu

2010-12-15

Bacterial luciferase contains an extended 29-residue mobile loop. Movements of this loop are governed by binding of either flavin mononucleotide (FMNH2) or polyvalent anions. To understand this process, loop dynamics were investigated using replica-exchange molecular dynamics that yielded conformational ensembles in either the presence or absence of FMNH2. The resulting data were analyzed using clustering and network analysis. We observed the closed conformations that are visited only in the simulations with the ligand. Yet the mobile loop is intrinsically flexible, and FMNH2 binding modifies the relative populations of conformations. This model provides unique information regarding the function of a crystallographically disordered segment of the loop near the binding site. Structures at or near the fringe of this network were compatible with flavin binding or release. Finally, we demonstrate that the crystallographically observed conformation of the mobile loop bound to oxidized flavin was influenced by crystal packing. Thus, our study has revealed what we believe are novel conformations of the mobile loop and additional context for experimentally determined structures. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Fluid mechanics of fusion lasers. Final report, September 11, 1978-June 5, 1980

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

Shwartz, J; Kulkarny, V A; Ausherman, D A

1980-01-01

Flow loop components required to operate continuous-flow, repetitively-pulsed CO/sub 2/ and KrF laser drivers for ICF were identified and their performance requirements were specified. It was found that the laser flow loops can have a major effect on the laser beam quality and overall efficiency. The pressure wave suppressor was identified as the most critical flow loop component. The performance of vented side-wall suppressors was evaluated both analytically and experimentally and found capable of meeting the performance requirements of the CO/sub 2/ and KrF fusion lasers. All other laser flow loop components are essentially similar to those used in conventional,more » low speed wind tunnels and are therefore well characterized and can be readily incorporated into fusion laser flow systems designs.« less

High-resolution retinal imaging through open-loop adaptive optics

NASA Astrophysics Data System (ADS)

Li, Chao; Xia, Mingliang; Li, Dayu; Mu, Quanquan; Xuan, Li

2010-07-01

Using the liquid crystal spatial light modulator (LC-SLM) as the wavefront corrector, an open-loop adaptive optics (AO) system for fundus imaging in vivo is constructed. Compared with the LC-SLM closed-loop AO system, the light energy efficiency is increased by a factor of 2, which is helpful for the safety of fundus illumination in vivo. In our experiment, the subjective accommodation method is used to precorrect the defocus aberration, and three subjects with different myopia 0, -3, and -5 D are tested. Although the residual wavefront error after correction cannot to detected, the fundus images adequately demonstrate that the imaging system reaches the resolution of a single photoreceptor cell through the open-loop correction. Without dilating and cyclopleging the eye, the continuous imaging for 8 s is recorded for one of the subjects.

Night glucose control with MD-Logic artificial pancreas in home setting: a single blind, randomized crossover trial-interim analysis.

PubMed

Nimri, Revital; Muller, Ido; Atlas, Eran; Miller, Shahar; Kordonouri, Olga; Bratina, Natasa; Tsioli, Christiana; Stefanija, Magdalena A; Danne, Thomas; Battelino, Tadej; Phillip, Moshe

2014-03-01

Artificial pancreas (AP) systems have shown an improvement in glucose control and a reduced risk of nocturnal hypoglycemia under controlled conditions but remain to be evaluated under daily-life conditions. To assess the feasibility, safety, and efficacy of the MD-Logic AP in controlling nocturnal glucose levels in the patient's home. Two-arm study, each covering four consecutive nights comparing the MD-Logic AP ('closed-loop' arm) with sensor-augmented pump therapy ('control' arm). Fifteen patients (mean age 19 ± 10.4 yr, A1c 7.5 ± 0.5% or 58 ± 5.9 mmol/mol, diabetes duration 9.9 ± 8.2 yr) were randomly assigned either to 'Group A' (first 'closed-loop', then 'control' arm) or to 'Group B' (vice versa). Investigators were masked to treatment intervention. Primary endpoints were the time spent with glucose levels below 70 mg/dL and the percentage of nights in which the mean overnight glucose levels were within 90-140 mg/dL. Endpoint analyses were based on unmodified sensor glucose readings of the four study nights. Time of glucose levels spent below 70 mg/dL was significantly shorter on the closed-loop nights than on control nights, median and interquartile range 3.8 (0, 11.6) and 48.7 (0.6, 67.9) min, respectively; p = 0.0034. The percentage of individual nights in which mean overnight glucose level was within 90-140 mg/dL was 67 (33, 88), and 50 (25, 75), under closed-loop and control nights, respectively, with no statistical difference. Secondary endpoint analyses demonstrated significant improvements in hypoglycemia parameters. No serious adverse events were reported. This interim analysis demonstrates the feasibility, safety, and efficiency of the MD-Logic AP system in home use, and demonstrates an improvement over sensor-augmented pump therapy. (ClinicalTrials.gov identifier NCT01726829). © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Neural signal processing and closed-loop control algorithm design for an implanted neural recording and stimulation system.

PubMed

Hamilton, Lei; McConley, Marc; Angermueller, Kai; Goldberg, David; Corba, Massimiliano; Kim, Louis; Moran, James; Parks, Philip D; Sang Chin; Widge, Alik S; Dougherty, Darin D; Eskandar, Emad N

2015-08-01

A fully autonomous intracranial device is built to continually record neural activities in different parts of the brain, process these sampled signals, decode features that correlate to behaviors and neuropsychiatric states, and use these features to deliver brain stimulation in a closed-loop fashion. In this paper, we describe the sampling and stimulation aspects of such a device. We first describe the signal processing algorithms of two unsupervised spike sorting methods. Next, we describe the LFP time-frequency analysis and feature derivation from the two spike sorting methods. Spike sorting includes a novel approach to constructing a dictionary learning algorithm in a Compressed Sensing (CS) framework. We present a joint prediction scheme to determine the class of neural spikes in the dictionary learning framework; and, the second approach is a modified OSort algorithm which is implemented in a distributed system optimized for power efficiency. Furthermore, sorted spikes and time-frequency analysis of LFP signals can be used to generate derived features (including cross-frequency coupling, spike-field coupling). We then show how these derived features can be used in the design and development of novel decode and closed-loop control algorithms that are optimized to apply deep brain stimulation based on a patient's neuropsychiatric state. For the control algorithm, we define the state vector as representative of a patient's impulsivity, avoidance, inhibition, etc. Controller parameters are optimized to apply stimulation based on the state vector's current state as well as its historical values. The overall algorithm and software design for our implantable neural recording and stimulation system uses an innovative, adaptable, and reprogrammable architecture that enables advancement of the state-of-the-art in closed-loop neural control while also meeting the challenges of system power constraints and concurrent development with ongoing scientific research designed to define brain network connectivity and neural network dynamics that vary at the individual patient level and vary over time.

Hall devices improve electric motor efficiency

NASA Technical Reports Server (NTRS)

Haeussermann, W.

1979-01-01

Efficiency of electric motors and generators is reduced by radial magnetic forces created by symmetric fields within device. Forces are sensed and counteracted by Hall devices on excitation or control windings. Hall generators directly measure and provide compensating control of anu asymmetry, eliminating additional measurements needed for calibration feedback control loop.

Efficient/reliable dc-to-dc inverter circuit

NASA Technical Reports Server (NTRS)

Pasciutti, E. R.

1970-01-01

Feedback loop, which contains an inductor in series with a saturable reactor, is added to a standard inverter circuit to permit the inverter power transistors to be switched in a controlled and efficient manner. This inverter is applicable where the power source has either high or low impedance properties.

A simplified fracture network model for studying the efficiency of a single well semi open loop heat exchanger in fractured crystalline rock

NASA Astrophysics Data System (ADS)

de La Bernardie, Jérôme; de Dreuzy, Jean-Raynald; Bour, Olivier; Thierion, Charlotte; Ausseur, Jean-Yves; Lesuer, Hervé; Le Borgne, Tanguy

2016-04-01

Geothermal energy is a renewable energy source particularly attractive due to associated low greenhouse gas emission rates. Crystalline rocks are in general considered of poor interest for geothermal applications at shallow depths (< 100m), because of the low permeability of the medium. In some cases, fractures may enhance permeability, but thermal energy storage at these shallow depths is still remaining very challenging because of the complexity of fractured media. The purpose of this study is to test the possibility of efficient thermal energy storage in shallow fractured rocks with a single well semi open loop heat exchanger (standing column well). For doing so, a simplified numerical model of fractured media is considered with few fractures. Here we present the different steps for building the model and for achieving the sensitivity analysis. First, an analytical and dimensional study on the equations has been achieved to highlight the main parameters that control the optimization of the system. In a second step, multiphysics software COMSOL was used to achieve numerical simulations in a very simplified model of fractured media. The objective was to test the efficiency of such a system to store and recover thermal energy depending on i) the few parameters controlling fracture network geometry (size and number of fractures) and ii) the frequency of cycles used to store and recover thermal energy. The results have then been compared to reference shallow geothermal systems already set up for porous media. Through this study, relationships between structure, heat exchanges and storage may be highlighted.

New insights into the structural and functional involvement of the gate loop in AcrB export activity.

PubMed

Ababou, Abdessamad

2018-02-01

AcrB is a major multidrug exporter in Escherichia coli and other Gram-negative bacteria. Its gate loop, located between the proximal and the distal pockets, have been reported to play important role in the export of many antibiotics. This loop location, rigidity and interactions with substrates have led recent reports to suggest that AcrB export mechanism operates in a sequential manner. First the substrate binds the proximal pocket in the access monomer, then it moves to bind the distal pocket in the binding monomer and subsequently it is extruded in the extrusion monomer. Recently, we have demonstrated that the gate loop is not required for the binding of Erythromycin but the integrity of this loop is important for an efficient export of this substrate. However, here we show that the antibiotic susceptibilities of the same AcrB gate loop mutants for Doxorubicin were unaffected, suggesting that this loop is not required for its export, and we demonstrate that this substrate may use principally the tunnel-1, located between transmembranes 8 and 9, more often than previously reported. To further explain our findings, here we address the gate loop mutations effects on AcrB solution energetics (fold, stability, molecular dynamics) and on the in vivo efflux of Erythromycin and Doxorubicin. Finally, we discuss the efflux and the discrepancy between the structural and the functional experiments for Erythromycin in these gate loop mutants. Copyright © 2017 Elsevier B.V. All rights reserved.

Decoupling of a tight-fit transceiver phased array for human brain imaging at 9.4T: Loop overlapping rediscovered.

PubMed

Avdievich, Nikolai I; Giapitzakis, Ioannis-Angelos; Pfrommer, Andreas; Henning, Anke

2018-02-01

To improve the decoupling of a transceiver human head phased array at ultra-high fields (UHF, ≥ 7T) and to optimize its transmit (Tx) and receive (Rx) performance, a single-row eight-element (1 × 8) tight-fit transceiver overlapped loop array was developed and constructed. Overlapping the loops increases the RF field penetration depth but can compromise decoupling by generating substantial mutual resistance. Based on analytical modeling, we optimized the loop geometry and relative positioning to simultaneously minimize the resistive and inductive coupling and constructed a 9.4T eight-loop transceiver head phased array decoupled entirely by overlapping loops. We demonstrated that both the magnetic and electric coupling between adjacent loops is compensated at the same time by overlapping and nearly perfect decoupling (below -30 dB) can be obtained without additional decoupling strategies. Tx-efficiency and SNR of the overlapped array outperformed that of a common UHF gapped array of similar dimensions. Parallel Rx-performance was also not compromised due to overlapping the loops. As a proof of concept we developed and constructed a 9.4T (400 MHz) overlapped transceiver head array based on results of the analytical modeling. We demonstrated that at UHF overlapping loops not only provides excellent decoupling but also improves both Tx- and Rx-performance. Magn Reson Med 79:1200-1211, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Co-Adapting Water Demand and Supply to Changing Climate in Agricultural Water Systems, A Case Study in Northern Italy

NASA Astrophysics Data System (ADS)

Giuliani, M.; Li, Y.; Mainardi, M.; Arias Munoz, C.; Castelletti, A.; Gandolfi, C.

2013-12-01

Exponentially growing water demands and increasing uncertainties in the hydrologic cycle due to changes in climate and land use will challenge water resources planning and management in the next decade. Improving agricultural productivity is particularly critical, being this sector the one characterized by the highest water demand. Moreover, to meet projected growth in human population and per-capita food demand, agricultural production will have to significantly increase in the next decades, even though water availability is expected to decrease due to climate change impacts. Agricultural systems are called to adapt their strategies (e.g., changing crop patterns and the corresponding water demand, or maximizing the efficiency in the water supply modifying irrigation scheduling and adopting high efficiency irrigation techniques) in order to re-optimize the use of limited water resources. Although many studies have assessed climate change impacts on agricultural practices and water management, most of them assume few scenarios of water demand or water supply separately, while an analysis of their reciprocal feedbacks is still missing. Moreover, current practices are generally established according to historical agreements and normative constraints and, in the absence of dramatic failures, the shift toward more efficient water management is not easily achievable. In this work, we propose to activate an information loop between farmers and water managers to improve the effectiveness of agricultural water management practices by matching the needs of the farmers with the design of water supply strategies. The proposed approach is tested on a real-world case study, namely the Lake Como serving the Muzza-Bassa Lodigiana irrigation district (Italy). A distributed-parameter, dynamic model of the system allows to simulate crop growth and the final yield over a range of hydro-climatic conditions, irrigation strategies and water-related stresses. The spatial component of the model is managed by a Web GIS to support the visualization of the results and the participation of the stakeholders. The activation of the information loop allows farmers to decide the most profitable crop option on the basis of an expected water supply. Knowing the farmers decisions, the water supply strategy (i.e., the regulation of Lake Como) is then optimized with respect to the actual irrigation demand of the crops. By recursively running this procedure, the farmers and the water manager will exchange information until the system converges to an equilibrium. Our results show that the proposed co-adaptation loop is able to enhance the efficiency of agricultural water management practices and foster crop production. Moreover, the analysis of the co-evolution of the two systems under change allows to estimate the potential for the approach to mitigate climate change adverse impacts.

Phase-locked loops. [in analog and digital circuits communication system

NASA Technical Reports Server (NTRS)

Gupta, S. C.

1975-01-01

An attempt to systematically outline the work done in the area of phase-locked loops which are now used in modern communication system design is presented. The analog phase-locked loops are well documented in several books but discrete, analog-digital, and digital phase-locked loop work is scattered. Apart from discussing the various analysis, design, and application aspects of phase-locked loops, a number of references are given in the bibliography.

Closed-loop fiber optic gyroscope with homodyne detection

NASA Astrophysics Data System (ADS)

Zhu, Yong; Qin, BingKun; Chen, Shufen

1996-09-01

Interferometric fiber optic gyroscope (IFOG) has been analyzed with autocontrol theory in this paper. An open-loop IFOG system is not able to restrain the bias drift, but a closed-loop IFOG system can do it very well using negative feedback in order to suppress zero drift. The result of our theoretic analysis and computer simulation indicate that the bias drift of a closed-loop system is smaller than an open- loop one.

Parametric study and optimization trends for the Von-Kármán-sodium dynamo experiment

NASA Astrophysics Data System (ADS)

Varela, J.

2018-05-01

We present magneto-hydrodynamic simulations of liquid sodium flow performed with the PLUTO compressible MHD code. We investigated the influence of the remanent magnetic field orientation and intensity, the impinging velocity field due to Ekman pumping as well as the impeller dimensions on the magnetic field collimation by helical flows in-between the impeller blades. For a simplified Cartesian geometry, we model the flow dynamics of a multi-blade impeller inspired by the Von-Kármán-Sodium experiment. This study shows that a remanent magnetic field oriented in the toroidal direction is the less efficient configuration to collimate the magnetic field, although if the radial or vertical components are not negligible, the collimation is significantly improved. As the intensity of the remanent magnetic field increases, the system magnetic energy becomes larger, but the magnetic field collimation efficiency remains the same, so the gain of magnetic energy is smaller as the remanent magnetic field intensity increases. The magnetic field collimation is modified if the impinging velocity field changes: the collimation is weaker if the impinging velocity increases from Γ = 0.8 to 0.9 and slightly larger if the impinging velocity decreases from Γ = 0.8 to 0.7. The analysis of the impeller dimensions points out that the most efficient configuration to collimate the magnetic field requires a ratio between the impeller blade height and the base longitude between 0.375 and 0.5. The largest enhancement of the hypothetical α2 dynamo loop, compared to the hypothetical Ω-α dynamo loop, is observed for the model that mimics the TM 73 impeller configuration rotating in the unscooping direction with a remanent magnetic field of 10-3 T orientated in the radial or vertical direction. The optimization trends obtained in the parametric analysis are also confirmed by simulations with a higher resolution and turbulence degree.

High performance liquid chromatography column efficiency enhancement by zero dead volume recycling and practical approach using park and recycle arrangement.

PubMed

Minarik, Marek; Franc, Martin; Minarik, Milan

2018-06-15

A new instrumental approach to recycling HPLC is described. The concept is based on fast reintroduction of incremental peak sections back onto the separation column. The re-circulation is performed within a closed loop containing only the column and two synchronized switching valves. By having HPLC pump out of the cycle, the method minimizes peak broadening due to dead volume. As a result the efficiency is dramatically increased allowing for the most demanding analytical applications. In addition, a parking loop is employed for temporary storage of analytes from the middle section of the separated mixture prior to their recycling. Copyright © 2018 Elsevier B.V. All rights reserved.

Extracting Loop Bounds for WCET Analysis Using the Instrumentation Point Graph

NASA Astrophysics Data System (ADS)

Betts, A.; Bernat, G.

2009-05-01

Every calculation engine proposed in the literature of Worst-Case Execution Time (WCET) analysis requires upper bounds on loop iterations. Existing mechanisms to procure this information are either error prone, because they are gathered from the end-user, or limited in scope, because automatic analyses target very specific loop structures. In this paper, we present a technique that obtains bounds completely automatically for arbitrary loop structures. In particular, we show how to employ the Instrumentation Point Graph (IPG) to parse traces of execution (generated by an instrumented program) in order to extract bounds relative to any loop-nesting level. With this technique, therefore, non-rectangular dependencies between loops can be captured, allowing more accurate WCET estimates to be calculated. We demonstrate the improvement in accuracy by comparing WCET estimates computed through our HMB framework against those computed with state-of-the-art techniques.

Alternative refrigerants and refrigeration cycles for domestic refrigerators

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

Sand, J.R.; Rice, C.L.; Vineyard, E.A.

1992-12-01

This project initially focused on using nonazeotropic refrigerant mixtures (NARMs) in a two-evaporator refrigerator-freezer design using two stages of liquid refrigerant subcooling. This concept was proposed and tested in 1975. The work suggested that the concept was 20% more efficient than the conventional one-evaporator refrigerator-freezer (RF) design. After considerable planning and system modeling based on using a NARM in a Lorenz-Meutzner (L-M) RF, the program scope was broadened to include investigation of a ``dual-loop`` concept where energy savings result from exploiting the less stringent operating conditions needed to satisfy cooling, of the fresh food section. A steady-state computer model (CYCLE-Z)more » capable of simulating conventional, dual loop, and L-M refrigeration cycles was developed. This model was used to rank the performance of 20 ozone-safe NARMs in the L-M refrigeration cycle while key system parameters were systematically varied. The results indicated that the steady-state efficiency of the L-M design was up to 25% greater than that of a conventional cycle. This model was also used to calculate the performance of other pure refrigerants relative to that of dichlorodifluoromethane, R-12, in conventional and dual-loop RF designs. Projected efficiency gains for these cycles were more modest, ranging from 0 to 10%. Individual compressor calorimeter tests of nine combinations of evaporator and condenser temperatures usually used to map RF compressor performance were carried out with R-12 and two candidate L-M NARMs in several compressors. Several models of a commercially produced two-evaporator RF were obtained as test units. Two dual-loop RF designs were built and tested as part of this project.« less

Thin-Wire Modeling Techniques Applied to Antenna Analysis.

DTIC Science & Technology

1974-10-11

Ol- MULT11 CRN LOOP ANTENNA ... 30 2.4.1 Balanced vs unbalanced operation ... 3 1 2.4.2 Horizontal vs vertical configuration ... 33 3.0...of the Ml A-l Mimloop ... 28 Hl; multiturn loop antenna of Ohio State University ...31 Configurations ot balanced and unbalanced MTLs ... 32...4. Evaluation of Multiturn Loop Antenna In each example the specific project is outlined and the antenna analysis problems of particular interest

Mechanical testing and finite element analysis of orthodontic teardrop loop.

PubMed

Coimbra, Maria Elisa Rodrigues; Penedo, Norman Duque; de Gouvêa, Jayme Pereira; Elias, Carlos Nelson; de Souza Araújo, Mônica Tirre; Coelho, Paulo Guilherme

2008-02-01

Understanding how teeth move in response to mechanical loads is an important aspect of orthodontic treatment. Treatment planning should include consideration of the appliances that will meet the desired loading of the teeth to result in optimized treatment outcomes. The purpose of this study was to evaluate the use of computer simulation to predict the force and the torsion obtained after the activation of tear drop loops of 3 heights. Seventy-five retraction loops were divided into 3 groups according to height (6, 7, and 8 mm). The loops were subjected to tensile load through displacements of 0.5, 1.0, 1.5, and 2.0 mm, and the resulting forces and torques were recorded. The loops were designed in AutoCAD software(2005; Autodesk Systems, Alpharetta, GA), and finite element analysis was performed with Ansys software(version 7.0; Swanson Analysis System, Canonsburg, PA). Statistical analysis of the mechanical experiment results was obtained by ANOVA and the Tukey post-hoc test (P < .01). The correlation test and the paired t test (P < .05) were used to compare the computer simulation with the mechanical experiment. The computer simulation accurately predicted the experimentally determined mechanical behavior of tear drop loops of different heights and should be considered an alternative for designing orthodontic appliances before treatment.

Simulation Speed Analysis and Improvements of Modelica Models for Building Energy Simulation

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

Jorissen, Filip; Wetter, Michael; Helsen, Lieve

This paper presents an approach for speeding up Modelica models. Insight is provided into how Modelica models are solved and what determines the tool’s computational speed. Aspects such as algebraic loops, code efficiency and integrator choice are discussed. This is illustrated using simple building simulation examples and Dymola. The generality of the work is in some cases verified using OpenModelica. Using this approach, a medium sized office building including building envelope, heating ventilation and air conditioning (HVAC) systems and control strategy can be simulated at a speed five hundred times faster than real time.

Integrated autopilot/autothrottle for the NASA TSRV B-737 aircraft: Design and verification by nonlinear simulation

NASA Technical Reports Server (NTRS)

Bruce, Kevin R.

1989-01-01

An integrated autopilot/autothrottle was designed for flight test on the NASA TSRV B-737 aircraft. The system was designed using a total energy concept and is attended to achieve the following: (1) fuel efficiency by minimizing throttle activity; (2) low development and implementation costs by designing the control modes around a fixed inner loop design; and (3) maximum safety by preventing stall and engine overboost. The control law was designed initially using linear analysis; the system was developed using nonlinear simulations. All primary design requirements were satisfied.

The loop structure and the RNA helicase p72/DDX17 influence the processing efficiency of the mice miR-132

PubMed Central

Remenyi, Judit; Bajan, Sarah; Fuller-Pace, Frances V.; Arthur, J. Simon C.; Hutvagner, Gyorgy

2016-01-01

miRNAs are small RNAs that are key regulators of gene expression in eukaryotic organisms. The processing of miRNAs is regulated by structural characteristics of the RNA and is also tightly controlled by auxiliary protein factors. Among them, RNA binding proteins play crucial roles to facilitate or inhibit miRNA maturation and can be controlled in a cell, tissue and species-specific manners or in response to environmental stimuli. In this study we dissect the molecular mechanism that promotes the overexpression of miR-132 in mice over its related, co-transcribed and co-regulated miRNA, miR-212. We have shown that the loop structure of miR-132 is a key determinant for its efficient processing in cells. We have also identified a range of RNA binding proteins that recognize the loop of miR-132 and influence both miR-132 and miR-212 processing. The DEAD box helicase p72/DDX17 was identified as a factor that facilitates the specific processing of miR-132. PMID:26947125

Electron acceleration in solar flares and the transition from nonthermal to thermal hard X-ray phases

NASA Technical Reports Server (NTRS)

Smith, D. F.

1985-01-01

Observations are reviewed which indicate that hard X-rays during the impulsive phase of a flare typically start with a primarily nonthermal phase which undergoes a transition to a primarily thermal phase as the flare progresses. Recent theoretical work on the modified two-stream instability as an efficient electron accelerator and modeling of thermal hard X-ray sources is considered. A scenario which is termed the dissipative thermal model is proposed to explain the observations. Fast tearing modes occurring in a loop give rise to cross-field ion motion. This in turn excites the modified two-stream instability which converts about 50 percent of the ion energy into accelerated electrons along the loop as long as the plasma beta is less than 0.3. These electrons impact the chromosphere and boil off a part of it which rises up the loop. This density increase coupled with the temperature increase due to tearing causes the beta to increase beyond 0.3 and efficient electron acceleration ceases. This leads to the primarily thermal phase.

Spatiotemporal Analysis of Coronal Loops Using Seismology of Damped Kink Oscillations and Forward Modeling of EUV Intensity Profiles

NASA Astrophysics Data System (ADS)

Pascoe, D. J.; Anfinogentov, S. A.; Goddard, C. R.; Nakariakov, V. M.

2018-06-01

The shape of the damping profile of kink oscillations in coronal loops has recently allowed the transverse density profile of the loop to be estimated. This requires accurate measurement of the damping profile that can distinguish the Gaussian and exponential damping regimes, otherwise there are more unknowns than observables. Forward modeling of the transverse intensity profile may also be used to estimate the width of the inhomogeneous layer of a loop, providing an independent estimate of one of these unknowns. We analyze an oscillating loop for which the seismological determination of the transverse structure is inconclusive except when supplemented by additional spatial information from the transverse intensity profile. Our temporal analysis describes the motion of a coronal loop as a kink oscillation damped by resonant absorption, and our spatial analysis is based on forward modeling the transverse EUV intensity profile of the loop under the isothermal and optically thin approximations. We use Bayesian analysis and Markov chain Monte Carlo sampling to apply our spatial and temporal models both individually and simultaneously to our data and compare the results with numerical simulations. Combining the two methods allows both the inhomogeneous layer width and density contrast to be calculated, which is not possible for the same data when each method is applied individually. We demonstrate that the assumption of an exponential damping profile leads to a significantly larger error in the inferred density contrast ratio compared with a Gaussian damping profile.

Air-Cooled Design of a Temperature-Swing Adsorption Compressor for Closed-Loop Air Revitalization Systems

NASA Technical Reports Server (NTRS)

Mulloth, Lila M.; Affleck, Dave L.; Rosen, Micha; LeVan, M. Douglas; Wang, Yuan; Cavalcante, Celio L.

2004-01-01

The air revitalization system of the International Space Station (ISS) operates in an open loop mode and relies on the resupply of oxygen and other consumables from earth for the life support of astronauts. A compressor is required for delivering the carbon dioxide from a removal assembly to a reduction unit to recover oxygen and thereby closing the air-loop. We have a developed a temperature-swing adsorption compressor (TSAC) for performing these tasks that is energy efficient, quiet, and has no rapidly moving parts. This paper discusses the mechanical design and the results of thermal model validation tests of a TSAC that uses air as the cooling medium.

Opto-Electronic Oscillator Stabilized By A Hyperfine Atomic Transition

NASA Technical Reports Server (NTRS)

Strekalov, Dmitry; Aveline, David; Matsko, Andrey B.; Thompson, Robert; Yu, Nan

2004-01-01

Opto-electronic oscillator (OEO) is a closed-loop system with part of the loop is implemented by an optical beam, and the rest by RF circuitry. The technological advantage of this approach over traditional all-RF loops in the gigahertz range comes from the that frequency filtering can be done far more efficiently in the optical range with compact, low power, and have superior stability. In this work, we report our preliminary results on using the phenomenon of coherent population trapping in (87) Rb vapor as an optical filter. Such a filter allows us to stabilize the OEO at the hyperfine splitting frequency of rubidium, thus implementing a novel type of frequency standard.

Run-time parallelization and scheduling of loops

NASA Technical Reports Server (NTRS)

Saltz, Joel H.; Mirchandaney, Ravi; Crowley, Kay

1991-01-01

Run-time methods are studied to automatically parallelize and schedule iterations of a do loop in certain cases where compile-time information is inadequate. The methods presented involve execution time preprocessing of the loop. At compile-time, these methods set up the framework for performing a loop dependency analysis. At run-time, wavefronts of concurrently executable loop iterations are identified. Using this wavefront information, loop iterations are reordered for increased parallelism. Symbolic transformation rules are used to produce: inspector procedures that perform execution time preprocessing, and executors or transformed versions of source code loop structures. These transformed loop structures carry out the calculations planned in the inspector procedures. Performance results are presented from experiments conducted on the Encore Multimax. These results illustrate that run-time reordering of loop indexes can have a significant impact on performance.

Effect of Variable Emittance Coatings on the Operation of a Miniature Loop Heat Pipe

NASA Technical Reports Server (NTRS)

Douglas, Donya M.; Ku, Jentung; Ottenstein, Laura; Swanson, Theodore; Hess, Steve; Darrin, Ann

2005-01-01

Abstract. As the size of spacecraft shrink to accommodate small and more efficient instruments, smaller launch vehicles, and constellation missions, all subsystems must also be made smaller. Under NASA NFL4 03-OSS-02, Space Technology-8 (ST 8), NASA Goddard Space Flight Center and Jet Propulsion Laboratory jointly conducted a Concept Definition study to develop a miniature loop heat pipe (MLHP) thermal management system design suitable for future small spacecraft. The proposed MLHP thermal management system consists of a miniature loop heat pipe (LHP) and deployable radiators that are coated with variable emittance coatings (VECs). As part of the Phase A study and proof of the design concept, variable emittance coatings were integrated with a breadboard miniature loop heat pipe. The miniature loop heat pipe was supplied by the Jet Propulsion Laboratory (PL), while the variable emittance technology were supplied by Johns Hopkins University Applied Physics Laboratory and Sensortex, Inc. The entire system was tested under vacuum at various temperature extremes and power loads. This paper summarizes the results of this testing and shows the effect of the VEC on the operation of a miniature loop heat pipe.

A flexible algorithm for calculating pair interactions on SIMD architectures

NASA Astrophysics Data System (ADS)

Páll, Szilárd; Hess, Berk

2013-12-01

Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have traditionally worked well, especially since compilers usually do a good job of unrolling the inner loop. In order to reach high performance on modern CPU and accelerator architectures, single-instruction multiple-data (SIMD) parallelization has become essential. Avoiding memory bottlenecks is also increasingly important and requires reducing the ratio of memory to arithmetic operations. Moreover, when pairs only interact within a certain cut-off distance, good SIMD utilization can only be achieved by reordering input and output data, which quickly becomes a limiting factor. Here we present an algorithm for SIMD parallelization based on grouping a fixed number of particles, e.g. 2, 4, or 8, into spatial clusters. Calculating all interactions between particles in a pair of such clusters improves data reuse compared to the traditional scheme and results in a more efficient SIMD parallelization. Adjusting the cluster size allows the algorithm to map to SIMD units of various widths. This flexibility not only enables fast and efficient implementation on current CPUs and accelerator architectures like GPUs or Intel MIC, but it also makes the algorithm future-proof. We present the algorithm with an application to molecular dynamics simulations, where we can also make use of the effective buffering the method introduces.

MULTI-STRAND CORONAL LOOP MODEL AND FILTER-RATIO ANALYSIS

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

Bourouaine, Sofiane; Marsch, Eckart, E-mail: bourouaine@mps.mpg.d

2010-01-10

We model a coronal loop as a bundle of seven separate strands or filaments. Each of the loop strands used in this model can independently be heated (near their left footpoints) by Alfven/ion-cyclotron waves via wave-particle interactions. The Alfven waves are assumed to penetrate the strands from their footpoints, at which we consider different wave energy inputs. As a result, the loop strands can have different heating profiles, and the differential heating can lead to a varying cross-field temperature in the total coronal loop. The simulation of Transition Region and Coronal Explorer (TRACE) observations by means of this loop modelmore » implies two uniform temperatures along the loop length, one inferred from the 171:195 filter ratio and the other from the 171:284 ratio. The reproduced flat temperature profiles are consistent with those inferred from the observed extreme-ultraviolet coronal loops. According to our model, the flat temperature profile is a consequence of the coronal loop consisting of filaments, which have different temperatures but almost similar emission measures in the cross-field direction. Furthermore, when we assume certain errors in the simulated loop emissions (e.g., due to photometric uncertainties in the TRACE filters) and use the triple-filter analysis, our simulated loop conditions become consistent with those of an isothermal plasma. This implies that the use of TRACE or EUV Imaging Telescope triple filters for observation of a warm coronal loop may not help in determining whether the cross-field isothermal assumption is satisfied or not.« less

Efficient computation of the genomic relationship matrix and other matrices used in single-step evaluation.

PubMed

Aguilar, I; Misztal, I; Legarra, A; Tsuruta, S

2011-12-01

Genomic evaluations can be calculated using a unified procedure that combines phenotypic, pedigree and genomic information. Implementation of such a procedure requires the inverse of the relationship matrix based on pedigree and genomic relationships. The objective of this study was to investigate efficient computing options to create relationship matrices based on genomic markers and pedigree information as well as their inverses. SNP maker information was simulated for a panel of 40 K SNPs, with the number of genotyped animals up to 30 000. Matrix multiplication in the computation of the genomic relationship was by a simple 'do' loop, by two optimized versions of the loop, and by a specific matrix multiplication subroutine. Inversion was by a generalized inverse algorithm and by a LAPACK subroutine. With the most efficient choices and parallel processing, creation of matrices for 30 000 animals would take a few hours. Matrices required to implement a unified approach can be computed efficiently. Optimizations can be either by modifications of existing code or by the use of efficient automatic optimizations provided by open source or third-party libraries. © 2011 Blackwell Verlag GmbH.

10 GHz dual loop opto-electronic oscillator without RF-amplifiers

NASA Astrophysics Data System (ADS)

Zhou, Weimin; Okusaga, Olukayode; Nelson, Craig; Howe, David; Carter, Gary

2008-02-01

We report the first demonstration of a 10 GHz dual-fiber-loop Opto-Electronic Oscillator (OEO) without RF-amplifiers. Using a recently developed highly efficient RF-Photonic link with RF-to-RF gain facilitated by a high power laser, highly efficient optical modulator and high power phototectectors, we have built an amplifier-less OEO that eliminates the phase noise produced by the electronic amplifier. The dual-loop approach can provide additional gain and reduce unwanted multi-mode spurs. However, we have observed RF phase noise produced by the high power laser include relative intensity noise (RIN) and noise related to the laser's electronic control system. In addition, stimulated Brillouin scattering limits the fiber loop's length to ~2km at the 40mW laser power needed to provide the RF gain which limits the system's quality factor, Q. We have investigated several different methods for solving these problems. One promising technique is the use of a multi-longitudinal-mode laser to carry the RF signal, maintaining the total optical power but reducing the optical power of each mode to eliminate the Brillouin scattering in a longer fiber thereby reducing the phase noise of the RF signal produced by the OEO. This work shows that improvement in photonic components increases the potential for more RF system applications such as an OEO's with higher performance and new capabilities.

Numerical analysis of stress effects on Frank loop evolution during irradiation in austenitic Fe&z.sbnd;Cr&z.sbnd;Ni alloy

NASA Astrophysics Data System (ADS)

Tanigawa, Hiroyasu; Katoh, Yutai; Kohyama, Akira

1995-08-01

Effects of applied stress on early stages of interstitial type Frank loop evolution were investigated by both numerical calculation and irradiation experiments. The final objective of this research is to propose a comprehensive model of complex stress effects on microstructural evolution under various conditions. In the experimental part of this work, the microstructural analysis revealed that the differences in resolved normal stress caused those in the nucleation rates of Frank loops on {111} crystallographic family planes, and that with increasing external applied stress the total nucleation rate of Frank loops was increased. A numerical calculation was carried out primarily to evaluate the validity of models of stress effects on nucleation processes of Frank loop evolution. The calculation stands on rate equuations which describe evolution of point defects, small points defect clusters and Frank loops. The rate equations of Frank loop evolution were formulated for {111} planes, considering effects of resolved normal stress to clustering processes of small point defects and growth processes of Frank loops, separately. The experimental results and the predictions from the numerical calculation qualitatively coincided well with each other.

Dynamic testing of a single-degree-of-freedom strapdown gyroscope

NASA Technical Reports Server (NTRS)

Lory, C. B.; Feldman, J.; Sinkiewicz, J. S., Jr.

1971-01-01

Test methods and results are presented for the equivalent average input rate of a single-degree-of-freedom gyroscope operated both open loop and with a ternary-logic pulse-torque-to-balance loop during multiaxis angular oscillation. For the open-loop tests, good agreement was obtained with theoretical results. Two-axis testing was performed for oscillations about the Input-Output axes, the Input-Spin axes, and the Spin-Output axes. These tests run in the torque-to-balance mode revealed significant departures from open-loop results in the induced drift rate. An analysis is developed explaining much of the closed-loop data presented. Test data for the gryoscope in a ternary torque-to-balance loop with constant input rates is presented. The tests demonstrate that the instrument rate linearity does not change with interrogation frequency from 3,600 to 14,400 Hz if the torque coil is tuned to offer a resistive load to the current switch. Analysis cited shows that gyroscope lag compensation eliminates multiple pulsing and other equivalent forms of degraded resolution in a wide variety of quantizing loops. This result is test verified for the ternary delta-modulator loop.

Investigation of air transportation technology at Ohio University, 1980. [general aviation aircraft and navigation aids

NASA Technical Reports Server (NTRS)

Mcfarland, R. H.

1981-01-01

Specific configurations of first and second order all digital phase locked loops were analyzed for both ideal and additive gaussian noise inputs. In addition, a design for a hardware digital phase locked loop capable of either first or second order operation was evaluated along with appropriate experimental data obtained from testing of the hardware loop. All parameters chosen for the analysis and the design of the digital phase locked loop were consistent with an application to an Omega navigation receiver although neither the analysis nor the design are limited to this application. For all cases tested, the experimental data showed close agreement with the analytical results indicating that the Markov chain model for first and second order digital phase locked loops are valid.

WPC North American Surface Analyses

Science.gov Websites

window and is a pdf file (requires Adobe Acrobat Reader to view). Create a Surface Analysis Loop North U.S. (South) Alaska Gulf of Alaska Color on White Black and White Display Loop Loop the sea-level

An area and power-efficient analog li-ion battery charger circuit.

PubMed

Do Valle, Bruno; Wentz, Christian T; Sarpeshkar, Rahul

2011-04-01

The demand for greater battery life in low-power consumer electronics and implantable medical devices presents a need for improved energy efficiency in the management of small rechargeable cells. This paper describes an ultra-compact analog lithium-ion (Li-ion) battery charger with high energy efficiency. The charger presented here utilizes the tanh basis function of a subthreshold operational transconductance amplifier to smoothly transition between constant-current and constant-voltage charging regimes without the need for additional area- and power-consuming control circuitry. Current-domain circuitry for end-of-charge detection negates the need for precision-sense resistors in either the charging path or control loop. We show theoretically and experimentally that the low-frequency pole-zero nature of most battery impedances leads to inherent stability of the analog control loop. The circuit was fabricated in an AMI 0.5-μm complementary metal-oxide semiconductor process, and achieves 89.7% average power efficiency and an end voltage accuracy of 99.9% relative to the desired target 4.2 V, while consuming 0.16 mm(2) of chip area. To date and to the best of our knowledge, this design represents the most area-efficient and most energy-efficient battery charger circuit reported in the literature.

Run-time parallelization and scheduling of loops

NASA Technical Reports Server (NTRS)

Saltz, Joel H.; Mirchandaney, Ravi; Crowley, Kay

1990-01-01

Run time methods are studied to automatically parallelize and schedule iterations of a do loop in certain cases, where compile-time information is inadequate. The methods presented involve execution time preprocessing of the loop. At compile-time, these methods set up the framework for performing a loop dependency analysis. At run time, wave fronts of concurrently executable loop iterations are identified. Using this wavefront information, loop iterations are reordered for increased parallelism. Symbolic transformation rules are used to produce: inspector procedures that perform execution time preprocessing and executors or transformed versions of source code loop structures. These transformed loop structures carry out the calculations planned in the inspector procedures. Performance results are presented from experiments conducted on the Encore Multimax. These results illustrate that run time reordering of loop indices can have a significant impact on performance. Furthermore, the overheads associated with this type of reordering are amortized when the loop is executed several times with the same dependency structure.

Near optimum digital phase locked loops.

NASA Technical Reports Server (NTRS)

Polk, D. R.; Gupta, S. C.

1972-01-01

Near optimum digital phase locked loops are derived utilizing nonlinear estimation theory. Nonlinear approximations are employed to yield realizable loop structures. Baseband equivalent loop gains are derived which under high signal to noise ratio conditions may be calculated off-line. Additional simplifications are made which permit the application of the Kalman filter algorithms to determine the optimum loop filter. Performance is evaluated by a theoretical analysis and by simulation. Theoretical and simulated results are discussed and a comparison to analog results is made.

Dynamic Modeling, Model-Based Control, and Optimization of Solid Oxide Fuel Cells

NASA Astrophysics Data System (ADS)

Spivey, Benjamin James

2011-07-01

Solid oxide fuel cells are a promising option for distributed stationary power generation that offers efficiencies ranging from 50% in stand-alone applications to greater than 80% in cogeneration. To advance SOFC technology for widespread market penetration, the SOFC should demonstrate improved cell lifetime and load-following capability. This work seeks to improve lifetime through dynamic analysis of critical lifetime variables and advanced control algorithms that permit load-following while remaining in a safe operating zone based on stress analysis. Control algorithms typically have addressed SOFC lifetime operability objectives using unconstrained, single-input-single-output control algorithms that minimize thermal transients. Existing SOFC controls research has not considered maximum radial thermal gradients or limits on absolute temperatures in the SOFC. In particular, as stress analysis demonstrates, the minimum cell temperature is the primary thermal stress driver in tubular SOFCs. This dissertation presents a dynamic, quasi-two-dimensional model for a high-temperature tubular SOFC combined with ejector and prereformer models. The model captures dynamics of critical thermal stress drivers and is used as the physical plant for closed-loop control simulations. A constrained, MIMO model predictive control algorithm is developed and applied to control the SOFC. Closed-loop control simulation results demonstrate effective load-following, constraint satisfaction for critical lifetime variables, and disturbance rejection. Nonlinear programming is applied to find the optimal SOFC size and steady-state operating conditions to minimize total system costs.

Efficacy of Code Optimization on Cache-based Processors

NASA Technical Reports Server (NTRS)

VanderWijngaart, Rob F.; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

The current common wisdom in the U.S. is that the powerful, cost-effective supercomputers of tomorrow will be based on commodity (RISC) micro-processors with cache memories. Already, most distributed systems in the world use such hardware as building blocks. This shift away from vector supercomputers and towards cache-based systems has brought about a change in programming paradigm, even when ignoring issues of parallelism. Vector machines require inner-loop independence and regular, non-pathological memory strides (usually this means: non-power-of-two strides) to allow efficient vectorization of array operations. Cache-based systems require spatial and temporal locality of data, so that data once read from main memory and stored in high-speed cache memory is used optimally before being written back to main memory. This means that the most cache-friendly array operations are those that feature zero or unit stride, so that each unit of data read from main memory (a cache line) contains information for the next iteration in the loop. Moreover, loops ought to be 'fat', meaning that as many operations as possible are performed on cache data-provided instruction caches do not overflow and enough registers are available. If unit stride is not possible, for example because of some data dependency, then care must be taken to avoid pathological strides, just ads on vector computers. For cache-based systems the issues are more complex, due to the effects of associativity and of non-unit block (cache line) size. But there is more to the story. Most modern micro-processors are superscalar, which means that they can issue several (arithmetic) instructions per clock cycle, provided that there are enough independent instructions in the loop body. This is another argument for providing fat loop bodies. With these restrictions, it appears fairly straightforward to produce code that will run efficiently on any cache-based system. It can be argued that although some of the important computational algorithms employed at NASA Ames require different programming styles on vector machines and cache-based machines, respectively, neither architecture class appeared to be favored by particular algorithms in principle. Practice tells us that the situation is more complicated. This report presents observations and some analysis of performance tuning for cache-based systems. We point out several counterintuitive results that serve as a cautionary reminder that memory accesses are not the only factors that determine performance, and that within the class of cache-based systems, significant differences exist.

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

None

Oberlin College’s Adam Joseph Lewis Center for Environmental Studies is a high-performance building featuring an expansive photovoltaic system and a closed-loop groundwater heat pump system. Designers incorporated energy-efficient components and materials

5-kWe Free-piston Stirling Engine Convertor

NASA Technical Reports Server (NTRS)

Chapman, Peter A.; Vitale, Nicholas A.; Walter, Thomas J.

2008-01-01

The high reliability, long life, and efficient operation of Free-Piston Stirling Engines (FPSEs) make them an attractive power system to meet future space power requirements with less mass, better efficiency, and less total heat exchanger area than other power convertor options. FPSEs are also flexible in configuration as they can be coupled with many potential heat sources and various heat input systems, heat rejection systems, and power management and distribution systems. Development of a 5-kWe Stirling Convertor Assembly (SCA) is underway to demonstrate the viability of an FPSE for space power. The design is a scaled-down version of the successful 12.5-kWe Component Test Power Converter (CTPC) developed under NAS3-25463. The ultimate efficiency target is 25% overall convertor efficiency (electrical power out over heat in). For the single cylinder prototype now in development, cost and time constraints required use of economical and readily available materials (steel versus beryllium) and components (a commercially available linear alternator) and thus lower efficiency. The working gas is helium at 150 bar mean pressure. The design consists of a displacer suspended on internally pumped gas bearings and a power piston/alternator supported on flexures. Non-contacting clearance seals are used between internal volumes. Heat to and from the prototype convertor is done via pumped liquid loops passing through shell and tube heat exchangers. The preliminary and detail designs of the convertor, controller, and support systems (heating loop, cooling loop, and helium supply system) are complete and all hardware is on order. Assembly and test of the prototype at Foster- Miller is planned for early 2008, when work will focus on characterizing convertor dynamics and steady-state operation to determine maximum power output and system efficiency. The device will then be delivered to Auburn University where assessments will include start-up and shutdown characterization and transient response to temperature and load variations. Future activities may include testing at NASA GRC.

Effects of two-loop contributions in the pseudofermion functional renormalization group method for quantum spin systems

NASA Astrophysics Data System (ADS)

Rück, Marlon; Reuther, Johannes

2018-04-01

We implement an extension of the pseudofermion functional renormalization group method for quantum spin systems that takes into account two-loop diagrammatic contributions. An efficient numerical treatment of the additional terms is achieved within a nested graph construction which recombines different one-loop interaction channels. In order to be fully self-consistent with respect to self-energy corrections, we also include certain three-loop terms of Katanin type. We first apply this formalism to the antiferromagnetic J1-J2 Heisenberg model on the square lattice and benchmark our results against the previous one-loop plus Katanin approach. Even though the renormalization group (RG) equations undergo significant modifications when including the two-loop terms, the magnetic phase diagram, comprising Néel ordered and collinear ordered phases separated by a magnetically disordered regime, remains remarkably unchanged. Only the boundary position between the disordered and the collinear phases is found to be moderately affected by two-loop terms. On the other hand, critical RG scales, which we associate with critical temperatures Tc, are reduced by a factor of ˜2 indicating that the two-loop diagrams play a significant role in enforcing the Mermin-Wagner theorem. Improved estimates for critical temperatures are also obtained for the Heisenberg ferromagnet on the three-dimensional simple cubic lattice where errors in Tc are reduced by ˜34 % . These findings have important implications for the quantum phase diagrams calculated within the previous one-loop plus Katanin approach which turn out to be already well converged.

The Strength of an Ig Switch Region is Determined by its Ability to Drive R-loop Formation and its Number of WGCW Sites

PubMed Central

Zhang, Zheng Z.; Pannunzio, Nicholas R.; Han, Li; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R.

2014-01-01

SUMMARY R-loops exist at the murine IgH switch regions and possibly other locations, but their functional importance is unclear. In biochemical systems, R-loop initiation requires DNA sequence regions containing clusters of G nucleotides, but cellular studies have not been done. Here, we vary the G-clustering, total switch region length, and the number of target sites (WGCW sites for the activation-induced deaminase) at synthetic switch regions in a murine B cell line to determine the effect on class switch recombination (CSR). G-clusters increase CSR, regardless of their immediate proximity to the WGCW sites. This increase is accompanied by an increase in R-loop formation. CSR efficiency correlates better with the absolute number of WGCW sites in the switch region rather than the total switch region length or density of WGCW sites. Thus, the overall strength of the switch region depends on G-clusters, which initiate R-loop formation, and on the number of WGCW sites. PMID:25017067

Development and Testing of a Temperature-swing Adsorption Compressor for Carbon Dioxide in Closed-loop Air Revitalization Systems

NASA Technical Reports Server (NTRS)

Mulloth, Lila M.; Rosen, Micha; Affleck, David; LeVan, M. Douglas; Wang, Yuan

2005-01-01

The air revitalization system of the International Space Station (ISS) operates in an open loop mode and relies on the resupply of oxygen and other consumables from earth for the life support of astronauts. A compressor is required for delivering the carbon dioxide from a removal assembly to a reduction unit to recover oxygen and thereby dosing the air-loop. We have developed a temperature-swing adsorption compressor (TSAC) that is energy efficient, quiet, and has no rapidly moving parts for performing these tasks. The TSAC is a solid-state compressor that has the capability to remove CO2 from a low- pressure source, and subsequently store, compress, and deliver at a higher pressure as required by a processor. The TSAC is an ideal interface device for CO2 removal and reduction units in the air revitalization loop of a spacecraft for oxygen recovery. This paper discusses the design and testing of a TSAC for carbon dioxide that has application in the ISS and future spacecraft for closing the air revitalization loop.

An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase

NASA Astrophysics Data System (ADS)

Pucheta-Martínez, Encarna; Saladino, Giorgio; Morando, Maria Agnese; Martinez-Torrecuadrada, Jorge; Lelli, Moreno; Sutto, Ludovico; D'Amelio, Nicola; Gervasio, Francesco Luigi

2016-04-01

Phosphorylation of the activation loop is a fundamental step in the activation of most protein kinases. In the case of the Src tyrosine kinase, a prototypical kinase due to its role in cancer and its historic importance, phosphorylation of tyrosine 416 in the activation loop is known to rigidify the structure and contribute to the switch from the inactive to a fully active form. However, whether or not phosphorylation is able per-se to induce a fully active conformation, that efficiently binds ATP and phosphorylates the substrate, is less clear. Here we employ a combination of solution NMR and enhanced-sampling molecular dynamics simulations to fully map the effects of phosphorylation and ATP/ADP cofactor loading on the conformational landscape of Src tyrosine kinase. We find that both phosphorylation and cofactor binding are needed to induce a fully active conformation. What is more, we find a complex interplay between the A-loop and the hinge motion where the phosphorylation of the activation-loop has a significant allosteric effect on the dynamics of the C-lobe.

2D Inversion of Transient Electromagnetic Method (TEM)

NASA Astrophysics Data System (ADS)

Bortolozo, Cassiano Antonio; Luís Porsani, Jorge; Acácio Monteiro dos Santos, Fernando

2017-04-01

A new methodology was developed for 2D inversion of Transient Electromagnetic Method (TEM). The methodology consists in the elaboration of a set of routines in Matlab code for modeling and inversion of TEM data and the determination of the most efficient field array for the problem. In this research, the 2D TEM modeling uses the finite differences discretization. To solve the inversion problem, were applied an algorithm based on Marquardt technique, also known as Ridge Regression. The algorithm is stable and efficient and it is widely used in geoelectrical inversion problems. The main advantage of 1D survey is the rapid data acquisition in a large area, but in regions with two-dimensional structures or that need more details, is essential to use two-dimensional interpretation methodologies. For an efficient field acquisition we used in an innovative form the fixed-loop array, with a square transmitter loop (200m x 200m) and 25m spacing between the sounding points. The TEM surveys were conducted only inside the transmitter loop, in order to not deal with negative apparent resistivity values. Although it is possible to model the negative values, it makes the inversion convergence more difficult. Therefore the methodology described above has been developed in order to achieve maximum optimization of data acquisition. Since it is necessary only one transmitter loop disposition in the surface for each series of soundings inside the loop. The algorithms were tested with synthetic data and the results were essential to the interpretation of the results with real data and will be useful in future situations. With the inversion of the real data acquired over the Paraná Sedimentary Basin (PSB) was successful realized a 2D TEM inversion. The results indicate a robust geoelectrical characterization for the sedimentary and crystalline aquifers in the PSB. Therefore, using a new and relevant approach for 2D TEM inversion, this research effectively contributed to map the most promising regions for groundwater exploration. In addition, there was the development of new geophysical software that can be applied as an important tool for many geological/hydrogeological applications and educational purposes.

The analysis of novel microRNA mimic sequences in cancer cells reveals lack of specificity in stem-loop RT-qPCR-based microRNA detection.

PubMed

Winata, Patrick; Williams, Marissa; McGowan, Eileen; Nassif, Najah; van Zandwijk, Nico; Reid, Glen

2017-11-17

MicroRNAs are frequently downregulated in cancer, and restoring expression has tumour suppressive activity in tumour cells. Our recent phase I clinical trial investigated microRNA-based therapy in patients with malignant pleural mesothelioma. Treatment with TargomiRs, microRNA mimics with novel sequence packaged in EGFR antibody-targeted bacterial minicells, revealed clear signs of clinical activity. In order to detect delivery of microRNA mimics to tumour cells in future clinical trials, we tested hydrolysis probe-based assays specific for the sequence of the novel mimics in transfected mesothelioma cell lines using RT-qPCR. The custom assays efficiently and specifically amplified the consensus mimics. However, we found that these assays gave a signal when total RNA from untransfected and control mimic-transfected cells were used as templates. Further investigation revealed that the reverse transcription step using stem-loop primers appeared to introduce substantial non-specific amplification with either total RNA or synthetic RNA templates. This suggests that reverse transcription using stem-loop primers suffers from an intrinsic lack of specificity for the detection of highly similar microRNAs in the same family, especially when analysing total RNA. These results suggest that RT-qPCR is unlikely to be an effective means to detect delivery of microRNA mimic-based drugs to tumour cells in patients.

Interface Matters: The Stiffness Route to Stability of a Thermophilic Tetrameric Malate Dehydrogenase

PubMed Central

Kalimeri, Maria; Girard, Eric; Madern, Dominique; Sterpone, Fabio

2014-01-01

In this work we investigate by computational means the behavior of two orthologous bacterial proteins, a mesophilic and a thermophilic tetrameric malate dehydrogenase (MalDH), at different temperatures. Namely, we quantify how protein mechanical rigidity at different length- and time-scales correlates to protein thermophilicity as commonly believed. In particular by using a clustering analysis strategy to explore the conformational space of the folded proteins, we show that at ambient conditions and at the molecular length-scale the thermophilic variant is indeed more rigid that the mesophilic one. This rigidification is the result of more efficient inter-domain interactions, the strength of which is further quantified via ad hoc free energy calculations. When considered isolated, the thermophilic domain is indeed more flexible than the respective mesophilic one. Upon oligomerization, the induced stiffening of the thermophilic protein propagates from the interface to the active site where the loop, controlling the access to the catalytic pocket, anchors down via an extended network of ion-pairs. On the contrary in the mesophilic tetramer the loop is highly mobile. Simulations at high temperature, could not re-activate the mobility of the loop in the thermophile. This finding opens questions on the similarities of the binding processes for these two homologues at their optimal working temperature and suggests for the thermophilic variant a possible cooperative role of cofactor/substrate. PMID:25437494

Interface matters: the stiffness route to stability of a thermophilic tetrameric malate dehydrogenase.

PubMed

Kalimeri, Maria; Girard, Eric; Madern, Dominique; Sterpone, Fabio

2014-01-01

In this work we investigate by computational means the behavior of two orthologous bacterial proteins, a mesophilic and a thermophilic tetrameric malate dehydrogenase (MalDH), at different temperatures. Namely, we quantify how protein mechanical rigidity at different length- and time-scales correlates to protein thermophilicity as commonly believed. In particular by using a clustering analysis strategy to explore the conformational space of the folded proteins, we show that at ambient conditions and at the molecular length-scale the thermophilic variant is indeed more rigid that the mesophilic one. This rigidification is the result of more efficient inter-domain interactions, the strength of which is further quantified via ad hoc free energy calculations. When considered isolated, the thermophilic domain is indeed more flexible than the respective mesophilic one. Upon oligomerization, the induced stiffening of the thermophilic protein propagates from the interface to the active site where the loop, controlling the access to the catalytic pocket, anchors down via an extended network of ion-pairs. On the contrary in the mesophilic tetramer the loop is highly mobile. Simulations at high temperature, could not re-activate the mobility of the loop in the thermophile. This finding opens questions on the similarities of the binding processes for these two homologues at their optimal working temperature and suggests for the thermophilic variant a possible cooperative role of cofactor/substrate.

Regenerative Hydride Heat Pump

NASA Technical Reports Server (NTRS)

Jones, Jack A.

1992-01-01

Hydride heat pump features regenerative heating and single circulation loop. Counterflow heat exchangers accommodate different temperatures of FeTi and LaNi4.7Al0.3 subloops. Heating scheme increases efficiency.

Closed-Loop Hybrid Gaze Brain-Machine Interface Based Robotic Arm Control with Augmented Reality Feedback

PubMed Central

Zeng, Hong; Wang, Yanxin; Wu, Changcheng; Song, Aiguo; Liu, Jia; Ji, Peng; Xu, Baoguo; Zhu, Lifeng; Li, Huijun; Wen, Pengcheng

2017-01-01

Brain-machine interface (BMI) can be used to control the robotic arm to assist paralysis people for performing activities of daily living. However, it is still a complex task for the BMI users to control the process of objects grasping and lifting with the robotic arm. It is hard to achieve high efficiency and accuracy even after extensive trainings. One important reason is lacking of sufficient feedback information for the user to perform the closed-loop control. In this study, we proposed a method of augmented reality (AR) guiding assistance to provide the enhanced visual feedback to the user for a closed-loop control with a hybrid Gaze-BMI, which combines the electroencephalography (EEG) signals based BMI and the eye tracking for an intuitive and effective control of the robotic arm. Experiments for the objects manipulation tasks while avoiding the obstacle in the workspace are designed to evaluate the performance of our method for controlling the robotic arm. According to the experimental results obtained from eight subjects, the advantages of the proposed closed-loop system (with AR feedback) over the open-loop system (with visual inspection only) have been verified. The number of trigger commands used for controlling the robotic arm to grasp and lift the objects with AR feedback has reduced significantly and the height gaps of the gripper in the lifting process have decreased more than 50% compared to those trials with normal visual inspection only. The results reveal that the hybrid Gaze-BMI user can benefit from the information provided by the AR interface, improving the efficiency and reducing the cognitive load during the grasping and lifting processes. PMID:29163123

Sythesis of MCMC and Belief Propagation

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

Ahn, Sungsoo; Chertkov, Michael; Shin, Jinwoo

Markov Chain Monte Carlo (MCMC) and Belief Propagation (BP) are the most popular algorithms for computational inference in Graphical Models (GM). In principle, MCMC is an exact probabilistic method which, however, often suffers from exponentially slow mixing. In contrast, BP is a deterministic method, which is typically fast, empirically very successful, however in general lacking control of accuracy over loopy graphs. In this paper, we introduce MCMC algorithms correcting the approximation error of BP, i.e., we provide a way to compensate for BP errors via a consecutive BP-aware MCMC. Our framework is based on the Loop Calculus (LC) approach whichmore » allows to express the BP error as a sum of weighted generalized loops. Although the full series is computationally intractable, it is known that a truncated series, summing up all 2-regular loops, is computable in polynomial-time for planar pair-wise binary GMs and it also provides a highly accurate approximation empirically. Motivated by this, we first propose a polynomial-time approximation MCMC scheme for the truncated series of general (non-planar) pair-wise binary models. Our main idea here is to use the Worm algorithm, known to provide fast mixing in other (related) problems, and then design an appropriate rejection scheme to sample 2-regular loops. Furthermore, we also design an efficient rejection-free MCMC scheme for approximating the full series. The main novelty underlying our design is in utilizing the concept of cycle basis, which provides an efficient decomposition of the generalized loops. In essence, the proposed MCMC schemes run on transformed GM built upon the non-trivial BP solution, and our experiments show that this synthesis of BP and MCMC outperforms both direct MCMC and bare BP schemes.« less

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.

PubMed

Di Palma, Francesco; Bottaro, Sandro; Bussi, Giovanni

2015-01-01

Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating its conformational changes upon ligand binding mostly remains to be elucidated. In this open framework it has been suggested that the ligand stabilizes the interaction of the distal "kissing loop" complex. Using accurate full-atom molecular dynamics with explicit solvent in combination with enhanced sampling techniques and advanced analysis methods it could be possible to provide a more detailed perspective on the formation of these tertiary contacts. In this work, we used umbrella sampling simulations to study the thermodynamics of the kissing loop complex in the presence and in the absence of the cognate ligand. We enforced the breaking/formation of the loop-loop interaction restraining the distance between the two loops. We also assessed the convergence of the results by using two alternative initialization protocols. A structural analysis was performed using a novel approach to analyze base contacts. Contacts between the two loops were progressively lost when larger inter-loop distances were enforced. Inter-loop Watson-Crick contacts survived at larger separation when compared with non-canonical pairing and stacking interactions. Intra-loop stacking contacts remained formed upon loop undocking. Our simulations qualitatively indicated that the ligand could stabilize the kissing loop complex. We also compared with previously published simulation studies. Kissing complex stabilization given by the ligand was compatible with available experimental data. However, the dependence of its value on the initialization protocol of the umbrella sampling simulations posed some questions on the quantitative interpretation of the results and called for better converged enhanced sampling simulations.

Black hole state counting in loop quantum gravity: a number-theoretical approach.

PubMed

Agulló, Iván; Barbero G, J Fernando; Díaz-Polo, Jacobo; Fernández-Borja, Enrique; Villaseñor, Eduardo J S

2008-05-30

We give an efficient method, combining number-theoretic and combinatorial ideas, to exactly compute black hole entropy in the framework of loop quantum gravity. Along the way we provide a complete characterization of the relevant sector of the spectrum of the area operator, including degeneracies, and explicitly determine the number of solutions to the projection constraint. We use a computer implementation of the proposed algorithm to confirm and extend previous results on the detailed structure of the black hole degeneracy spectrum.

Thermoelectric power generator with intermediate loop

DOEpatents

Bell, Lon E; Crane, Douglas Todd

2013-05-21

A thermoelectric power generator is disclosed for use to generate electrical power from heat, typically waste heat. An intermediate heat transfer loop forms a part of the system to permit added control and adjustability in the system. This allows the thermoelectric power generator to more effectively and efficiently generate power in the face of dynamically varying temperatures and heat flux conditions, such as where the heat source is the exhaust of an automobile, or any other heat source with dynamic temperature and heat flux conditions.

Thermoelectric power generator with intermediate loop

DOEpatents

Bel,; Lon, E [Altadena, CA; Crane, Douglas Todd [Pasadena, CA

2009-10-27

A thermoelectric power generator is disclosed for use to generate electrical power from heat, typically waste heat. An intermediate heat transfer loop forms a part of the system to permit added control and adjustability in the system. This allows the thermoelectric power generator to more effectively and efficiently generate power in the face of dynamically varying temperatures and heat flux conditions, such as where the heat source is the exhaust of an automobile, or any other heat source with dynamic temperature and heat flux conditions.

Gene silencing efficiency and INF-β induction effects of splicing miRNA 155-based artificial miRNA with pre-miRNA stem-loop structures.

PubMed

Sin, Onsam; Mabiala, Prudence; Liu, Ye; Sun, Ying; Hu, Tao; Liu, Qingzhen; Guo, Deyin

2012-02-01

Artificial microRNA (miRNA) expression vectors have been developed and used for RNA interference. The secondary structure of artificial miRNA is important for RNA interference efficacy. We designed two groups of six artificial splicing miRNA 155-based miRNAs (SM155-based miRNAs) with the same target in the coding region or 3' UTR of a target gene and studied their RNA silencing efficiency and interferon β (IFN-β) induction effects. SM155-based miRNA with a mismatch at the +1 position and a bulge at the +11, +12 positions in a miRNA precursor stem-loop structure showed the highest gene silencing efficiency and lowest IFN-β induction effect (increased IFN-β mRNA level by 10% in both target cases), regardless of the specificity of the target sequence, suggesting that pSM155-based miRNA with this design could be a valuable miRNA expression vector.

Role of the DELSEED Loop in Torque Transmission of F1-ATPase

PubMed Central

Tanigawara, Mizue; Tabata, Kazuhito V.; Ito, Yuko; Ito, Jotaro; Watanabe, Rikiya; Ueno, Hiroshi; Ikeguchi, Mitsunori; Noji, Hiroyuki

2012-01-01

F1-ATPase is an ATP-driven rotary motor that generates torque at the interface between the catalytic β-subunits and the rotor γ-subunit. The β-subunit inwardly rotates the C-terminal domain upon nucleotide binding/dissociation; hence, the region of the C-terminal domain that is in direct contact with γ—termed the DELSEED loop—is thought to play a critical role in torque transmission. We substituted all the DELSEED loop residues with alanine to diminish specific DELSEED loop-γ interactions and with glycine to disrupt the loop structure. All the mutants rotated unidirectionally with kinetic parameters comparable to those of the wild-type F1, suggesting that the specific interactions between DELSEED loop and γ is not involved in cooperative interplays between the catalytic β-subunits. Glycine substitution mutants generated half the torque of the wild-type F1, whereas the alanine mutant generated comparable torque. Fluctuation analyses of the glycine/alanine mutants revealed that the γ-subunit was less tightly held in the α3β3-stator ring of the glycine mutant than in the wild-type F1 and the alanine mutant. Molecular dynamics simulation showed that the DELSEED loop was disordered by the glycine substitution, whereas it formed an α-helix in the alanine mutant. Our results emphasize the importance of loop rigidity for efficient torque transmissions. PMID:23009846

Effects of human chromosome 12 on interactions between Tat and TAR of human immunodeficiency virus type 1.

PubMed Central

Alonso, A; Cujec, T P; Peterlin, B M

1994-01-01

Rates of transcriptions of the human immunodeficiency virus are greatly increased by the viral trans activator Tat. In vitro, Tat binds to the 5' bulge of the trans-activation response (TAR) RNA stem-loop, which is present in all viral transcripts. In human cells, the central loop in TAR and its cellular RNA-binding proteins are also critical for the function of Tat. Previously, we demonstrated that in rodent cells (CHO cells), but not in those which contain the human chromosome 12 (CHO12 cells), Tat-TAR interactions are compromised. In this study, we examined the roles of the bulge and loop in TAR in Tat trans activation in these cells. Whereas low levels of trans activation depended solely on interactions between Tat and the bulge in CHO cells, high levels of trans activation depended also on interactions between Tat and the loop in CHO12 cells. Since the TAR loop binding proteins in these two cell lines were identical and different from their human counterpart, the human chromosome 12 does not encode TAR loop binding proteins. In vivo binding competition studies with TAR decoys confirmed that the binding of Tat to TAR is more efficient in CHO12 cells. Thus, the protein(s) encoded on human chromosome 12 helps to tether Tat to TAR via its loop, which results in high levels of trans activation. Images PMID:8083988

Analysis and design of a 3rd order velocity-controlled closed-loop for MEMS vibratory gyroscopes.

PubMed

Wu, Huan-ming; Yang, Hai-gang; Yin, Tao; Jiao, Ji-wei

2013-09-18

The time-average method currently available is limited to analyzing the specific performance of the automatic gain control-proportional and integral (AGC-PI) based velocity-controlled closed-loop in a micro-electro-mechanical systems (MEMS) vibratory gyroscope, since it is hard to solve nonlinear functions in the time domain when the control loop reaches to 3rd order. In this paper, we propose a linearization design approach to overcome this limitation by establishing a 3rd order linear model of the control loop and transferring the analysis to the frequency domain. Order reduction is applied on the built linear model's transfer function by constructing a zero-pole doublet, and therefore mathematical expression of each control loop's performance specification is obtained. Then an optimization methodology is summarized, which reveals that a robust, stable and swift control loop can be achieved by carefully selecting the system parameters following a priority order. Closed-loop drive circuits are designed and implemented using 0.35 μm complementary metal oxide semiconductor (CMOS) process, and experiments carried out on a gyroscope prototype verify the optimization methodology that an optimized stability of the control loop can be achieved by constructing the zero-pole doublet, and disturbance rejection capability (D.R.C) of the control loop can be improved by increasing the integral term.

Automated fluid analysis apparatus and techniques

DOEpatents

Szecsody, James E.

2004-03-16

An automated device that couples a pair of differently sized sample loops with a syringe pump and a source of degassed water. A fluid sample is mounted at an inlet port and delivered to the sample loops. A selected sample from the sample loops is diluted in the syringe pump with the degassed water and fed to a flow through detector for analysis. The sample inlet is also directly connected to the syringe pump to selectively perform analysis without dilution. The device is airtight and used to detect oxygen-sensitive species, such as dithionite in groundwater following a remedial injection to treat soil contamination.

Integration of Haptics in Agricultural Robotics

NASA Astrophysics Data System (ADS)

Kannan Megalingam, Rajesh; Sreekanth, M. M.; Sivanantham, Vinu; Sai Kumar, K.; Ghanta, Sriharsha; Surya Teja, P.; Reddy, Rajesh G.

2017-08-01

Robots can differentiate with open loop system and closed loop system robots. We face many problems when we do not have a feedback from robots. In this research paper, we are discussing all possibilities to achieve complete closed loop system for Multiple-DOF Robotic Arm, which is used in a coconut tree climbing and cutting robot by introducing a Haptic device. We are working on various sensors like tactile, vibration, force and proximity sensors for getting feedback. For monitoring the robotic arm achieved by graphical user interference software which simulates the working of the robotic arm, send the feedback of all the real time analog values which are produced by various sensors and provide real-time graphs for estimate the efficiency of the Robot.

Analysis of wave propagation and wavefront sensing in target-in-the-loop beam control systems

NASA Astrophysics Data System (ADS)

Vorontsov, Mikhail A.; Kolosov, Valeri V.

2004-10-01

Target-in-the-loop (TIL) wave propagation geometry represents perhaps the most challenging case for adaptive optics applications that are related with maximization of irradiance power density on extended remotely located surfaces in the presence of dynamically changing refractive index inhomogeneities in the propagation medium. We introduce a TIL propagation model that uses a combination of the parabolic equation describing outgoing wave propagation, and the equation describing evolution of the mutual intensity function (MIF) for the backscattered (returned) wave. The resulting evolution equation for the MIF is further simplified by the use of the smooth refractive index approximation. This approximation enables derivation of the transport equation for the returned wave brightness function, analyzed here using method characteristics (brightness function trajectories). The equations for the brightness function trajectories (ray equations) can be efficiently integrated numerically. We also consider wavefront sensors that perform sensing of speckle-averaged characteristics of the wavefront phase (TIL sensors). Analysis of the wavefront phase reconstructed from Shack-Hartmann TIL sensor measurements shows that an extended target introduces a phase modulation (target-induced phase) that cannot be easily separated from the atmospheric turbulence-related phase aberrations. We also show that wavefront sensing results depend on the extended target shape, surface roughness, and the outgoing beam intensity distribution on the target surface.

Determination of the force systems produced by different configurations of tear drop orthodontic loops.

PubMed

Thiesen, Guilherme; Shimizu, Roberto Hideo; do Valle, Caio Vinicius Martins; do Valle-Corotti, Karyna Martins; Pereira, Jefferson Ricardo; Conti, Paulo Cesar Rodrigues

2013-03-15

To determine the mechanical characteristics of teardrop loop with and without helix fabricated using different metal alloy compositions (stainless steel and beta-titanium), submitted to different intensities of bends preactivation (0° and 40°), and with different cross-sectional dimension of the wire used to build these loops (0.017 x 0.025-in and 0.019 x 0.025-in). Eighty loops used to close spaces were submitted to mechanical tests. The magnitudes of horizontal force, the moment/force ratio, and the load/deflection ratio produced by the specimens were quantified. Loops were submitted to a total activation of 5.0 mm and the values were registered for each 1.0 mm of activation. For statistic data analysis, a analysis of variance was performed and a Tukey's Multiple Comparison test was used as supplement, considering a 5% level of significance. In general, teardrop loops with helix produced lower magnitudes of horizontal force and load/deflection ratio, and higher moment/force ratio than teardrop loops without helix. Among all analyzed variables, metal alloy composition presented greater influence in the horizontal force and in the load/deflection ratio. The moment/force ratio showed to be more influenced by the preactivation of loops for space closure.

Flare parameters inferred from a 3D loop model data base

NASA Astrophysics Data System (ADS)

Cuambe, Valente A.; Costa, J. E. R.; Simões, P. J. A.

2018-06-01

We developed a data base of pre-calculated flare images and spectra exploring a set of parameters which describe the physical characteristics of coronal loops and accelerated electron distribution. Due to the large number of parameters involved in describing the geometry and the flaring atmosphere in the model used, we built a large data base of models (˜250 000) to facilitate the flare analysis. The geometry and characteristics of non-thermal electrons are defined on a discrete grid with spatial resolution greater than 4 arcsec. The data base was constructed based on general properties of known solar flares and convolved with instrumental resolution to replicate the observations from the Nobeyama radio polarimeter spectra and Nobeyama radioheliograph (NoRH) brightness maps. Observed spectra and brightness distribution maps are easily compared with the modelled spectra and images in the data base, indicating a possible range of solutions. The parameter search efficiency in this finite data base is discussed. 8 out of 10 parameters analysed for 1000 simulated flare searches were recovered with a relative error of less than 20 per cent on average. In addition, from the analysis of the observed correlation between NoRH flare sizes and intensities at 17 GHz, some statistical properties were derived. From these statistics, the energy spectral index was found to be δ ˜ 3, with non-thermal electron densities showing a peak distribution ⪅107 cm-3, and Bphotosphere ⪆ 2000 G. Some bias for larger loops with heights as great as ˜2.6 × 109 cm, and looptop events were noted. An excellent match of the spectrum and the brightness distribution at 17 and 34 GHz of the 2002 May 31 flare is presented as well.

Estimating the Expected Value of Sample Information Using the Probabilistic Sensitivity Analysis Sample

PubMed Central

Oakley, Jeremy E.; Brennan, Alan; Breeze, Penny

2015-01-01

Health economic decision-analytic models are used to estimate the expected net benefits of competing decision options. The true values of the input parameters of such models are rarely known with certainty, and it is often useful to quantify the value to the decision maker of reducing uncertainty through collecting new data. In the context of a particular decision problem, the value of a proposed research design can be quantified by its expected value of sample information (EVSI). EVSI is commonly estimated via a 2-level Monte Carlo procedure in which plausible data sets are generated in an outer loop, and then, conditional on these, the parameters of the decision model are updated via Bayes rule and sampled in an inner loop. At each iteration of the inner loop, the decision model is evaluated. This is computationally demanding and may be difficult if the posterior distribution of the model parameters conditional on sampled data is hard to sample from. We describe a fast nonparametric regression-based method for estimating per-patient EVSI that requires only the probabilistic sensitivity analysis sample (i.e., the set of samples drawn from the joint distribution of the parameters and the corresponding net benefits). The method avoids the need to sample from the posterior distributions of the parameters and avoids the need to rerun the model. The only requirement is that sample data sets can be generated. The method is applicable with a model of any complexity and with any specification of model parameter distribution. We demonstrate in a case study the superior efficiency of the regression method over the 2-level Monte Carlo method. PMID:25810269

Multiple substitutions lead to increased loop flexibility and expanded specificity in Acinetobacter baumannii carbapenemase OXA-239.

PubMed

Harper, Thomas M; June, Cynthia M; Taracila, Magdalena A; Bonomo, Robert A; Powers, Rachel A; Leonard, David A

2018-01-11

OXA-239 is a class D carbapenemase isolated from an Acinetobacter baumannii strain found in Mexico. This enzyme is a variant of OXA-23 with three amino acid substitutions in or near the active site. These substitutions cause OXA-239 to hydrolyze late-generation cephalosporins and the monobactam aztreonam with greater efficiency than OXA-23. OXA-239 activity against the carbapenems doripenem and imipenem is reduced ∼3-fold and 20-fold, respectively. Further analysis demonstrated that two of the substitutions (P225S and D222N) are largely responsible for the observed alteration of kinetic parameters, while the third (S109L) may serve to stabilize the protein. Structures of OXA-239 with cefotaxime, doripenem and imipenem bound as acyl-intermediates were determined. These structures reveal that OXA-239 has increased flexibility in a loop that contains P225S and D222N. When carbapenems are bound, the conformation of this loop is essentially identical with that observed previously for OXA-23, with a narrow active site that makes extensive contacts to the ligand. When cefotaxime is bound, the loop can adopt a different conformation that widens the active site to allow binding of that bulky drug. This alternate conformation is made possible by P225S and further stabilized by D222N. Taken together, these results suggest that the three substitutions were selected to expand the substrate specificity profile of OXA-23 to cephalosporins and monobactams. The loss of activity against imipenem, however, suggests that there may be limits to the plasticity of class D enzymes with regard to evolving active sites that can effectively bind multiple classes of β-lactam drugs. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Exploring the Mechanism of Zanamivir Resistance in a Neuraminidase Mutant: A Molecular Dynamics Study

PubMed Central

Han, Nanyu; Liu, Xuewei; Mu, Yuguang

2012-01-01

It is critical to understand the molecular basis of the drug resistance of influenza viruses to efficiently treat this infectious disease. Recently, H1N1 strains of influenza A carrying a mutation of Q136K in neuraminidase were found. The new strain showed a strong Zanamivir neutralization effect. In this study, normal molecular dynamics simulations and metadynamics simulations were employed to explore the mechanism of Zanamivir resistance. The wild-type neuraminidase contained a 310 helix before the 150 loop, and there was interaction between the 150 and 430 loops. However, the helix and the interaction between the two loops were disturbed in the mutant protein due to interaction between K136 and nearby residues. Hydrogen-bond network analysis showed weakened interaction between the Zanamivir drug and E276/D151 on account of the electrostatic interaction between K136 and D151. Metadynamics simulations showed that the free energy landscape was different in the mutant than in the wild-type neuraminidase. Conformation with the global minimum of free energy for the mutant protein was different from the wild-type conformation. While the drug fit completely into the active site of the wild-type neuraminidase, it did not match the active site of the mutant variant. This study indicates that the altered hydrogen-bond network and the deformation of the 150 loop are the key factors in development of Zanamivir resistance. Furthermore, the Q136K mutation has a variable effect on conformation of different N1 variants, with conformation of the 1918 N1 variant being more profoundly affected than that of the other N1 variants studied in this paper. This observation warrants further experimental investigation. PMID:22970161

Bayesian, maximum parsimony and UPGMA models for inferring the phylogenies of antelopes using mitochondrial markers.

PubMed

Khan, Haseeb A; Arif, Ibrahim A; Bahkali, Ali H; Al Farhan, Ahmad H; Al Homaidan, Ali A

2008-10-06

This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to BA, MP and UPGMA models for comparing the topologies of respective phylogenetic trees. The 16S rRNA region possessed the highest frequency of conserved sequences (97.65%) followed by cyt-b (94.22%) and d-loop (87.29%). There were few transitions (2.35%) and none transversions in 16S rRNA as compared to cyt-b (5.61% transitions and 0.17% transversions) and d-loop (11.57% transitions and 1.14% transversions) while comparing the four taxa. All the three mitochondrial segments clearly differentiated the genus Addax from Oryx using the BA or UPGMA models. The topologies of all the gamma-corrected Bayesian trees were identical irrespective of the marker type. The UPGMA trees resulting from 16S rRNA and d-loop sequences were also identical (Oryx dammah grouped with Oryx leucoryx) to Bayesian trees except that the UPGMA tree based on cyt-b showed a slightly different phylogeny (Oryx dammah grouped with Oryx gazella) with a low bootstrap support. However, the MP model failed to differentiate the genus Addax from Oryx. These findings demonstrate the efficiency and robustness of BA and UPGMA methods for phylogenetic analysis of antelopes using mitochondrial markers.

Bayesian, Maximum Parsimony and UPGMA Models for Inferring the Phylogenies of Antelopes Using Mitochondrial Markers

PubMed Central

Khan, Haseeb A.; Arif, Ibrahim A.; Bahkali, Ali H.; Al Farhan, Ahmad H.; Al Homaidan, Ali A.

2008-01-01

This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to BA, MP and UPGMA models for comparing the topologies of respective phylogenetic trees. The 16S rRNA region possessed the highest frequency of conserved sequences (97.65%) followed by cyt-b (94.22%) and d-loop (87.29%). There were few transitions (2.35%) and none transversions in 16S rRNA as compared to cyt-b (5.61% transitions and 0.17% transversions) and d-loop (11.57% transitions and 1.14% transversions) while comparing the four taxa. All the three mitochondrial segments clearly differentiated the genus Addax from Oryx using the BA or UPGMA models. The topologies of all the gamma-corrected Bayesian trees were identical irrespective of the marker type. The UPGMA trees resulting from 16S rRNA and d-loop sequences were also identical (Oryx dammah grouped with Oryx leucoryx) to Bayesian trees except that the UPGMA tree based on cyt-b showed a slightly different phylogeny (Oryx dammah grouped with Oryx gazella) with a low bootstrap support. However, the MP model failed to differentiate the genus Addax from Oryx. These findings demonstrate the efficiency and robustness of BA and UPGMA methods for phylogenetic analysis of antelopes using mitochondrial markers. PMID:19204824

The development of a closed-loop flight controller with panel method integration for gust alleviation using biomimetic feathers on aircraft wings

NASA Astrophysics Data System (ADS)

Blower, Christopher J.; Lee, Woody; Wickenheiser, Adam M.

2012-04-01

This paper presents the development of a biomimetic closed-loop flight controller that integrates gust alleviation and flight control into a single distributed system. Modern flight controllers predominantly rely on and respond to perturbations in the global states, resulting in rotation or displacement of the entire aircraft prior to the response. This bio-inspired gust alleviation system (GAS) employs active deflection of electromechanical feathers that react to changes in the airflow, i.e. the local states. The GAS design is a skeletal wing structure with a network of featherlike panels installed on the wing's surfaces, creating the airfoil profile and replacing the trailing-edge flaps. In this study, a dynamic model of the GAS-integrated wing is simulated to compute gust-induced disturbances. The system implements continuous adjustment to flap orientation to perform corrective responses to inbound gusts. MATLAB simulations, using a closed-loop LQR integrated with a 2D adaptive panel method, allow analysis of the morphing structure's aerodynamic data. Non-linear and linear dynamic models of the GAS are compared to a traditional single control surface baseline wing. The feedback loops synthesized rely on inertial changes in the global states; however, variations in number and location of feather actuation are compared. The bio-inspired system's distributed control effort allows the flight controller to interchange between the single and dual trailing edge flap profiles, thereby offering an improved efficiency to gust response in comparison to the traditional wing configuration. The introduction of aero-braking during continuous gusting flows offers a 25% reduction in x-velocity deviation; other flight parameters can be reduced in magnitude and deviation through control weighting optimization. Consequently, the GAS demonstrates enhancements to maneuverability and stability in turbulent intensive environments.

Identification of processed Chinese medicinal materials using DNA mini-barcoding.

PubMed

Song, Ming; Dong, Gang-Qiang; Zhang, Ya-Qin; Liu, Xia; Sun, Wei

2017-07-01

Most of Chinese medicinal herbs are subjected to traditional processing procedures, including stir-frying, charring, steaming, boiling, and calcining before they are released into dispensaries. The marketing and identification of processed medicinal materials is a growing issue in the marketplace. However, conventional methods of identification have limitations, while DNA mini-barcoding, based on the sequencing of a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In the present study, six DNA barcode loci including ITS2, psbA-trnH, rbcL, matK, trnL (UAA) intron and its P6 loop, were employed for the authentication of 45 processed samples belonging to 15 species. We evaluated the amplification efficiency of each locus. We also examined the identification accuracy of the potential mini-barcode locus, of trnL (UAA) intron P6 loop. Our results showed that the five primary barcode loci were successfully amplified in only 8.89%-20% of the processed samples, while the amplification rates of the trnL (UAA) intron P6 loop were higher, at 75.56% successful amplification. We compared the mini-barcode sequences with Genbank using the Blast program. The analysis showed that 45.23% samples could be identified to genus level, while only one sample could be identified to the species level. We conclude that trnL (UAA) p6 loop is a candidate mini-barcode that has shown its potential and may become a universal mini-barcode as complementary barcode for authenticity testing and will play an important role in medicinal materials control. Copyright © 2017 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

Exploring the mechanism of zanamivir resistance in a neuraminidase mutant: a molecular dynamics study.

PubMed

Han, Nanyu; Liu, Xuewei; Mu, Yuguang

2012-01-01

It is critical to understand the molecular basis of the drug resistance of influenza viruses to efficiently treat this infectious disease. Recently, H1N1 strains of influenza A carrying a mutation of Q136K in neuraminidase were found. The new strain showed a strong Zanamivir neutralization effect. In this study, normal molecular dynamics simulations and metadynamics simulations were employed to explore the mechanism of Zanamivir resistance. The wild-type neuraminidase contained a 3(10) helix before the 150 loop, and there was interaction between the 150 and 430 loops. However, the helix and the interaction between the two loops were disturbed in the mutant protein due to interaction between K136 and nearby residues. Hydrogen-bond network analysis showed weakened interaction between the Zanamivir drug and E276/D151 on account of the electrostatic interaction between K136 and D151. Metadynamics simulations showed that the free energy landscape was different in the mutant than in the wild-type neuraminidase. Conformation with the global minimum of free energy for the mutant protein was different from the wild-type conformation. While the drug fit completely into the active site of the wild-type neuraminidase, it did not match the active site of the mutant variant. This study indicates that the altered hydrogen-bond network and the deformation of the 150 loop are the key factors in development of Zanamivir resistance. Furthermore, the Q136K mutation has a variable effect on conformation of different N1 variants, with conformation of the 1918 N1 variant being more profoundly affected than that of the other N1 variants studied in this paper. This observation warrants further experimental investigation.

Loran digital phase-locked loop and RF front-end system error analysis

NASA Technical Reports Server (NTRS)

Mccall, D. L.

1979-01-01

An analysis of the system performance of the digital phase locked loops (DPLL) and RF front end that are implemented in the MINI-L4 Loran receiver is presented. Three of the four experiments deal with the performance of the digital phase locked loops. The other experiment deals with the RF front end and DPLL system error which arise in the front end due to poor signal to noise ratios. The ability of the DPLLs to track the offsets is studied.

Thermal Analysis of Post-eruption Loops from 80,000 to 1.6 million K

NASA Technical Reports Server (NTRS)

Kucera, T.; Landi, E.

2006-01-01

We analyze the thermal properties of a set of post eruptive loops which appeared after a prominence eruption on April 30, 2004. The event was observed by TRACE and SOHO/SUMER. The SUMER data was taken from a single slit location with a 90 second cadence and included a number of lines spanning the temperature range 80,000 to 1.6 million K. We perform a differential emission measure analysis of the loops in order to study their thermal evolution.

75 FR 75721 - Environmental Impact Statement: Billings County, North Dakota

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-06

...- of-Way Engineer, Federal Highway Administration, 1471 Interstate Loop, Bismarck, North Dakota 58503... agricultural, commercial, and industrial vehicles and equipment. The safe and efficient movement of people and...

A Numerical Study for Groundwater Flow, Heat and Solute Transport Associated with Operation of Open-loop Geothermal System in Alluvial Aquifer

NASA Astrophysics Data System (ADS)

Park, D. K.; Bae, G. O.; Lee, K. K.

2014-12-01

The open-loop geothermal system directly uses a relatively stable temperature of groundwater for cooling and heating in buildings and thus has been known as an eco-friendly, energy-saving, and cost-efficient technique. The facility for this system was installed at a site located near Paldang-dam in Han-river, Korea. Because of the well-developed alluvium, the site might be appropriate to application of this system requiring extraction and injection of a large amount of groundwater. A simple numerical experiment assuming various hydrogeologic conditions demonstrated that regional groundwater flow direction was the most important factor for efficient operation of facility in this site having a highly permeable layer. However, a comparison of river stage data and groundwater level measurements showed that the daily and seasonal controls of water level at Paldang-dam have had a critical influence on the regional groundwater flow in the site. Moreover, nitrate concentrations measured in the monitoring wells gave indication of the effect of agricultural activities around the facility on the groundwater quality. The facility operation, such as extraction and injection of groundwater, will obviously affect transport of the agricultural contaminant and, maybe, it will even cause serious problems in the normal operation. Particularly, the high-permeable layer in this aquifer must be a preferential path for quick spreadings of thermal and contaminant plumes. The objective of this study was to find an efficient, safe and stable operation plan of the open-loop geothermal system installed in this site having the complicated conditions of highly permeable layer, variable regional groundwater flow, and agricultural contamination. Numerical simulations for groundwater flow, heat and solute transport were carried out to analyze all the changes in groundwater level and flow, temperature, and quality according to the operation, respectively. Results showed that an operation plan for only the thermal efficiency of system cannot be the best in aspect of safe and stable operation related to groundwater quality. All these results concluded that it is essential to understand various and site-specific conditions of the site in a more integrated approach for the successful application of the open-loop geothermal system.

Effect of lysine to arginine mutagenesis in the V3 loop of HIV-1 gp120 on viral entry efficiency and neutralization.

PubMed

Schwalbe, Birco; Schreiber, Michael

2015-01-01

HIV-1 infection is characterized by an ongoing replication leading to T-lymphocyte decline which is paralleled by the switch from CCR5 to CXCR4 coreceptor usage. To predict coreceptor usage, several computer algorithms using gp120 V3 loop sequence data have been developed. In these algorithms an occupation of the V3 positions 11 and 25, by one of the amino acids lysine (K) or arginine (R), is an indicator for CXCR4 usage. Amino acids R and K dominate at these two positions, but can also be identified at positions 9 and 10. Generally, CXCR4-viruses possess V3 sequences, with an overall positive charge higher than the V3 sequences of R5-viruses. The net charge is calculated by subtracting the number of negatively charged amino acids (D, aspartic acid and E, glutamic acid) from the number of positively charged ones (K and R). In contrast to D and E, which are very similar in their polar and acidic properties, the characteristics of the R guanidinium group differ significantly from the K ammonium group. However, in coreceptor predictive computer algorithms R and K are both equally rated. The study was conducted to analyze differences in infectivity and coreceptor usage because of R-to-K mutations at the V3 positions 9, 10 and 11. V3 loop mutants with all possible RRR-to-KKK triplets were constructed and analyzed for coreceptor usage, infectivity and neutralization by SDF-1α and RANTES. Virus mutants R9R10R11 showed the highest infectivity rates, and were inhibited more efficiently in contrast to the K9K10K11 viruses. They also showed higher efficiency in a virus-gp120 paired infection assay. Especially V3 loop position 9 was relevant for a switch to higher infectivity when occupied by R. Thus, K-to-R exchanges play a role for enhanced viral entry efficiency and should therefore be considered when the viral phenotype is predicted based on V3 sequence data.

Effect of Lysine to Arginine Mutagenesis in the V3 Loop of HIV-1 gp120 on Viral Entry Efficiency and Neutralization

PubMed Central

Schwalbe, Birco; Schreiber, Michael

2015-01-01

HIV-1 infection is characterized by an ongoing replication leading to T-lymphocyte decline which is paralleled by the switch from CCR5 to CXCR4 coreceptor usage. To predict coreceptor usage, several computer algorithms using gp120 V3 loop sequence data have been developed. In these algorithms an occupation of the V3 positions 11 and 25, by one of the amino acids lysine (K) or arginine (R), is an indicator for CXCR4 usage. Amino acids R and K dominate at these two positions, but can also be identified at positions 9 and 10. Generally, CXCR4-viruses possess V3 sequences, with an overall positive charge higher than the V3 sequences of R5-viruses. The net charge is calculated by subtracting the number of negatively charged amino acids (D, aspartic acid and E, glutamic acid) from the number of positively charged ones (K and R). In contrast to D and E, which are very similar in their polar and acidic properties, the characteristics of the R guanidinium group differ significantly from the K ammonium group. However, in coreceptor predictive computer algorithms R and K are both equally rated. The study was conducted to analyze differences in infectivity and coreceptor usage because of R-to-K mutations at the V3 positions 9, 10 and 11. V3 loop mutants with all possible RRR-to-KKK triplets were constructed and analyzed for coreceptor usage, infectivity and neutralization by SDF-1α and RANTES. Virus mutants R9R10R11 showed the highest infectivity rates, and were inhibited more efficiently in contrast to the K9K10K11 viruses. They also showed higher efficiency in a virus-gp120 paired infection assay. Especially V3 loop position 9 was relevant for a switch to higher infectivity when occupied by R. Thus, K-to-R exchanges play a role for enhanced viral entry efficiency and should therefore be considered when the viral phenotype is predicted based on V3 sequence data. PMID:25785610

The 5′-tail of antisense RNAII of pMV158 plays a critical role in binding to the target mRNA and in translation inhibition of repB

PubMed Central

López-Aguilar, Celeste; Romero-López, Cristina; Espinosa, Manuel; Berzal-Herranz, Alfredo; del Solar, Gloria

2015-01-01

Rolling-circle replication of streptococcal plasmid pMV158 is controlled by the concerted action of two trans-acting elements, namely transcriptional repressor CopG and antisense RNAII, which inhibit expression of the repB gene encoding the replication initiator protein. The pMV158-encoded antisense RNAII exerts its activity of replication control by inhibiting translation of the essential repB gene. RNAII is the smallest and simplest among the characterized antisense RNAs involved in control of plasmid replication. Structure analysis of RNAII revealed that it folds into an 8-bp-long stem containing a 1-nt bulge and closed by a 6-nt apical loop. This hairpin is flanked by a 17-nt-long single-stranded 5′-tail and an 8-nt-long 3′-terminal U-rich stretch. Here, the 3′ and 5′ regions of the 5′-tail of RNAII are shown to play a critical role in the binding to the target mRNA and in the inhibition of repB translation, respectively. In contrast, the apical loop of the single hairpin of RNAII plays a rather secondary role and the upper stem region hardly contributes to the binding or inhibition processes. The entire 5′-tail is required for efficient inhibition of repB translation, though only the 8-nt-long region adjacent to the hairpin seems to be essential for rapid binding to the mRNA. These results show that a “kissing” interaction involving base-pairing between complementary hairpin loops in RNAII and mRNA is not critical for efficient RNA/RNA binding or repB translation inhibition. A singular binding mechanism is envisaged whereby initial pairing between complementary single-stranded regions in the antisense and sense RNAs progresses upwards into the corresponding hairpin stems to form the intermolecular duplex. PMID:26175752

The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.

PubMed

Tsuchiya, Yuko; Mizuguchi, Kenji

2016-04-01

Of the complementarity-determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen-binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen-binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen-binding tendencies of all the CDR loops. © 2016 The Protein Society.

A digital wireless system for closed-loop inhibition of nociceptive signals

NASA Astrophysics Data System (ADS)

Zuo, Chao; Yang, Xiaofei; Wang, Yang; Hagains, Christopher E.; Li, Ai-Ling; Peng, Yuan B.; Chiao, J.-C.

2012-10-01

Neurostimulation of the spinal cord or brain has been used to inhibit nociceptive signals in pain management applications. Nevertheless, most of the current neurostimulation models are based on open-loop system designs. There is a lack of closed-loop systems for neurostimulation in research with small freely-moving animals and in future clinical applications. Based on our previously developed analog wireless system for closed-loop neurostimulation, a digital wireless system with real-time feedback between recorder and stimulator modules has been developed to achieve multi-channel communication. The wireless system includes a wearable recording module, a wearable stimulation module and a transceiver connected to a computer for real-time and off-line data processing, display and storage. To validate our system, wide dynamic range neurons in the spinal cord dorsal horn have been recorded from anesthetized rats in response to graded mechanical stimuli (brush, pressure and pinch) applied in the hind paw. The identified nociceptive signals were used to automatically trigger electrical stimulation at the periaqueductal gray in real time to inhibit their own activities by the closed-loop design. Our digital wireless closed-loop system has provided a simplified and efficient method for further study of pain processing in freely-moving animals and potential clinical application in patients. Groups 1, 2 and 3 contributed equally to this project.

Loop and void damage during heavy ion irradiation on nanocrystalline and coarse grained tungsten: Microstructure, effect of dpa rate, temperature, and grain size

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

El-Atwani, O.; Esquivel, E.; Efe, M.

Displacement damage, through heavy ion irradiation was studied on two tungsten grades (coarse grained tungsten (CGW) and nanocrystalline and ultrafine grained tungsten (NCW)) using different displacement per atom rates and different irradiation temperatures (RT and 1050 K). Percentage of <111> and <100> type loops at the irradiation conditions was determined. Irradiation damage in the microstructure was quantified using average loop areas and densities (method A) and loop areal fraction in the grain matrices under 2-beam diffraction conditions (method B). Average values of <111> and <100> loops were calculated from method A. Loop coalescence was shown to occur for CGW atmore » 0.25 dpa. Using both methods of quantifying microstructural damage, no effect of dpa rate was observed and damage in CGW was shown to be the same at RT and 1050 K. Swelling from voids observed at 1050 K was quantified. The loop damage in NCW was compared to CGW at the same diffraction and imaging conditions. NCW was shown to possess enhanced irradiation resistance at RT regarding loop damage and higher swelling resistance at 1050 K compared to CGW. For irradiation at 1050 K, the NCW was shown to have a similar defect densities to the CGW which is attributed to higher surface effects in the CGW, vacancy loop growth to voids and a better sink efficiency in the CGW deduced from the vacancy distribution profiles from Kinetic Monte Carlo simulations. Loop density and swelling was shown to have similar values in grains sizes that range from 80-600 nm. No loop or void denuded zones occurred at any of the irradiation conditions. This work has a collection of experiments and conclusions that are of vital importance to materials and nuclear communities.« less

Loop and void damage during heavy ion irradiation on nanocrystalline and coarse grained tungsten: Microstructure, effect of dpa rate, temperature, and grain size

DOE PAGES

El-Atwani, O.; Esquivel, E.; Efe, M.; ...

2018-02-20

Displacement damage, through heavy ion irradiation was studied on two tungsten grades (coarse grained tungsten (CGW) and nanocrystalline and ultrafine grained tungsten (NCW)) using different displacement per atom rates and different irradiation temperatures (RT and 1050 K). Percentage of <111> and <100> type loops at the irradiation conditions was determined. Irradiation damage in the microstructure was quantified using average loop areas and densities (method A) and loop areal fraction in the grain matrices under 2-beam diffraction conditions (method B). Average values of <111> and <100> loops were calculated from method A. Loop coalescence was shown to occur for CGW atmore » 0.25 dpa. Using both methods of quantifying microstructural damage, no effect of dpa rate was observed and damage in CGW was shown to be the same at RT and 1050 K. Swelling from voids observed at 1050 K was quantified. The loop damage in NCW was compared to CGW at the same diffraction and imaging conditions. NCW was shown to possess enhanced irradiation resistance at RT regarding loop damage and higher swelling resistance at 1050 K compared to CGW. For irradiation at 1050 K, the NCW was shown to have a similar defect densities to the CGW which is attributed to higher surface effects in the CGW, vacancy loop growth to voids and a better sink efficiency in the CGW deduced from the vacancy distribution profiles from Kinetic Monte Carlo simulations. Loop density and swelling was shown to have similar values in grains sizes that range from 80-600 nm. No loop or void denuded zones occurred at any of the irradiation conditions. This work has a collection of experiments and conclusions that are of vital importance to materials and nuclear communities.« less

Telecommunications Policy Research Conference. Competition in the Local Loop Section. Papers.

ERIC Educational Resources Information Center

Telecommunications Policy Research Conference, Inc., Washington, DC.

Four papers consider competition, new technology and economics of local telephone companies in a deregulated environment: (1) "An Engineering and Policy Analysis of Fiber Introduction into the Residential Subscriber Loop" (Marvin Sirbu, Frank Ferrante, and David Reed); (2) "Competition in the Local Loop: Pricing Carrier Access"…

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics

PubMed Central

Kurkcuoglu, Zeynep; Bakan, Ahmet; Kocaman, Duygu; Bahar, Ivet; Doruker, Pemra

2012-01-01

Catalytic loop motions facilitate substrate recognition and binding in many enzymes. While these motions appear to be highly flexible, their functional significance suggests that structure-encoded preferences may play a role in selecting particular mechanisms of motions. We performed an extensive study on a set of enzymes to assess whether the collective/global dynamics, as predicted by elastic network models (ENMs), facilitates or even defines the local motions undergone by functional loops. Our dataset includes a total of 117 crystal structures for ten enzymes of different sizes and oligomerization states. Each enzyme contains a specific functional/catalytic loop (10–21 residues long) that closes over the active site during catalysis. Principal component analysis (PCA) of the available crystal structures (including apo and ligand-bound forms) for each enzyme revealed the dominant conformational changes taking place in these loops upon substrate binding. These experimentally observed loop reconfigurations are shown to be predominantly driven by energetically favored modes of motion intrinsically accessible to the enzyme in the absence of its substrate. The analysis suggests that robust global modes cooperatively defined by the overall enzyme architecture also entail local components that assist in suitable opening/closure of the catalytic loop over the active site. PMID:23028297

Molecular dynamics simulation of hepatitis C virus IRES IIId domain: structural behavior, electrostatic and energetic analysis.

PubMed

Golebiowski, Jérôme; Antonczak, Serge; Di-Giorgio, Audrey; Condom, Roger; Cabrol-Bass, Daniel

2004-02-01

The dynamic behavior of the HCV IRES IIId domain is analyzed by means of a 2.6-ns molecular dynamics simulation, starting from an NMR structure. The simulation is carried out in explicit water with Na+ counterions, and particle-mesh Ewald summation is used for the electrostatic interactions. In this work, we analyze selected patterns of the helix that are crucial for IRES activity and that could be considered as targets for the intervention of inhibitors, such as the hexanucleotide terminal loop (more particularly its three consecutive guanines) and the loop-E motif. The simulation has allowed us to analyze the dynamics of the loop substructure and has revealed a behavior among the guanine bases that might explain the different role of the third guanine of the GGG triplet upon molecular recognition. The accessibility of the loop-E motif and the loop major and minor groove is also examined, as well as the effect of Na+ or Mg2+ counterion within the simulation. The electrostatic analysis reveals several ion pockets, not discussed in the experimental structure. The positions of these ions are useful for locating specific electrostatic recognition sites for potential inhibitor binding.

Analysis of an all-digital maximum likelihood carrier phase and clock timing synchronizer for eight phase-shift keying modulation

NASA Astrophysics Data System (ADS)

Degaudenzi, Riccardo; Vanghi, Vieri

1994-02-01

In all-digital Trellis-Coded 8PSK (TC-8PSK) demodulator well suited for VLSI implementation, including maximum likelihood estimation decision-directed (MLE-DD) carrier phase and clock timing recovery, is introduced and analyzed. By simply removing the trellis decoder the demodulator can efficiently cope with uncoded 8PSK signals. The proposed MLE-DD synchronization algorithm requires one sample for the phase and two samples per symbol for the timing loop. The joint phase and timing discriminator characteristics are analytically derived and numerical results checked by means of computer simulations. An approximated expression for steady-state carrier phase and clock timing mean square error has been derived and successfully checked with simulation findings. Synchronizer deviation from the Cramer Rao bound is also discussed. Mean acquisition time for the digital synchronizer has also been computed and checked, using the Monte Carlo simulation technique. Finally, TC-8PSK digital demodulator performance in terms of bit error rate and mean time to lose lock, including digital interpolators and synchronization loops, is presented.

Mutational analysis of three predicted 5'-proximal stem-loop structures in the genome of tick-borne encephalitis virus indicates different roles in RNA replication and translation

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

Rouha, Harald; Hoenninger, Verena M.; Thurner, Caroline

2011-08-15

Flavivirus gene expression is modulated by RNA secondary structure elements at the terminal ends of the viral RNA molecule. For tick-borne encephalitis virus (TBEV), four stem-loop (SL) elements have been predicted in the first 180 nucleotides of the viral genome: 5'-SL1, 5'-SL2, 5'-SL3 and 5'-SL4. The last three of these appear to be unique to tick-borne flaviviruses. Here, we report their characterization by mutagenesis in a TBEV luciferase reporter system. By manipulating their thermodynamic properties, we found that an optimal stability of the 5'-SL2 is required for efficient RNA replication. 5'-SL3 formation is also important for viral RNA replication, butmore » although it contains the viral start codon, its formation is dispensable for RNA translation. 5'-SL4 appears to facilitate both RNA translation and replication. Our data suggest that maintenance of the balanced thermodynamic stability of these SL elements is important for temporal regulation of its different functions.« less

Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression

PubMed Central

Aze, Antoine; Sannino, Vincenzo; Soffientini, Paolo; Bachi, Angela; Costanzo, Vincenzo

2016-01-01

Half of human genome is made of repetitive DNA. However, mechanisms underlying replication of chromosome regions containing repetitive DNA are poorly understood. We reconstituted replication of defined human chromosome segments using Bacterial Artificial Chromosomes (BACs) in Xenopus laevis egg extract. Using this approach we characterized chromatin assembly and replication dynamics of centromeric alpha-satellite DNA. Proteomic analysis of centromeric chromatin revealed replication dependent enrichment of a network of DNA repair factors among which the MSH2-6 complex, which was required for efficient centromeric DNA replication. However, contrary to expectations, the ATR dependent checkpoint monitoring DNA replication fork arrest could not be activated on highly repetitive DNA due to inability of single stranded DNA binding protein RPA to accumulate on chromatin. Electron microscopy of centromeric DNA and supercoil mapping revealed the presence of Topoisomerase I dependent DNA loops embedded in a protein matrix enriched for SMC2-4 proteins. This arrangement suppressed ATR signalling by preventing RPA hyper-loading, facilitating replication of centromeric DNA. These findings have important implications on our understanding of repetitive DNA metabolism and centromere organization under normal and stressful conditions. PMID:27111843

Does microbial biomass affect pelagic ecosystem efficiency? An experimental study.

PubMed

Wehr, J D; Le, J; Campbell, L

1994-01-01

Bacteria and other microorganisms in the pelagic zone participate in the recycling of organic matter and nutrients within the water column. The microbial loop is thought to enhance ecosystem efficiency through rapid recycling and reduced sinking rates, thus reducing the loss of nutrients contained in organisms remaining within the photic zone. We conducted experiments with lake communities in 5400-liter mesocosms, and measured the flux of materials and nutrients out of the water column. A factorial design manipulated 8 nutrient treatments: 4 phosphorus levels × 2 nitrogen levels. Total sedimentation rates were greatest in high-N mesocosms; within N-surplus communities, [Symbol: see text]1 µM P resulted in 50% increase in total particulate losses. P additions without added N had small effects on nutrient losses from the photic zone; +2 µM P tanks received 334 mg P per tank, yet after 14 days lost only 69 mg more particulate-P than did control communities. Nutrient treatments resulted in marked differences in phytoplankton biomass (twofold N effect, fivefold P effect in +N mesocosms only), bacterioplankton densities (twofold N-effect, twofold P effects in -N and +N mesocosms), and the relative importance of autotrophic picoplankton (maximum in high NY mesocosms). Multiple regression analysis found that of 8 plankton and water chemistry variables, the ratio of autotrophic picoplankton to total phytoplankton (measured as chlorophyll α) explained the largest portion of the total variation in sedimentation loss rates (65% of P-flux, 57% of N-flux, 26% of total flux). In each case, systems with greater relative importance of autotrophic picoplankton had significantly reduced loss rates. In contrast, greater numbers of planktonic bacteria were associated with increased sedimentation rates and lower system efficiency. We suggest that different microbial components may have contrasting effects on the presumed enhanced efficiency provided by the microbial loop.

Possibility-based robust design optimization for the structural-acoustic system with fuzzy parameters

NASA Astrophysics Data System (ADS)

Yin, Hui; Yu, Dejie; Yin, Shengwen; Xia, Baizhan

2018-03-01

The conventional engineering optimization problems considering uncertainties are based on the probabilistic model. However, the probabilistic model may be unavailable because of the lack of sufficient objective information to construct the precise probability distribution of uncertainties. This paper proposes a possibility-based robust design optimization (PBRDO) framework for the uncertain structural-acoustic system based on the fuzzy set model, which can be constructed by expert opinions. The objective of robust design is to optimize the expectation and variability of system performance with respect to uncertainties simultaneously. In the proposed PBRDO, the entropy of the fuzzy system response is used as the variability index; the weighted sum of the entropy and expectation of the fuzzy response is used as the objective function, and the constraints are established in the possibility context. The computations for the constraints and objective function of PBRDO are a triple-loop and a double-loop nested problem, respectively, whose computational costs are considerable. To improve the computational efficiency, the target performance approach is introduced to transform the calculation of the constraints into a double-loop nested problem. To further improve the computational efficiency, a Chebyshev fuzzy method (CFM) based on the Chebyshev polynomials is proposed to estimate the objective function, and the Chebyshev interval method (CIM) is introduced to estimate the constraints, thereby the optimization problem is transformed into a single-loop one. Numerical results on a shell structural-acoustic system verify the effectiveness and feasibility of the proposed methods.

Experimental validation of the predicted binding site of Escherichia coli K1 outer membrane protein A to human brain microvascular endothelial cells: identification of critical mutations that prevent E. coli meningitis.

PubMed

Pascal, Tod A; Abrol, Ravinder; Mittal, Rahul; Wang, Ying; Prasadarao, Nemani V; Goddard, William A

2010-11-26

Escherichia coli K1, the most common cause of meningitis in neonates, has been shown to interact with GlcNAc1-4GlcNAc epitopes of Ecgp96 on human brain microvascular endothelial cells (HBMECs) via OmpA (outer membrane protein A). However, the precise domains of extracellular loops of OmpA interacting with the chitobiose epitopes have not been elucidated. We report the loop-barrel model of these OmpA interactions with the carbohydrate moieties of Ecgp96 predicted from molecular modeling. To test this model experimentally, we generated E. coli K1 strains expressing OmpA with mutations of residues predicted to be critical for interaction with the HBMEC and tested E. coli invasion efficiency. For these same mutations, we predicted the interaction free energies (including explicit calculation of the entropy) from molecular dynamics (MD), finding excellent correlation (R(2) = 90%) with experimental invasion efficiency. Particularly important is that mutating specific residues in loops 1, 2, and 4 to alanines resulted in significant inhibition of E. coli K1 invasion in HBMECs, which is consistent with the complete lack of binding found in the MD simulations for these two cases. These studies suggest that inhibition of the interactions of these residues of Loop 1, 2, and 4 with Ecgp96 could provide a therapeutic strategy to prevent neonatal meningitis due to E. coli K1.

Tunable, Electrically Small, Inductively Coupled Antenna for Transportable Ionospheric Heating

NASA Astrophysics Data System (ADS)

Esser, Benedikt; Mauch, Daniel; Dickens, James; Mankowski, John; Neuber, Andreas

2018-04-01

An electrically small antenna is evaluated for use as the principle radiating element in a mobile ionospheric heating array. Consisting of a small loop antenna inductively coupled to a capacitively loaded loop, the electrically small antenna provides high efficiency with the capability of being tuned within the range of ionospheric heating. At a factor 60 smaller in area than a High-Frequency Active Auroral Research Program element, this antenna provides a compact, efficient radiating element for mobile ionospheric heating. A prototype antenna at 10 MHz was built to study large-scale feasibility and possible use with photoconductive semiconductor switch-based drivers. Based on the experimental study, the design has been extrapolated to a small 6 × 4 array of antennas. At a total power input of 16.1 MW this array is predicted to provide 3.6-GW effective radiated power typically required for ionospheric heating. Array cross talk is addressed, including effects upon individual antenna port parameters. Tuning within the range of ionospheric heating, 3-10 MHz, is made possible without the use of lossy dielectrics through a large capacitive area suited to tune the antenna. Considerations for high power operation across the band are provided including a method of driving the antenna with a simple switcher requiring no radio frequency cabling. Source matching may be improved via adjustment of the coupling between small loop antenna and capacitively loaded loop improving |S11| from -1 to -21 dB at 3 MHz.

Integrand Reduction Reloaded: Algebraic Geometry and Finite Fields

NASA Astrophysics Data System (ADS)

Sameshima, Ray D.; Ferroglia, Andrea; Ossola, Giovanni

2017-01-01

The evaluation of scattering amplitudes in quantum field theory allows us to compare the phenomenological prediction of particle theory with the measurement at collider experiments. The study of scattering amplitudes, in terms of their symmetries and analytic properties, provides a theoretical framework to develop techniques and efficient algorithms for the evaluation of physical cross sections and differential distributions. Tree-level calculations have been known for a long time. Loop amplitudes, which are needed to reduce the theoretical uncertainty, are more challenging since they involve a large number of Feynman diagrams, expressed as integrals of rational functions. At one-loop, the problem has been solved thanks to the combined effect of integrand reduction, such as the OPP method, and unitarity. However, plenty of work is still needed at higher orders, starting with the two-loop case. Recently, integrand reduction has been revisited using algebraic geometry. In this presentation, we review the salient features of integrand reduction for dimensionally regulated Feynman integrals, and describe an interesting technique for their reduction based on multivariate polynomial division. We also show a novel approach to improve its efficiency by introducing finite fields. Supported in part by the National Science Foundation under Grant PHY-1417354.

Comparative study of control strategies for hybrid GSHP system in the cooling dominated climate

DOE PAGES

Wang, Shaojie; Liu, Xiaobing; Gates, Steve

2015-01-06

The ground source heat pump (GSHP) system is one of the most energy efficient HVAC technologies in the current market. However, the heat imbalance may degrade the ability of the ground loop heat exchanger (GLHX) to absorb or reject heat. The hybrid GSHP system, which combines a geothermal well field with a supplemental boiler or cooling tower, can balance the loads imposed on the ground loop heat exchangers to minimize its size while retaining superior energy efficiency. This paper presents a recent simulation-based study with an intention to compare multiple common control strategies used in hybrid GSHP systems, including fixedmore » setpoint, outside air reset, load reset, and wetbulb reset. A small office in Oklahoma City conditioned by a hybrid GSHP system was simulated with the latest version of eQUEST 3.7 [1]. In the end, the simulation results reveal that the hybrid GSHP system has the excellent capability to meet the cooling and heating setpoints during the occupied hours, balance thermal loads on the ground loop, as well as improve the thermal comfort of the occupants with the reduced size well field.« less

A Power-Efficient Wireless System With Adaptive Supply Control for Deep Brain Stimulation.

PubMed

Lee, Hyung-Min; Park, Hangue; Ghovanloo, Maysam

2013-09-01

A power-efficient wireless stimulating system for a head-mounted deep brain stimulator (DBS) is presented. A new adaptive rectifier generates a variable DC supply voltage from a constant AC power carrier utilizing phase control feedback, while achieving high AC-DC power conversion efficiency (PCE) through active synchronous switching. A current-controlled stimulator adopts closed-loop supply control to automatically adjust the stimulation compliance voltage by detecting stimulation site potentials through a voltage readout channel, and improve the stimulation efficiency. The stimulator also utilizes closed-loop active charge balancing to maintain the residual charge at each site within a safe limit, while receiving the stimulation parameters wirelessly from the amplitude-shift-keyed power carrier. A 4-ch wireless stimulating system prototype was fabricated in a 0.5-μm 3M2P standard CMOS process, occupying 2.25 mm². With 5 V peak AC input at 2 MHz, the adaptive rectifier provides an adjustable DC output between 2.5 V and 4.6 V at 2.8 mA loading, resulting in measured PCE of 72 ~ 87%. The adaptive supply control increases the stimulation efficiency up to 30% higher than a fixed supply voltage to 58 ~ 68%. The prototype wireless stimulating system was verified in vitro .

A Power-Efficient Wireless System With Adaptive Supply Control for Deep Brain Stimulation

PubMed Central

Lee, Hyung-Min; Park, Hangue; Ghovanloo, Maysam

2014-01-01

A power-efficient wireless stimulating system for a head-mounted deep brain stimulator (DBS) is presented. A new adaptive rectifier generates a variable DC supply voltage from a constant AC power carrier utilizing phase control feedback, while achieving high AC-DC power conversion efficiency (PCE) through active synchronous switching. A current-controlled stimulator adopts closed-loop supply control to automatically adjust the stimulation compliance voltage by detecting stimulation site potentials through a voltage readout channel, and improve the stimulation efficiency. The stimulator also utilizes closed-loop active charge balancing to maintain the residual charge at each site within a safe limit, while receiving the stimulation parameters wirelessly from the amplitude-shift-keyed power carrier. A 4-ch wireless stimulating system prototype was fabricated in a 0.5-μm 3M2P standard CMOS process, occupying 2.25 mm². With 5 V peak AC input at 2 MHz, the adaptive rectifier provides an adjustable DC output between 2.5 V and 4.6 V at 2.8 mA loading, resulting in measured PCE of 72 ~ 87%. The adaptive supply control increases the stimulation efficiency up to 30% higher than a fixed supply voltage to 58 ~ 68%. The prototype wireless stimulating system was verified in vitro. PMID:24678126

Secondary Heat Exchanger Design and Comparison for Advanced High Temperature Reactor

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

Piyush Sabharwall; Ali Siahpush; Michael McKellar

2012-06-01

The goals of next generation nuclear reactors, such as the high temperature gas-cooled reactor and advance high temperature reactor (AHTR), are to increase energy efficiency in the production of electricity and provide high temperature heat for industrial processes. The efficient transfer of energy for industrial applications depends on the ability to incorporate effective heat exchangers between the nuclear heat transport system and the industrial process heat transport system. The need for efficiency, compactness, and safety challenge the boundaries of existing heat exchanger technology, giving rise to the following study. Various studies have been performed in attempts to update the secondarymore » heat exchanger that is downstream of the primary heat exchanger, mostly because its performance is strongly tied to the ability to employ more efficient conversion cycles, such as the Rankine super critical and subcritical cycles. This study considers two different types of heat exchangers—helical coiled heat exchanger and printed circuit heat exchanger—as possible options for the AHTR secondary heat exchangers with the following three different options: (1) A single heat exchanger transfers all the heat (3,400 MW(t)) from the intermediate heat transfer loop to the power conversion system or process plants; (2) Two heat exchangers share heat to transfer total heat of 3,400 MW(t) from the intermediate heat transfer loop to the power conversion system or process plants, each exchanger transfers 1,700 MW(t) with a parallel configuration; and (3) Three heat exchangers share heat to transfer total heat of 3,400 MW(t) from the intermediate heat transfer loop to the power conversion system or process plants. Each heat exchanger transfers 1,130 MW(t) with a parallel configuration. A preliminary cost comparison will be provided for all different cases along with challenges and recommendations.« less

Space Shuttle program communication and tracking systems interface analysis

NASA Technical Reports Server (NTRS)

Dodds, J. G.; Holmes, J. K.; Huth, G. K.; Iwasaki, R. S.; Nilsen, P. W.; Polydoros, A.; Sampaio, D. R.; Udalov, S.

1984-01-01

The Space Shuttle Program Communications and Tracking Systems Interface Analysis began April 18, 1983. During this time, the shuttle communication and tracking systems began flight testing. Two areas of analysis documented were a result of observations made during flight tests. These analyses involved the Ku-band communication system. First, there was a detailed analysis of the interface between the solar max data format and the Ku-band communication system including the TDRSS ground station. The second analysis involving the Ku-band communication system was an analysis of the frequency lock loop of the Gunn oscillator used to generate the transmit frequency. The stability of the frequency lock loop was investigated and changes to the design were reviewed to alleviate the potential loss of data due the loop losing lock and entering the reacquisition mode. Other areas of investigation were the S-band antenna analysis and RF coverage analysis.

Satellite laser ranging using superconducting nanowire single-photon detectors at 1064  nm wavelength.

PubMed

Xue, Li; Li, Zhulian; Zhang, Labao; Zhai, Dongsheng; Li, Yuqiang; Zhang, Sen; Li, Ming; Kang, Lin; Chen, Jian; Wu, Peiheng; Xiong, Yaoheng

2016-08-15

Satellite laser ranging operating at 1064 nm wavelength using superconducting nanowire single-photon detectors (SNSPDs) is successfully demonstrated. A SNSPD with an intrinsic quantum efficiency of 80% and a dark count rate of 100 cps at 1064 nm wavelength is developed and introduced to Yunnan Observatory in China. With improved closed-loop telescope systems (field of view of about 26^''), satellites including Cryosat, Ajisai, and Glonass with ranges of 1600 km, 3100 km, and 19,500 km, respectively, are experimentally ranged with mean echo rates of 1200/min, 4200/min, and 320/min, respectively. To the best of our knowledge, this is the first demonstration of laser ranging for satellites using SNSPDs at 1064 nm wavelength. Theoretical analysis of the detection efficiency and the mean echo rate for typical satellites indicate that it is possible for a SNSPD to range satellites from low Earth orbit to geostationary Earth orbit.

Direct LAMP Assay without Prior DNA Purification for Sex Determination of Papaya.

PubMed

Tsai, Chi-Chu; Shih, Huei-Chuan; Ko, Ya-Zhu; Wang, Ren-Huang; Li, Shu-Ju; Chiang, Yu-Chung

2016-09-24

Papaya (Carica papaya L.) is an economically important tropical fruit tree with hermaphrodite, male and female sex types. Hermaphroditic plants are the major type used for papaya production because their fruits have more commercial advantages than those of female plants. Sex determination of the seedlings, or during the early growth stages, is very important for the papaya seedling industry. Thus far, the only method for determining the sex type of a papaya at the seedling stage has been DNA analysis. In this study, a molecular technique-based on DNA analysis-was developed for detecting male-hermaphrodite-specific markers to examine the papaya's sex type. This method is based on the loop-mediated isothermal amplification (LAMP) and does not require prior DNA purification. The results show that the method is an easy, efficient, and inexpensive way to determine a papaya's sex. This is the first report on the LAMP assay, using intact plant materials-without DNA purification-as samples for the analysis of sex determination of papaya. We found that using high-efficiency DNA polymerase was essential for successful DNA amplification, using trace intact plant material as a template DNA source.

The application of cluster analysis in the intercomparison of loop structures in RNA.

PubMed

Huang, Hung-Chung; Nagaswamy, Uma; Fox, George E

2005-04-01

We have developed a computational approach for the comparison and classification of RNA loop structures. Hairpin or interior loops identified in atomic resolution RNA structures were intercompared by conformational matching. The root-mean-square deviation (RMSD) values between all pairs of RNA fragments of interest, even if from different molecules, are calculated. Subsequently, cluster analysis is performed on the resulting matrix of RMSD distances using the unweighted pair group method with arithmetic mean (UPGMA). The cluster analysis objectively reveals groups of folds that resemble one another. To demonstrate the utility of the approach, a comprehensive analysis of all the terminal hairpin tetraloops that have been observed in 15 RNA structures that have been determined by X-ray crystallography was undertaken. The method found major clusters corresponding to the well-known GNRA and UNCG types. In addition, two tetraloops with the unusual primary sequence UMAC (M is A or C) were successfully assigned to the GNRA cluster. Larger loop structures were also examined and the clustering results confirmed the occurrence of variations of the GNRA and UNCG tetraloops in these loops and provided a systematic means for locating them. Nineteen examples of larger loops that closely resemble either the GNRA or UNCG tetraloop were found in the large ribosomal RNAs. When the clustering approach was extended to include all structures in the SCOR database, novel relationships were detected including one between the ANYA motif and a less common folding of the GAAA tetraloop sequence.

The application of cluster analysis in the intercomparison of loop structures in RNA

PubMed Central

HUANG, HUNG-CHUNG; NAGASWAMY, UMA; FOX, GEORGE E.

2005-01-01

We have developed a computational approach for the comparison and classification of RNA loop structures. Hairpin or interior loops identified in atomic resolution RNA structures were intercompared by conformational matching. The root-mean-square deviation (RMSD) values between all pairs of RNA fragments of interest, even if from different molecules, are calculated. Subsequently, cluster analysis is performed on the resulting matrix of RMSD distances using the unweighted pair group method with arithmetic mean (UPGMA). The cluster analysis objectively reveals groups of folds that resemble one another. To demonstrate the utility of the approach, a comprehensive analysis of all the terminal hairpin tetraloops that have been observed in 15 RNA structures that have been determined by X-ray crystallography was undertaken. The method found major clusters corresponding to the well-known GNRA and UNCG types. In addition, two tetraloops with the unusual primary sequence UMAC (M is A or C) were successfully assigned to the GNRA cluster. Larger loop structures were also examined and the clustering results confirmed the occurrence of variations of the GNRA and UNCG tetraloops in these loops and provided a systematic means for locating them. Nineteen examples of larger loops that closely resemble either the GNRA or UNCG tetraloop were found in the large ribosomal RNAs. When the clustering approach was extended to include all structures in the SCOR database, novel relationships were detected including one between the ANYA motif and a less common folding of the GAAA tetraloop sequence. PMID:15769871

Multiple roles of mobile active center loops in the E1 component of the Escherichia coli pyruvate dehydrogenase complex - Linkage of protein dynamics to catalysis

PubMed Central

Jordan, Frank; Arjunan, Palaniappa; Kale, Sachin; Nemeria, Natalia S.; Furey, William

2009-01-01

The region encompassing residues 401–413 on the E1 component of the pyruvate dehydrogenase multienzyme complex from Escherichia coli comprises a loop (the inner loop) which was not seen in the X-ray structure in the presence of thiamin diphosphate, the required cofactor for the enzyme. This loop is seen in the presence of a stable analogue of the pre-decarboxylation intermediate, the covalent adduct between the substrate analogue methyl acetylphosphonate and thiamin diphosphate, C2α-phosphonolactylthiamin diphosphate. It has been shown that the residue H407 and several other residues on this loop are required to reduce the mobility of the loop so electron density corresponding to it can be seen once the pre-decarboxylation intermediate is formed. Concomitantly, the loop encompassing residues 541–557 (the outer loop) appears to work in tandem with the inner loop and there is a hydrogen bond between the two loops ensuring their correlated motion. The inner loop was shown to: a) sequester the active center from carboligase side reactions; b) assist the interaction between the E1 and the E2 components, thereby affecting the overall reaction rate of the entire multienzyme complex; c) control substrate access to the active center. Using viscosity effects on kinetics it was shown that formation of the pre-decarboxylation intermediate is specifically affected by loop movement. A cysteine-less variant was created for the E1 component, onto which cysteines were substituted at selected loop positions. Introducing an electron spin resonance spin label and an 19F NMR label onto these engineered cysteines, the loop mobility was examined: a) both methods suggested that in the absence of ligand, the loop exists in two conformations; b) line-shape analysis of the NMR signal at different temperatures, enabled estimation of the rate constant for loop movement, and this rate constant was found to be of the same order of magnitude as the turnover number for the enzyme under the same conditions. Furthermore, this analysis gave important insights into rate-limiting thermal loop dynamics. Overall, the results suggest that the dynamic properties correlate with catalytic events on the E1 component of the pyruvate dehydrogenase complex. PMID:20160956

Model-Driven Safety Analysis of Closed-Loop Medical Systems

PubMed Central

Pajic, Miroslav; Mangharam, Rahul; Sokolsky, Oleg; Arney, David; Goldman, Julian; Lee, Insup

2013-01-01

In modern hospitals, patients are treated using a wide array of medical devices that are increasingly interacting with each other over the network, thus offering a perfect example of a cyber-physical system. We study the safety of a medical device system for the physiologic closed-loop control of drug infusion. The main contribution of the paper is the verification approach for the safety properties of closed-loop medical device systems. We demonstrate, using a case study, that the approach can be applied to a system of clinical importance. Our method combines simulation-based analysis of a detailed model of the system that contains continuous patient dynamics with model checking of a more abstract timed automata model. We show that the relationship between the two models preserves the crucial aspect of the timing behavior that ensures the conservativeness of the safety analysis. We also describe system design that can provide open-loop safety under network failure. PMID:24177176

Model-Driven Safety Analysis of Closed-Loop Medical Systems.

PubMed

Pajic, Miroslav; Mangharam, Rahul; Sokolsky, Oleg; Arney, David; Goldman, Julian; Lee, Insup

2012-10-26

In modern hospitals, patients are treated using a wide array of medical devices that are increasingly interacting with each other over the network, thus offering a perfect example of a cyber-physical system. We study the safety of a medical device system for the physiologic closed-loop control of drug infusion. The main contribution of the paper is the verification approach for the safety properties of closed-loop medical device systems. We demonstrate, using a case study, that the approach can be applied to a system of clinical importance. Our method combines simulation-based analysis of a detailed model of the system that contains continuous patient dynamics with model checking of a more abstract timed automata model. We show that the relationship between the two models preserves the crucial aspect of the timing behavior that ensures the conservativeness of the safety analysis. We also describe system design that can provide open-loop safety under network failure.

Engineering the thermostability of β-glucuronidase from Penicillium purpurogenum Li-3 by loop transplant.

PubMed

Feng, Xudong; Tang, Heng; Han, Beijia; Zhang, Liang; Lv, Bo; Li, Chun

2016-12-01

In this study, we proposed a loop transplant strategy to improve the thermostability of Penicillium purpurogenum Li-3 β-glucuronidase expressed in Escherichia coli (abbreviated to PGUS-E). Firstly, three unstable surface loops of PGUS-E to be replaced were identified with regards to B-factor values and in-depth structure analysis: loops 205-211, 258-263, and 25-31. Then, based on B-factor analysis, eight stable loops for substitution were selected from two typical thermophilic glycosidases which had low homology with PGUS-E (less than 25 %). By analyzing the common features of these stable loops, it was found that they shared a common residue skeleton DXXTX(X)R, based on this, three chimera loops were also manually designed: RSQTSND, RSSTQRD, and DDQTSR. All these loops were introduced to replace the unstable loops of PGUS-E by homology structure modeling, and only mutants with increased hydrogen bonds number and good compatibility with the local mutated region were further subjected to experimental verification. By using this strategy, 10 mutants were experimentally generated, among which three mutants, M1, M3, and M8, were obtained which showed 11.8, 3.3, and 9.4 times higher half-life at 70 °C than that of wild-type (8.5 min). Finally, the MD simulation indicated that the increased hydrogen bonds, decreased flexibility of N-terminal, and increased π-π stacking interaction were responsible for the improved thermostability.

A computer method for schedule processing and quick-time updating.

NASA Technical Reports Server (NTRS)

Mccoy, W. H.

1972-01-01

A schedule analysis program is presented which can be used to process any schedule with continuous flow and with no loops. Although generally thought of as a management tool, it has applicability to such extremes as music composition and computer program efficiency analysis. Other possibilities for its use include the determination of electrical power usage during some operation such as spacecraft checkout, and the determination of impact envelopes for the purpose of scheduling payloads in launch processing. At the core of the described computer method is an algorithm which computes the position of each activity bar on the output waterfall chart. The algorithm is basically a maximal-path computation which gives to each node in the schedule network the maximal path from the initial node to the given node.

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

Not Available

Oberlin Colleges Adam Joseph Lewis Center for Environmental Studies is a high-performance building featuring an expansive photovoltaic system and a closed-loop groundwater heat pump system. Designers incorporated energy-efficient components and materials that are local, non-toxic, and durable.

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

None

Oberlin College's Adam Joseph Lewis Center for Environmental Studies is a high-performance building featuring an expansive photovoltaic system and a closed-loop groundwater heat pump system. Designers incorporated energy-efficient components and materials that are local, non-toxic, and durable.

Active control of thermoacoustic amplification in a thermo-acousto-electric engine

NASA Astrophysics Data System (ADS)

Olivier, Come; Penelet, Guillaume; Poignand, Gaelle; Lotton, Pierrick

2014-05-01

In this paper, a new approach is proposed to control the operation of a thermoacoustic Stirling electricity generator. This control basically consists in adding an additional acoustic source to the device, connected through a feedback loop to a reference microphone, a phase-shifter, and an audio amplifier. Experiments are performed to characterize the impact of the feedback loop (and especially that of the controlled phase-shift) on the overall efficiency of the thermal to electric energy conversion performed by the engine. It is demonstrated that this external forcing of thermoacoustic self-sustained oscillations strongly impacts the performance of the engine, and that it is possible under some circumstances to improve the efficiency of the thermo-electric transduction, compared to the one reached without active control. Applicability and further directions of investigation are also discussed.

Recycling and source reduction for long duration space habitation

NASA Technical Reports Server (NTRS)

Hightower, T. M.

1992-01-01

A direct mathematical approach has been established for characterizing the performance of closed-loop life support systems. The understanding that this approach gives clearly illustrates the options available for increasing the performance of a life support system by changing various parameters. New terms are defined and utilized, such as Segregation Factor, Resource Recovery Efficiency, Overall Reclamation Efficiency, Resupply Reduction Factor, and Life Support Extension Factor. The effects of increases in expendable system supplies required due to increases in life support system complexity are shown. Minimizing resupply through increased recycling and source reduction is illustrated. The effects of recycling upon resupply launch cost is also shown. Finally, material balance analyses have been performed based on quantity and composition data for both supplies and wastes, to illustrate the use of this approach by comparing ten different closed-loop life support system cases.

Fate of pharmaceuticals and pesticides in fly larvae composting.

PubMed

Lalander, C; Senecal, J; Gros Calvo, M; Ahrens, L; Josefsson, S; Wiberg, K; Vinnerås, B

2016-09-15

A novel and efficient organic waste management strategy currently gaining great attention is fly larvae composting. High resource recovery efficiency can be achieved in this closed-looped system, but pharmaceuticals and pesticides in waste could potentially accumulate in every loop of the treatment system and spread to the environment. This study evaluated the fate of three pharmaceuticals (carbamazepine, roxithromycin, trimethoprim) and two pesticides (azoxystrobin, propiconazole) in a fly larvae composting system and in a control treatment with no larvae. It was found that the half-life of all five substances was shorter in the fly larvae compost (<10% of control) and no bioaccumulation was detected in the larvae. Fly larvae composting could thus impede the spread of pharmaceuticals and pesticides into the environment. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Membrane Tension Acts Through PLD2 and mTORC2 to Limit Actin Network Assembly During Neutrophil Migration

PubMed Central

Diz-Muñoz, Alba; Thurley, Kevin; Chintamen, Sana; Altschuler, Steven J.; Fletcher, Daniel A.; Weiner, Orion D.

2016-01-01

For efficient polarity and migration, cells need to regulate the magnitude and spatial distribution of actin assembly. This process is coordinated by reciprocal interactions between the actin cytoskeleton and mechanical forces. Actin polymerization-based protrusion increases tension in the plasma membrane, which in turn acts as a long-range inhibitor of actin assembly. These interactions form a negative feedback circuit that limits the magnitude of membrane tension in neutrophils and prevents expansion of the existing front and the formation of secondary fronts. It has been suggested that the plasma membrane directly inhibits actin assembly by serving as a physical barrier that opposes protrusion. Here we show that efficient control of actin polymerization-based protrusion requires an additional mechanosensory feedback cascade that indirectly links membrane tension with actin assembly. Specifically, elevated membrane tension acts through phospholipase D2 (PLD2) and the mammalian target of rapamycin complex 2 (mTORC2) to limit actin nucleation. In the absence of this pathway, neutrophils exhibit larger leading edges, higher membrane tension, and profoundly defective chemotaxis. Mathematical modeling suggests roles for both the direct (mechanical) and indirect (biochemical via PLD2 and mTORC2) feedback loops in organizing cell polarity and motility—the indirect loop is better suited to enable competition between fronts, whereas the direct loop helps spatially organize actin nucleation for efficient leading edge formation and cell movement. This circuit is essential for polarity, motility, and the control of membrane tension. PMID:27280401

Vectorized Jiles-Atherton hysteresis model

NASA Astrophysics Data System (ADS)

Szymański, Grzegorz; Waszak, Michał

2004-01-01

This paper deals with vector hysteresis modeling. A vector model consisting of individual Jiles-Atherton components placed along principal axes is proposed. The cross-axis coupling ensures general vector model properties. Minor loops are obtained using scaling method. The model is intended for efficient finite element method computations defined in terms of magnetic vector potential. Numerical efficiency is ensured by differential susceptibility approach.

Coronal Loop Evolution Observed with AIA and Hi-C

NASA Technical Reports Server (NTRS)

Mulu-Moore, Fana; Winebarger, A.; Cirtain, J.; Kobayashi, K.; Korreck, K.; Golub, L.; Kuzin. S.; Walsh, R.; DeForest, C.; DePontieu, B.;

Deciphering the structural framework of glycine receptor anchoring by gephyrin

PubMed Central

Kim, Eun Young; Schrader, Nils; Smolinsky, Birthe; Bedet, Cécile; Vannier, Christian; Schwarz, Günter; Schindelin, Hermann

2006-01-01

Glycine is the major inhibitory neurotransmitter in the spinal cord and brain stem. Gephyrin is required to achieve a high concentration of glycine receptors (GlyRs) in the postsynaptic membrane, which is crucial for efficient glycinergic signal transduction. The interaction between gephyrin and the GlyR involves the E-domain of gephyrin and a cytoplasmic loop located between transmembrane segments three and four of the GlyR β subunit. Here, we present crystal structures of the gephyrin E-domain with and without the GlyR β-loop at 2.4 and 2.7 Å resolutions, respectively. The GlyR β-loop is bound in a symmetric ‘key and lock' fashion to each E-domain monomer in a pocket adjacent to the dimer interface. Structure-guided mutagenesis followed by in vitro binding and in vivo colocalization assays demonstrate that a hydrophobic interaction formed by Phe 330 of gephyrin and Phe 398 and Ile 400 of the GlyR β-loop is crucial for binding. PMID:16511563

Closed loop insulin delivery in diabetes.

PubMed

Battelino, Tadej; Omladič, Jasna Šuput; Phillip, Moshe

2015-06-01

The primary goal of type 1 diabetes treatment is attaining near-normal glucose values. This currently remains out of reach for most people with type 1 diabetes despite intensified insulin treatment in the form of insulin analogues, educational interventions, continuous glucose monitoring, and sensor augmented insulin pump. The main remaining problem is risk of hypoglycaemia, which cannot be sufficiently reduced in all patient groups. Additionally, patients' burn-out often develops with years of tedious day-to-day diabetes management, rendering available diabetes-related technology less efficient. Over the past 40 years, several attempts have been made towards computer-programmed insulin delivery in the form of closed loop, with faster developments especially in the past decade. Automated insulin delivery has reduced human error in glycaemic control and considerably lessened the burden of routine self-management. In this chapter, data from randomized controlled trials with closed-loop insulin delivery that included type 1 diabetes population are summarized, and an evidence-based vision for possible routine utilization of closed loop is provided. Copyright © 2015 Elsevier Ltd. All rights reserved.

Acquisition and Tracking Behavior of Phase-Locked Loops

NASA Technical Reports Server (NTRS)

Viterbi, A. J.

1958-01-01

Phase-locked or APC loops have found increasing applications in recent years as tracking filters, synchronizing devices, and narrowband FM discriminators. Considerable work has been performed to determine the noise-squelching properties of the loop when it is operating in or near phase lock and is functioning as a linear coherent detector. However, insufficient consideration has been devoted to the non-linear behavior of the loop when it is out of lock and in the process of pulling in. Experimental evidence has indicated that there is a strong tendency for phase-locked loops to achieve lock under most circumstances. However, the analysis which has appeared in the literature iis limited to the acquisition of a constant frequency reference signal with only one phase-locked loop filter configuration. This work represents an investigation of frequency acquisition properties of phase-locked loops for a variety of reference-signal behavior and loop configurations

A class of all digital phase locked loops - Modeling and analysis

NASA Technical Reports Server (NTRS)

Reddy, C. P.; Gupta, S. C.

1973-01-01

An all digital phase locked loop which tracks the phase of the incoming signal once per carrier cycle is proposed. The different elements and their functions, and the phase lock operation are explained in detail. The general digital loop operation is governed by a nonlinear difference equation from which a suitable model is developed. The lock range for the general model is derived. The performance of the digital loop for phase step and frequency step inputs for different levels of quantization without loop filter are studied. The analytical results are checked by simulating the actual system on the digital computer.

The Bacteroides sp. 3_1_23 Pif1 protein is a multifunctional helicase.

PubMed

Liu, Na-Nv; Duan, Xiao-Lei; Ai, Xia; Yang, Yan-Tao; Li, Ming; Dou, Shuo-Xing; Rety, Stephane; Deprez, Eric; Xi, Xu-Guang

2015-10-15

ScPif1 DNA helicase is the prototypical member of a 5'-to-3' helicase superfamily conserved from bacteria to human and plays various roles in the maintenance of genomic homeostasis. While many studies have been performed with eukaryotic Pif1 helicases, including yeast and human Pif1 proteins, the potential functions and biochemical properties of prokaryotic Pif1 helicases remain largely unknown. Here, we report the expression, purification and biochemical analysis of Pif1 helicase from Bacteroides sp. 3_1_23 (BsPif1). BsPif1 binds to a large panel of DNA substrates and, in particular, efficiently unwinds partial duplex DNAs with 5'-overhang, fork-like substrates, D-loop and flap-like substrates, suggesting that BsPif1 may act at stalled DNA replication forks and enhance Okazaki fragment maturation. Like its eukaryotic homologues, BsPif1 resolves R-loop structures and unwinds DNA-RNA hybrids. Furthermore, BsPif1 efficiently unfolds G-quadruplexes and disrupts nucleoprotein complexes. Altogether, these results highlight that prokaryotic Pif1 helicases may resolve common issues that arise during DNA transactions. Interestingly, we found that BsPif1 is different from yeast Pif1, but resembles more human Pif1 with regard to substrate specificity, helicase activity and mode of action. These findings are discussed in the context of the possible functions of prokaryotic Pif1 helicases in vivo. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Three-dimensional geometry of coronal loops inferred by the Principal Component Analysis

NASA Astrophysics Data System (ADS)

Nisticò, Giuseppe; Nakariakov, Valery

We propose a new method for the determination of the three dimensional (3D) shape of coronal loops from stereoscopy. The common approach requires to find a 1D geometric curve, as circumference or ellipse, that best-fits the 3D tie-points which sample the loop shape in a given coordinate system. This can be easily achieved by the Principal Component (PC) analysis. It mainly consists in calculating the eigenvalues and eigenvectors of the covariance matrix of the 3D tie-points: the eigenvalues give a measure of the variability of the distribution of the tie-points, and the corresponding eigenvectors define a new cartesian reference frame directly related to the loop. The eigenvector associated with the smallest eigenvalues defines the normal to the loop plane, while the other two determine the directions of the loop axes: the major axis is related to the largest eigenvalue, and the minor axis with the second one. The magnitude of the axes is directly proportional to the square roots of these eigenvalues. The technique is fast and easily implemented in some examples, returning best-fitting estimations of the loop parameters and 3D reconstruction with a reasonable small number of tie-points. The method is suitable for serial reconstruction of coronal loops in active regions, providing a useful tool for comparison between observations and theoretical magnetic field extrapolations from potential or force-free fields.

Tuning and performance evaluation of PID controller for superheater steam temperature control of 200 MW boiler using gain phase assignment algorithm

NASA Astrophysics Data System (ADS)

Begum, A. Yasmine; Gireesh, N.

2018-04-01

In superheater, steam temperature is controlled in a cascade control loop. The cascade control loop consists of PI and PID controllers. To improve the superheater steam temperature control the controller's gains in a cascade control loop has to be tuned efficiently. The mathematical model of the superheater is derived by sets of nonlinear partial differential equations. The tuning methods taken for study here are designed for delay plus first order transfer function model. Hence from the dynamical model of the superheater, a FOPTD model is derived using frequency response method. Then by using Chien-Hrones-Reswick Tuning Algorithm and Gain-Phase Assignment Algorithm optimum controller gains has been found out based on the least value of integral time weighted absolute error.

Multimegawatt potassium Rankine power for nuclear electric power

NASA Technical Reports Server (NTRS)

Rovang, Richard D.; Mills, Joseph C.; Baumeister, Ernie B.

1991-01-01

A cermet fueled potassium rankine power system concept has been developed for various power ranges and operating lifetimes. This concept utilizes a single primary lithium loop to transport thermal energy from the reactor to the boiler. Multiple, independent potassium loops are employed to achieve the required reliability of 99 percent. The potassium loops are two phase systems which expand heated potassium vapor through multistage turboalternators to produce a 10-kV dc electrical output. Condensation occurs by-way-of a shear-flow condenser, producing a 100 percent liquid potassium stream which is pumped back to the boiler. Waste heat is rejected by an advanced carbon-carbon radiator at approximately 1000 K. Overall system efficiencies of 19.3 percent to 20.5 percent were calculated depending on mission life and power level.

Introducing uncertainty analysis of nucleation and crystal growth models in Process Analytical Technology (PAT) system design of crystallization processes.

PubMed

Samad, Noor Asma Fazli Abdul; Sin, Gürkan; Gernaey, Krist V; Gani, Rafiqul

2013-11-01

This paper presents the application of uncertainty and sensitivity analysis as part of a systematic model-based process monitoring and control (PAT) system design framework for crystallization processes. For the uncertainty analysis, the Monte Carlo procedure is used to propagate input uncertainty, while for sensitivity analysis, global methods including the standardized regression coefficients (SRC) and Morris screening are used to identify the most significant parameters. The potassium dihydrogen phosphate (KDP) crystallization process is used as a case study, both in open-loop and closed-loop operation. In the uncertainty analysis, the impact on the predicted output of uncertain parameters related to the nucleation and the crystal growth model has been investigated for both a one- and two-dimensional crystal size distribution (CSD). The open-loop results show that the input uncertainties lead to significant uncertainties on the CSD, with appearance of a secondary peak due to secondary nucleation for both cases. The sensitivity analysis indicated that the most important parameters affecting the CSDs are nucleation order and growth order constants. In the proposed PAT system design (closed-loop), the target CSD variability was successfully reduced compared to the open-loop case, also when considering uncertainty in nucleation and crystal growth model parameters. The latter forms a strong indication of the robustness of the proposed PAT system design in achieving the target CSD and encourages its transfer to full-scale implementation. Copyright © 2013 Elsevier B.V. All rights reserved.

Environmental impacts of open loop geothermal system on groundwater

NASA Astrophysics Data System (ADS)

Kwon, Koo-Sang; Park, Youngyun; Yun, Sang Woong; Lee, Jin-Yong

2013-04-01

Application of renewable energies such as sunlight, wind, rain, tides, waves and geothermal heat has gradually increased to reduce emission of CO2 which is supplied from combustion of fossil fuel. The geothermal energy of various renewable energies has benefit to be used to cooling and heating systems and has good energy efficiency compared with other renewable energies. However, open loop system of geothermal heat pump system has possibility that various environmental problems are induced because the system directly uses groundwater to exchange heat. This study was performed to collect data from many documents such as papers and reports and to summarize environmental impacts for application of open loop system. The environmental impacts are classified into change of hydrogeological factors such as water temperature, redox condition, EC, change of microbial species, well contamination and depletion of groundwater. The change of hydrogeological factors can induce new geological processes such as dissolution and precipitation of some minerals. For examples, increase of water temperature can change pH and Eh. These variations can change saturation index of some minerals. Therefore, dissolution and precipitation of some minerals such as quartz and carbonate species and compounds including Fe and Mn can induce a collapse and a clogging of well. The well contamination and depletion of groundwater can reduce available groundwater resources. These environmental impacts will be different in each region because hydrogeological properties and scale, operation period and kind of the system. Therefore, appropriate responses will be considered for each environmental impact. Also, sufficient study will be conducted to reduce the environmental impacts and to improve geothermal energy efficiency during the period that a open loop system is operated. This work was supported by the Energy Efficiency and Resources of the Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Korea government Ministry of Knowledge Economy (No.20123040110010).

Control-structure interaction in precision pointing servo loops

NASA Technical Reports Server (NTRS)

Spanos, John T.

1989-01-01

The control-structure interaction problem is addressed via stability analysis of a generic linear servo loop model. With the plant described by the rigid body mode and a single elastic mode, structural flexibility is categorized into one of three types: (1) appendage, (2) in-the-loop minimum phase, and (3) in-the-loop nonminimum phase. Closing the loop with proportional-derivative (PD) control action and introducing sensor roll-off dynamics in the feedback path, stability conditions are obtained. Trade studies are conducted with modal frequency, modal participation, modal damping, loop bandwidth, and sensor bandwidth treated as free parameters. Results indicate that appendage modes are most likely to produce instability if they are near the sensor rolloff, whereas in-the-loop modes are most dangerous near the loop bandwidth. The main goal of this paper is to provide a fundamental understanding of the control-structure interaction problem so that it may benefit the design of complex spacecraft and pointing system servo loops. In this framework, the JPL Pathfinder gimbal pointer is considered as an example.

Contributions to the initial development of a microelectromechanical loop heat pipe, which is based on coherent porous silicon

NASA Astrophysics Data System (ADS)

Cytrynowicz, Debra G.

The research project itself was the initiation of the development of a planar miniature loop heat pipe based on a capillary wick structure made of coherent porous silicon. Work on this project fell into four main categories, which were component fabrication, test system construction, characterization testing and test data collection, performance analysis and thermal modeling. Component fabrication involved the production of various components for the evaporator. When applicable, these components were to be produced by microelectronic and MEMS or microelectromechanical fabrication techniques. Required work involved analyses and, where necessary, modifications to the wafer processing sequence, the photo-electrochemical etching process, system and controlling computer program to make it more reliable, flexible and efficient. The development of more than one wick production process was also extremely necessary in the event of equipment failure. Work on developing this alternative also involved investigations into various details of the photo-electrochemical etching process itself. Test system construction involved the actual assembly of open and closed loop test systems. Characterization involved developing and administering a series of tests to evaluate the performance of the wicks and test systems. Although there were some indications that the devices were operating according to loop heat pipe theory, they were transient and unstable. Performance analysis involved the construction of a transparent evaporator, which enabled the visual observation of the phenomena, which occurred in the evaporator during operation. It also involved investigating the effect of the quartz wool secondary wick on the operation of the device. Observations made during the visualization study indicated that the capillary and boiling limits were being reached at extremely low values of input power. The work was performed in a collaborative effort between the Biomedical Nanotechnology Research Laboratory at the University of Toledo, the Center for Microelectronics and Sensors and MEMS at the University of Cincinnati and the Thermo-Mechanical Systems Branch of the Power and On-Board Propulsion Division at the John H. Glenn Research Center of the National Aeronautics and Space Administration in Cleveland, Ohio. Work on the project produced six publications, which presented various details on component fabrication, tests system construction and characterization and thermal modeling.

Thermal Management of a Nitrogen Cryogenic Loop Heat Pipe

NASA Astrophysics Data System (ADS)

Gully, Ph.; Yan, T.

2010-04-01

Efficient thermal links are needed to ease the distribution of the cold power in satellites. Loop heat pipes are widely used at room temperature as passive thermal links based on a two-phase flow generated by capillary forces. Transportation of the cold power at cryogenic temperatures requires a specific design. In addition to the main loop, the cryogenic loop heat pipe (CLHP) features a hot reservoir and a secondary loop with a cold reservoir and a secondary evaporator which allows the cool down and the thermal management of the thermal link in normal cold operation. We have studied the influence of a heated cold reservoir and investigated the effect of parasitic heat loads on the performance of a nitrogen CLHP at around 80 K. It is shown that heating of the cold reservoir with a small amount of power (0.1 W) allows controlling the system temperature difference, which can be kept constant at a very low level (1 K) regardless of the transferred cold power (0-10 W). Parasitic heat loads have a significant effect on the thermal resistance, and the power applied on the secondary evaporator has to be increased up to 4 W to get stable operation.

One-loop matching and running with covariant derivative expansion

DOE PAGES

Henning, Brian; Lu, Xiaochuan; Murayama, Hitoshi

2018-01-24

We develop tools for performing effective field theory (EFT) calculations in a manifestly gauge-covariant fashion. We clarify how functional methods account for one-loop diagrams resulting from the exchange of both heavy and light fields, as some confusion has recently arisen in the literature. To efficiently evaluate functional traces containing these “mixed” one-loop terms, we develop a new covariant derivative expansion (CDE) technique that is capable of evaluating a much wider class of traces than previous methods. The technique is detailed in an appendix, so that it can be read independently from the rest of this work. We review the well-knownmore » matching procedure to one-loop order with functional methods. What we add to this story is showing how to isolate one-loop terms coming from diagrams involving only heavy propagators from diagrams with mixed heavy and light propagators. This is done using a non-local effective action, which physically connects to the notion of “integrating out” heavy fields. Lastly, we show how to use a CDE to do running analyses in EFTs, i.e. to obtain the anomalous dimension matrix. We demonstrate the methodologies by several explicit example calculations.« less

One-loop matching and running with covariant derivative expansion

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

Henning, Brian; Lu, Xiaochuan; Murayama, Hitoshi

We develop tools for performing effective field theory (EFT) calculations in a manifestly gauge-covariant fashion. We clarify how functional methods account for one-loop diagrams resulting from the exchange of both heavy and light fields, as some confusion has recently arisen in the literature. To efficiently evaluate functional traces containing these “mixed” one-loop terms, we develop a new covariant derivative expansion (CDE) technique that is capable of evaluating a much wider class of traces than previous methods. The technique is detailed in an appendix, so that it can be read independently from the rest of this work. We review the well-knownmore » matching procedure to one-loop order with functional methods. What we add to this story is showing how to isolate one-loop terms coming from diagrams involving only heavy propagators from diagrams with mixed heavy and light propagators. This is done using a non-local effective action, which physically connects to the notion of “integrating out” heavy fields. Lastly, we show how to use a CDE to do running analyses in EFTs, i.e. to obtain the anomalous dimension matrix. We demonstrate the methodologies by several explicit example calculations.« less

One-loop matching and running with covariant derivative expansion

NASA Astrophysics Data System (ADS)

Henning, Brian; Lu, Xiaochuan; Murayama, Hitoshi

2018-01-01

We develop tools for performing effective field theory (EFT) calculations in a manifestly gauge-covariant fashion. We clarify how functional methods account for one-loop diagrams resulting from the exchange of both heavy and light fields, as some confusion has recently arisen in the literature. To efficiently evaluate functional traces containing these "mixed" one-loop terms, we develop a new covariant derivative expansion (CDE) technique that is capable of evaluating a much wider class of traces than previous methods. The technique is detailed in an appendix, so that it can be read independently from the rest of this work. We review the well-known matching procedure to one-loop order with functional methods. What we add to this story is showing how to isolate one-loop terms coming from diagrams involving only heavy propagators from diagrams with mixed heavy and light propagators. This is done using a non-local effective action, which physically connects to the notion of "integrating out" heavy fields. Lastly, we show how to use a CDE to do running analyses in EFTs, i.e. to obtain the anomalous dimension matrix. We demonstrate the methodologies by several explicit example calculations.

RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination.

PubMed

Ribeiro de Almeida, Claudia; Dhir, Somdutta; Dhir, Ashish; Moghaddam, Amin E; Sattentau, Quentin; Meinhart, Anton; Proudfoot, Nicholas J

2018-05-17

Class switch recombination (CSR) at the immunoglobulin heavy-chain (IgH) locus is associated with the formation of R-loop structures over switch (S) regions. While these often occur co-transcriptionally between nascent RNA and template DNA, we now show that they also form as part of a post-transcriptional mechanism targeting AID to IgH S-regions. This depends on the RNA helicase DDX1 that is also required for CSR in vivo. DDX1 binds to G-quadruplex (G4) structures present in intronic switch transcripts and converts them into S-region R-loops. This in turn targets the cytidine deaminase enzyme AID to S-regions so promoting CSR. Notably R-loop levels over S-regions are diminished by chemical stabilization of G4 RNA or by the expression of a DDX1 ATPase-deficient mutant that acts as a dominant-negative protein to reduce CSR efficiency. In effect, we provide evidence for how S-region transcripts interconvert between G4 and R-loop structures to promote CSR in the IgH locus. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

PubMed

Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

2010-01-01

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

Analysis of a novel sensor interrogation technique based on fiber cavity ring-down (CRD) loop and OTDR

NASA Astrophysics Data System (ADS)

Yüksel, Kivilcim; Yilmaz, Anil

2018-07-01

We present the analysis of a remote sensor based on fiber Cavity Ring-Down (CRD) loop interrogated by an Optical Time Domain Reflectometer (OTDR) taking into account both practical limitations and the related signal processing. A commercial OTDR is used for both pulse generation and sensor output detection. This allows obtaining a compact and simple design for intensity-based sensor applications. This novel sensor interrogation approach is experimentally demonstrated by placing a variable attenuator inside the fiber loop that mimics a sensor head.

Polymeric heat pipe wick

NASA Technical Reports Server (NTRS)

Seidenberg, Benjamin

1988-01-01

A wick for use in a capillary loop pump heat pipe is described. The wick material is an essentially uniformly porous, permeable, open-cell, polyethylene thermoplastic foam having an ultrahigh average molecular weight of from approximately 1 to 5 million, and an average pore size of about 10 to 12 microns. A representative material having these characteristics is POREX UF, which has an average molecular weight of about 3 million. This material is fully compatible with the FREONs and anhydrous ammonia and allows for the use of these very efficient working fluids in capillary loops.

Automatic design of conformal cooling channels in injection molding tooling

NASA Astrophysics Data System (ADS)

Zhang, Yingming; Hou, Binkui; Wang, Qian; Li, Yang; Huang, Zhigao

2018-02-01

The generation of cooling system plays an important role in injection molding design. A conformal cooling system can effectively improve molding efficiency and product quality. This paper provides a generic approach for building conformal cooling channels. The centrelines of these channels are generated in two steps. First, we extract conformal loops based on geometric information of product. Second, centrelines in spiral shape are built by blending these loops. We devise algorithms to implement the entire design process. A case study verifies the feasibility of this approach.

Gas engine heat pump cycle analysis. Volume 1: Model description and generic analysis

NASA Astrophysics Data System (ADS)

Fischer, R. D.

1986-10-01

The task has prepared performance and cost information to assist in evaluating the selection of high voltage alternating current components, values for component design variables, and system configurations and operating strategy. A steady-state computer model for performance simulation of engine-driven and electrically driven heat pumps was prepared and effectively used for parametric and seasonal performance analyses. Parametric analysis showed the effect of variables associated with design of recuperators, brine coils, domestic hot water heat exchanger, compressor size, engine efficiency, insulation on exhaust and brine piping. Seasonal performance data were prepared for residential and commercial units in six cities with system configurations closely related to existing or contemplated hardware of the five GRI engine contractors. Similar data were prepared for an advanced variable-speed electric unit for comparison purposes. The effect of domestic hot water production on operating costs was determined. Four fan-operating strategies and two brine loop configurations were explored.

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.

PubMed

Olson, Mark A; Feig, Michael; Brooks, Charles L

2008-04-15

This article examines ab initio methods for the prediction of protein loops by a computational strategy of multiscale conformational sampling and physical energy scoring functions. Our approach consists of initial sampling of loop conformations from lattice-based low-resolution models followed by refinement using all-atom simulations. To allow enhanced conformational sampling, the replica exchange method was implemented. Physical energy functions based on CHARMM19 and CHARMM22 parameterizations with generalized Born (GB) solvent models were applied in scoring loop conformations extracted from the lattice simulations and, in the case of all-atom simulations, the ensemble of conformations were generated and scored with these models. Predictions are reported for 25 loop segments, each eight residues long and taken from a diverse set of 22 protein structures. We find that the simulations generally sampled conformations with low global root-mean-square-deviation (RMSD) for loop backbone coordinates from the known structures, whereas clustering conformations in RMSD space and scoring detected less favorable loop structures. Specifically, the lattice simulations sampled basins that exhibited an average global RMSD of 2.21 +/- 1.42 A, whereas clustering and scoring the loop conformations determined an RMSD of 3.72 +/- 1.91 A. Using CHARMM19/GB to refine the lattice conformations improved the sampling RMSD to 1.57 +/- 0.98 A and detection to 2.58 +/- 1.48 A. We found that further improvement could be gained from extending the upper temperature in the all-atom refinement from 400 to 800 K, where the results typically yield a reduction of approximately 1 A or greater in the RMSD of the detected loop. Overall, CHARMM19 with a simple pairwise GB solvent model is more efficient at sampling low-RMSD loop basins than CHARMM22 with a higher-resolution modified analytical GB model; however, the latter simulation method provides a more accurate description of the all-atom energy surface, yet demands a much greater computational cost. (c) 2007 Wiley Periodicals, Inc.

NASA Marshall Space Flight Center Improves Cooling System Performance: Best Management Practice Case Study #10: Cooling Towers (Fact Sheet)

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

Not Available

National Aeronautics and Space Administration's (NASA) Marshall Space Flight Center (MSFC) has a longstanding sustainability program that revolves around energy and water efficiency as well as environmental protection. MSFC identified a problematic cooling loop with six separate compressor heat exchangers and a history of poor efficiency. The facility engineering team at MSFC partnered with Flozone Services, Incorporated to implement a comprehensive water treatment platform to improve the overall efficiency of the system.

Study of the post-flare loops on 29 July 1973. II - Physical parameters in the X-ray loops

NASA Technical Reports Server (NTRS)

Petrasso, R. D.; Nolte, J. T.; Gerassimenko, M.; Krieger, A. S.; Krogstad, R.; Seguin, F. H.; Svestka, Z.

1979-01-01

We use the filter ratio method of analysis to determine spatially resolved values of plasma parameters in the X-ray emitting post-flare loop system which developed on 29 and 30 July 1973. We find that the loops were hotter and had higher plasma pressure at their tops than near their footpoints. The loop tops were at nearly the same temperature at different places 3 hr after the flare maximum and were also at nearly this same temperature 3 and 8 hr later. Variations in brightness transverse to the loops were due to variations in emission measure. We show by consideration of radiative losses alone that energy must have been added to the hottest part of the flare, at the tops of the loops, late in the decay phase of the flare.

Coronal Loop Temperatures Obtained with Hinode XRT: A Toothpaste-Tube Analogy

NASA Astrophysics Data System (ADS)

Schmelz, J. T.; Saar, S. H.; Weber, M. A.; Deluca, E. E.; Golub, L.

2009-12-01

Multi-filter data observed by the Hinode X-Ray Telescope on 10 and 2007 July 13 were used to investigate the thermal properties of coronal loops. At several positions along the loops, differential emission measure analysis revealed a strong peak at log T = 6.1 (which would predict the presence of a TRACE loop) and a much weaker hot component (which we speculated might be a nanoflare signature). TRACE observations, however, did not reveal the predicted loop, so we were forced to re-examine our assumptions. Good differential emission measure results require high- and low-temperature constraints, but our data sets did not contain images from the thinnest and thickest filters, which would be most likely to provide these constraints. Since differential emission measure programs aim to match observed intensities and get low values of χ2, they may place emission measure in high- and low-temperature bins where it does not belong. We draw an analogy to squeezing the toothpaste tube in the middle. Our analysis was repeated for a loop observed on 2007 May 13 when the instrument acquired data in 11 filters and filter combinations, including both the thinnest and thickest filters. These results show that the loop is multi-thermal, with significant emission measure in the range 6.0 < log T < 6.5.

Nailfold capillary patterns in healthy subjects: a real issue in capillaroscopy.

PubMed

Ingegnoli, Francesca; Gualtierotti, Roberta; Lubatti, Chiara; Bertolazzi, Chiara; Gutierrez, Marwin; Boracchi, Patrizia; Fornili, Marco; De Angelis, Rossella

2013-11-01

Nailfold capillaroscopy has been extensively applied in a broad spectrum of pathologic conditions, but very few data have been published in healthy individuals. The aim of this study was to describe the nailfold capillary findings on a large series of healthy subjects using the video-capillaroscopy technique. Nailfold capillaries were studied based on their morphology, dimensions and density. Then, to evaluate jointly the association between different capillary findings in groups of subjects which were homogeneous for their characteristics, cluster analysis was performed. The results (median) of capillary measurements were as follows: loop length 207μm, external diameter 39μm, internal diameter 17μm, apical diameter 17μm, and intercapillary distance 143μm. Based on the cluster analysis three major "normal" morphologic capillaroscopic patterns were depicted: 1) the "normal" pattern mainly with 2 to 5 U-shaped loops/mm and ≤2 tortuous loops/mm; 2) the "perfect normal" pattern with ≥5 U-shaped loops/mm and 3) the "unusual normal" with at least 1 meandering or bushy loop, or at least 1 microhemorrhage, or with >4 crossed loops/mm. Regarding the loop measurements, the majority of subjects had a median of 7capillaries/mm with a median length of 198μm. © 2013 Elsevier Inc. All rights reserved.

Phase-locked loops. [analog, hybrid, discrete and digital systems

NASA Technical Reports Server (NTRS)

Gupta, S. C.

1974-01-01

The basic analysis and design procedures are described for the realization of analog phase-locked loops (APLL), hybrid phase-locked loops (HPLL), discrete phase-locked loops, and digital phase-locked loops (DPLL). Basic configurations are diagrammed, and performance curves are given. A discrete communications model is derived and developed. The use of the APLL as an optimum angle demodulator and the Kalman-Bucy approach to APLL design are discussed. The literature in the area of phase-locked loops is reviewed, and an extensive bibliography is given. Although the design of APLLs is fairly well documented, work on discrete, hybrid, and digital PLLs is scattered, and more will have to be done in the future to pinpoint the formal design of DPLLs.

Design and implementation of a hybrid digital phase-locked loop with a TMS320C25: An application to a transponder receiver breadboard

NASA Technical Reports Server (NTRS)

Yeh, H.-G.; Nguyen, T. M.

1994-01-01

Design, modeling, analysis, and simulation of a phase-locked loop (PLL) with a digital loop filter are presented in this article. A TMS320C25 digital signal processor (DSP) is used to implement this digital loop filter. In order to keep the compatibility, the main design goal was to replace the analog PLL (APLL) of the Deep-Space Transponder (DST) receiver breadboard's loop filter with a digital loop filter without changing anything else. This replacement results in a hybrid digital PLL (HDPLL). Both the original APLL and the designed HDPLL are Type I second-order systems. The real-time performance of the HDPLL and the receiver is provided and evaluated.

Genetic distance of Malaysian mousedeer based on mitochondrial DNA cytochrome oxidase I (COI) and D-loop region sequences

NASA Astrophysics Data System (ADS)

Bakar, Mohamad-Azam Akmal Abu; Rovie-Ryan, Jeffrine Japning; Ampeng, Ahmad; Yaakop, Salmah; Nor, Shukor Md; Md-Zain, Badrul Munir

2018-04-01

Mousedeer is one of the primitive mammals that can be found mainly in Southeast-Asia region. There are two species of mousedeer in Malaysia which are Tragulus kanchil and Tragulus napu. Both species can be distinguish by size, coat coloration, and throat pattern but clear diagnosis still cannot be found. The objective of the study is to show the genetic distance relationship between T. kanchil and T. napu and their population based on mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and D-loop region. There are 42 sample of mousedeer were used in this study collected by PERHILITAN from different locality. Another 29 D-loop sequence were retrieved from Genbank for comparative analysis. All sample were amplified using universal primer and species-specific primer for COI and D-loop genes via PCR process. The amplified sequences were analyzed to determine genetic distance of T. kanchil and T. napu. From the analysis, the average genetic distance between T. kanchil and T. napu based on locus COI and D-loop were 0.145 and 0.128 respectively. The genetic distance between populations of T. kanchil based on locus COI was between 0.003-0.013. For locus D-loop, genetic distance analysis showed distance in relationship between west-coast populations to east-coast population of T. kanchil. COI and D-loop mtDNA region provided a clear picture on the relationship within the mousedeer species. Last but not least, conservation effort toward protecting this species can be done by study the molecular genetics and prevent the extinction of this species.

Reduction of Phase Ambiguity in an Offset-QPSK Receiver

NASA Technical Reports Server (NTRS)

Berner, Jeff; Kinman, Peter

2004-01-01

Proposed modifications of an offset-quadri-phase-shift keying (offset-QPSK) transmitter and receiver would reduce the amount of signal processing that must be done in the receiver to resolve the QPSK fourfold phase ambiguity. Resolution of the phase ambiguity is necessary in order to synchronize, with the received carrier signal, the signal generated by a local oscillator in a carrier-tracking loop in the receiver. Without resolution of the fourfold phase ambiguity, the loop could lock to any of four possible phase points, only one of which has the proper phase relationship with the carrier. The proposal applies, more specifically, to an offset-QPSK receiver that contains a carrier-tracking loop like that shown in Figure 1. This carrier-tracking loop does not resolve or reduce the phase ambiguity. A carrier-tracking loop of a different design optimized for the reception of offset QPSK could reduce the phase ambiguity from fourfold to twofold, but would be more complex. Alternatively, one could resolve the fourfold phase ambiguity by use of differential coding in the transmitter, at a cost of reduced power efficiency. The proposed modifications would make it possible to reduce the fourfold phase ambiguity to twofold, with no loss in power efficiency and only relatively simple additional signal-processing steps in the transmitter and receiver. The twofold phase ambiguity would then be resolved by use of a unique synchronization word, as is commonly done in binary phase-shift keying (BPSK). Although the mathematical and signal-processing principles underlying the modifications are too complex to explain in detail here, the modifications themselves would be relatively simple and are best described with the help of simple block diagrams (see Figure 2). In the transmitter, one would add a unit that would periodically invert bits going into the QPSK modulator; in the receiver, one would add a unit that would effect different but corresponding inversions of bits coming out of the QPSK demodulator. The net effect of all the inversions would be that depending on which lock point the carrier-tracking loop had selected, all the output bits would be either inverted or non-inverted together; hence, the ambiguity would be reduced from fourfold to twofold, as desired.

Virtual solar field - An opportunity to optimize transient processes in line-focus CSP power plants

NASA Astrophysics Data System (ADS)

Noureldin, Kareem; Hirsch, Tobias; Pitz-Paal, Robert

2017-06-01

Optimizing solar field operation and control is a key factor to improve the competitiveness of line-focus solar thermal power plants. However, the risks of assessing new and innovative control strategies on operational power plants hinder such optimizations and result in applying more conservative control schemes. In this paper, we describe some applications for a whole solar field transient in-house simulation tool developed at the German Aerospace Centre (DLR), the Virtual Solar Field (VSF). The tool offers a virtual platform to simulate real solar fields while coupling the thermal and hydraulic conditions of the field with high computational efficiency. Using the tool, developers and operator can probe their control strategies and assess the potential benefits while avoiding the high risks and costs. In this paper, we study the benefits gained from controlling the loop valves and of using direct normal irradiance maps and forecasts for the field control. Loop valve control is interesting for many solar field operators since it provides a high degree of flexibility to the control of the solar field through regulating the flow rate in each loop. This improves the reaction to transient condition, such as passing clouds and field start-up in the morning. Nevertheless, due to the large number of loops and the sensitivity of the field control to the valve settings, this process needs to be automated and the effect of changing the setting of each valve on the whole field control needs to be taken into account. We used VSF to implement simple control algorithms to control the loop valves and to study the benefits that could be gained from using active loop valve control during transient conditions. Secondly, we study how using short-term highly spatially-resolved DNI forecasts provided by cloud cameras could improve the plant energy yield. Both cases show an improvement in the plant efficiency and outlet temperature stability. This paves the road for further investigations of new control strategies or for optimizations of the currently implemented ones.

MaTrace: tracing the fate of materials over time and across products in open-loop recycling.

PubMed

Nakamura, Shinichiro; Kondo, Yasushi; Kagawa, Shigemi; Matsubae, Kazuyo; Nakajima, Kenichi; Nagasaka, Tetsuya

2014-07-01

Even for metals, open-loop recycling is more common than closed-loop recycling due, among other factors, to the degradation of quality in the end-of-life (EoL) phase. Open-loop recycling is subject to loss of functionality of original materials, dissipation in forms that are difficult to recover, and recovered metals might need dilution with primary metals to meet quality requirements. Sustainable management of metal resources calls for the minimization of these losses. Imperative to this is quantitative tracking of the fate of materials across different stages, products, and losses. A new input-output analysis (IO) based model of dynamic material flow analysis (MFA) is presented that can trace the fate of materials over time and across products in open-loop recycling taking explicit consideration of losses and the quality of scrap into account. Application to car steel recovered from EoL vehicles (ELV) showed that after 50 years around 80% of the steel is used in products, mostly buildings and civil engineering (infrastructure), with the rest mostly resided in unrecovered obsolete infrastructure and refinery losses. Sensitivity analysis was conducted to evaluate the effects of changes in product lifespan, and the quality of scrap.

Subsurface Thermal Energy Storage for Improved Heating and Air Conditioning Efficiency

DTIC Science & Technology

2016-11-21

This project involved a field demonstration of subsurface thermal energy storage for improving the geothermal heat pump air conditioning efficiency... geothermal heat pump systems, undesirable heating of the ground may occur. This demonstration was performed at the MCAS, Beaufort, SC, where several...buildings with geothermal heat pump systems were exhibiting excessively high ground loop temperatures. These buildings were retrofitted with dry fluid

The Inverse Optimal Control Problem for a Three-Loop Missile Autopilot

NASA Astrophysics Data System (ADS)

Hwang, Donghyeok; Tahk, Min-Jea

2018-04-01

The performance characteristics of the autopilot must have a fast response to intercept a maneuvering target and reasonable robustness for system stability under the effect of un-modeled dynamics and noise. By the conventional approach, the three-loop autopilot design is handled by time constant, damping factor and open-loop crossover frequency to achieve the desired performance requirements. Note that the general optimal theory can be also used to obtain the same gain as obtained from the conventional approach. The key idea of using optimal control technique for feedback gain design revolves around appropriate selection and interpretation of the performance index for which the control is optimal. This paper derives an explicit expression, which relates the weight parameters appearing in the quadratic performance index to the design parameters such as open-loop crossover frequency, phase margin, damping factor, or time constant, etc. Since all set of selection of design parameters do not guarantee existence of optimal control law, explicit inequalities, which are named the optimality criteria for the three-loop autopilot (OC3L), are derived to find out all set of design parameters for which the control law is optimal. Finally, based on OC3L, an efficient gain selection procedure is developed, where time constant is set to design objective and open-loop crossover frequency and phase margin as design constraints. The effectiveness of the proposed technique is illustrated through numerical simulations.

Identification and characterization of the sodium-binding site of activated protein C.

PubMed

He, X; Rezaie, A R

1999-02-19

Activated protein C (APC) requires both Ca2+ and Na+ for its optimal catalytic function. In contrast to the Ca2+-binding sites, the Na+-binding site(s) of APC has not been identified. Based on a recent study with thrombin, the 221-225 loop is predicted to be a potential Na+-binding site in APC. The sequence of this loop is not conserved in trypsin. We engineered a Gla domainless form of protein C (GDPC) in which the 221-225 loop was replaced with the corresponding loop of trypsin. We found that activated GDPC (aGDPC) required Na+ (or other alkali cations) for its amidolytic activity with dissociation constant (Kd(app)) = 44.1 +/- 8.6 mM. In the presence of Ca2+, however, the requirement for Na+ by aGDPC was eliminated, and Na+ stimulated the cleavage rate 5-6-fold with Kd(app) = 2.3 +/- 0.3 mM. Both cations were required for efficient factor Va inactivation by aGDPC. In the presence of Ca2+, the catalytic function of the mutant was independent of Na+. Unlike aGDPC, the mutant did not discriminate among monovalent cations. We conclude that the 221-225 loop is a Na+-binding site in APC and that an allosteric link between the Na+ and Ca2+ binding loops modulates the structure and function of this anticoagulant enzyme.

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

Pallan, Pradeep S.; Marshall, William S.; Harp, Joel

To understand the role of structural elements of RNA pseudoknots in controlling the extent of -1-type ribosomal frameshifting, we determined the crystal structure of a high-efficiency frameshifting mutant of the pseudoknot from potato leaf roll virus (PLRV). Correlations of the structure with available in vitro frameshifting data for PLRV pseudoknot mutants implicate sequence and length of a stem-loop linker as modulators of frameshifting efficiency. Although the sequences and overall structures of the RNA pseudoknots from PLRV and beet western yellow virus (BWYV) are similar, nucleotide deletions in the linker and adjacent minor groove loop abolish frameshifting only with the latter.more » Conversely, mutant PLRV pseudoknots with up to four nucleotides deleted in this region exhibit nearly wild-type frameshifting efficiencies. The crystal structure helps rationalize the different tolerances for deletions in the PLRV and BWYV RNAs, and we have used it to build a three-dimensional model of the PRLV pseudoknot with a four-nucleotide deletion. The resulting structure defines a minimal RNA pseudoknot motif composed of 22 nucleotides capable of stimulating -1-type ribosomal frameshifts.« less

Scaling considerations for a multi-megawatt class supercritical CO2 brayton cycle and commercialization.

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

Fleming, Darryn D.; Holschuh, Thomas Vernon,; Conboy, Thomas M.

2013-11-01

Small-scale supercritical CO2 demonstration loops are successful at identifying the important technical issues that one must face in order to scale up to larger power levels. The Sandia National Laboratories supercritical CO2 Brayton cycle test loops are identifying technical needs to scale the technology to commercial power levels such as 10 MWe. The small size of the Sandia 1 MWth loop has demonstration of the split flow loop efficiency and effectiveness of the Printed Circuit Heat Exchangers (PCHXs) leading to the design of a fully recuperated, split flow, supercritical CO2 Brayton cycle demonstration system. However, there were many problems thatmore » were encountered, such as high rotational speeds in the units. Additionally, the turbomachinery in the test loops need to identify issues concerning the bearings, seals, thermal boundaries, and motor controller problems in order to be proved a reliable power source in the 300 kWe range. Although these issues were anticipated in smaller demonstration units, commercially scaled hardware would eliminate these problems caused by high rotational speeds at small scale. The economic viability and development of the future scalable 10 MWe solely depends on the interest of DOE and private industry. The Intellectual Property collected by Sandia proves that the ~10 MWe supercritical CO2 power conversion loop to be very beneficial when coupled to a 20 MWth heat source (either solar, geothermal, fossil, or nuclear). This paper will identify a commercialization plan, as well as, a roadmap from the simple 1 MWth supercritical CO2 development loop to a power producing 10 MWe supercritical CO2 Brayton loop.« less

Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.

PubMed

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.

Dynameomics: Data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction

PubMed Central

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

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.

PubMed

Arnautova, Yelena A; Abagyan, Ruben A; Totrov, Maxim

2011-02-01

We report the development of internal coordinate mechanics force field (ICMFF), new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε = 2) instead of vacuum, (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions, and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the C(α) atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. ICMFF was combined with a solvent-accessible surface area solvation model optimized using a large set of loop decoys. Conformational sampling was carried out using the biased probability Monte Carlo method. Average/median backbone root-mean-square deviations of the lowest energy conformations from the native structures were 0.25/0.21 Å for four residues loops, 0.84/0.46 Å for eight residue loops, and 1.16/0.73 Å for 12 residue loops. To our knowledge, these results are significantly better than or comparable with those reported to date for any loop modeling method that does not take crystal packing into account. Moreover, the accuracy of our method is on par with the best previously reported results obtained considering the crystal environment. We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method. © 2010 Wiley-Liss, Inc.

Implementation of the Vocera Communication System in a Quaternary Perioperative Environment.

PubMed

Friend, Tynan H; Jennings, Samantha J; Copenhaver, Martin S; Levine, Wilton C

2017-01-01

In the hospital, fast and efficient communication among clinicians and other employees is paramount to ensure optimal patient care, workflow efficiency, patient safety and patient comfort. The implementation of the wireless Vocera® Badge, a hands-free wearable device distributed to perioperative team members, has increased communication efficiency across the perioperative environment at Massachusetts General Hospital (MGH). This quality improvement project, based upon identical pre- and post-implementation surveys, used qualitative and quantitative analysis to determine if and how the Vocera system affected the timeliness of information flow, ease of communication, and operating room noise levels throughout the perioperative environment. Overall, the system increased the speed of information flow and eased communication between coworkers yet was perceived to have raised the overall noise level in and around the operating rooms (ORs). The perceived increase in noise was outweighed by the closed-loop communication between clinicians. Further education of the system's features in regard to speech recognition and privacy along with expected conversation protocol are necessary to ensure hassle-free communication for all staff.

Degradation in finite-harmonic subcarrier demodulation

NASA Technical Reports Server (NTRS)

Feria, Y.; Townes, S.; Pham, T.

1995-01-01

Previous estimates on the degradations due to a subcarrier loop assume a square-wave subcarrier. This article provides a closed-form expression for the degradations due to the subcarrier loop when a finite number of harmonics are used to demodulate the subcarrier, as in the case of the buffered telemetry demodulator. We compared the degradations using a square wave and using finite harmonics in the subcarrier demodulation and found that, for a low loop signal-to-noise ratio, using finite harmonics leads to a lower degradation. The analysis is under the assumption that the phase noise in the subcarrier (SC) loop has a Tikhonov distribution. This assumption is valid for first-order loops.

A class of all digital phase locked loops - Modelling and analysis.

NASA Technical Reports Server (NTRS)

Reddy, C. P.; Gupta, S. C.

1972-01-01

An all digital phase locked loop which tracks the phase of the incoming signal once per carrier cycle is proposed. The different elements and their functions, and the phase lock operation are explained in detail. The general digital loop operation is governed by a non-linear difference equation from which a suitable model is developed. The lock range for the general model is derived. The performance of the digital loop for phase step, and frequency step inputs for different levels of quantization without loop filter, are studied. The analytical results are checked by simulating the actual system on the digital computer.

Performance improvement of a binary quantized all-digital phase-locked loop with a new aided-acquisition technique

NASA Astrophysics Data System (ADS)

Sandoz, J.-P.; Steenaart, W.

1984-12-01

The nonuniform sampling digital phase-locked loop (DPLL) with sequential loop filter, in which the correction sizes are controlled by the accumulated differences of two additional phase comparators, is graphically analyzed. In the absence of noise and frequency drift, the analysis gives some physical insight into the acquisition and tracking behavior. Taking noise into account, a mathematical model is derived and a random walk technique is applied to evaluate the rms phase error and the mean acquisition time. Experimental results confirm the appropriate simplifying hypotheses used in the numerical analysis. Two related performance measures defined in terms of the rms phase error and the acquisition time for a given SNR are used. These measures provide a common basis for comparing different digital loops and, to a limited extent, also with a first-order linear loop. Finally, the behavior of a modified DPLL under frequency deviation in the presence of Gaussian noise is tested experimentally and by computer simulation.

Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure

PubMed Central

Koczyk, Grzegorz; Berezovsky, Igor N.

2008-01-01

Domain hierarchy and closed loops (DHcL) (http://sitron.bccs.uib.no/dhcl/) is a web server that delineates energy hierarchy of protein domain structure and detects domains at different levels of this hierarchy. The server also identifies closed loops and van der Waals locks, which constitute a structural basis for the protein domain hierarchy. The DHcL can be a useful tool for an express analysis of protein structures and their alternative domain decompositions. The user submits a PDB identifier(s) or uploads a 3D protein structure in a PDB format. The results of the analysis are the location of domains at different levels of hierarchy, closed loops, van der Waals locks and their interactive visualization. The server maintains a regularly updated database of domains, closed loop and van der Waals locks for all X-ray structures in PDB. DHcL server is available at: http://sitron.bccs.uib.no/dhcl. PMID:18502776

Interplex modulation and a suppressed-carrier tracking loop for coherent communications systems

NASA Technical Reports Server (NTRS)

Butman, S.; Timor, U.

1974-01-01

Simple addition to hardware and new mode of operation of transmitter and receiver in coherent, PCM/PSK/PM configuration greatly improves channel efficiency. Procedure reduces amount of power lost to intermodulation products.

An Efficient Solution Method for Multibody Systems with Loops Using Multiple Processors

NASA Technical Reports Server (NTRS)

Ghosh, Tushar K.; Nguyen, Luong A.; Quiocho, Leslie J.

2015-01-01

This paper describes a multibody dynamics algorithm formulated for parallel implementation on multiprocessor computing platforms using the divide-and-conquer approach. The system of interest is a general topology of rigid and elastic articulated bodies with or without loops. The algorithm divides the multibody system into a number of smaller sets of bodies in chain or tree structures, called "branches" at convenient joints called "connection points", and uses an Order-N (O (N)) approach to formulate the dynamics of each branch in terms of the unknown spatial connection forces. The equations of motion for the branches, leaving the connection forces as unknowns, are implemented in separate processors in parallel for computational efficiency, and the equations for all the unknown connection forces are synthesized and solved in one or several processors. The performances of two implementations of this divide-and-conquer algorithm in multiple processors are compared with an existing method implemented on a single processor.

A 1microW 85nV/ radicalHz pseudo open-loop preamplifier with programmable band-pass filter for neural interface system.

PubMed

Chang, Sun-Il; Yoon, Euisik

2009-01-01

We report an energy efficient pseudo open-loop amplifier with programmable band-pass filter developed for neural interface systems. The proposed amplifier consumes 400nA at 2.5V power supply. The measured thermal noise level is 85nV/ radicalHz and input-referred noise is 1.69microV(rms) from 0.3Hz to 1 kHz. The amplifier has a noise efficiency factor of 2.43, the lowest in the differential topologies reported up to date to our knowledge. By programming the switched-capacitor frequency and bias current, we could control the bandwidth of the preamplifier from 138 mHz to 2.2 kHz to meet various application requirements. The entire preamplifier including band-pass filters has been realized in a small area of 0.043mm(2) using a 0.25microm CMOS technology.

A mechanically tunable and efficient ceramic probe for MR-microscopy at 17 Tesla

NASA Astrophysics Data System (ADS)

Kurdjumov, Sergei; Glybovski, Stanislav; Hurshkainen, Anna; Webb, Andrew; Abdeddaim, Redha; Ciobanu, Luisa; Melchakova, Irina; Belov, Pavel

2017-09-01

In this contribution we propose and study numerically a new probe (radiofrequency coil) for magnetic resonance mi-croscopy in the field of 17T. The probe is based on two coupled donut resonators made of a high-permittivity and low-loss ceramics excited by a non-resonant inductively coupled loop attached to a coaxial cable. By full-wave numerical simulation it was shown that the probe can be precisely tuned to the Larmor frequency of protons (723 MHz) by adjusting a gap between the two resonators. Moreover, the impedance of the probe can be matched by varying the distance from one of the resonators to the loop. As a result, a compact and mechanically tunable resonant probe was demonstrated for 17 Tesla applications using no lumped capacitors for tuning and matching. The new probe was numerically compared to a conventional solenoidal probe showing better efficiency.

High efficiency Brayton cycles using LNG

DOEpatents

Morrow, Charles W [Albuquerque, NM

2006-04-18

A modified, closed-loop Brayton cycle power conversion system that uses liquefied natural gas as the cold heat sink media. When combined with a helium gas cooled nuclear reactor, achievable efficiency can approach 68 76% (as compared to 35% for conventional steam cycle power cooled by air or water). A superheater heat exchanger can be used to exchange heat from a side-stream of hot helium gas split-off from the primary helium coolant loop to post-heat vaporized natural gas exiting from low and high-pressure coolers. The superheater raises the exit temperature of the natural gas to close to room temperature, which makes the gas more attractive to sell on the open market. An additional benefit is significantly reduced costs of a LNG revaporization plant, since the nuclear reactor provides the heat for vaporization instead of burning a portion of the LNG to provide the heat.

A 16-channel combined loop-dipole transceiver array for 7 Tesla body MRI.

PubMed

Ertürk, M Arcan; Raaijmakers, Alexander J E; Adriany, Gregor; Uğurbil, Kâmil; Metzger, Gregory J

2017-02-01

To develop a 16-channel transceive body imaging array at 7.0 T with improved transmit, receive, and specific absorption rate (SAR) performance by combining both loop and dipole elements and using their respective and complementary near and far field characteristics. A 16-channel radiofrequency (RF) coil array consisting of eight loop-dipole blocks (16LD) was designed and constructed. Transmit and receive performance was quantitatively investigated in phantom and human model simulations, and experiments on five healthy volunteers inside the prostate. Comparisons were made with 16-channel microstrip line (16ML) and 10-channel fractionated dipole antenna (10DA) arrays. The 16LD was used to acquire anatomic and functional images of the prostate, kidneys, and heart. The 16LD provided > 14% improvements in the signal-to-noise ratio (SNR), peak B1+, B1+ transmit, and SAR efficiencies over the 16ML and 10DA in simulations inside the prostate. Experimentally, the 16LD had > 20% higher SNR and B1+ transmit efficiency compared with other arrays, and achieved up to 51.8% higher peak B1+ compared with 10DA. Combining loop and dipole elements provided a body imaging array with high channel count and density while limiting inter-element coupling. The 16LD improved both near and far-field performance compared with existing 7.0T body arrays and provided high-quality MRI of the prostate kidneys and heart. Magn Reson Med 77:884-894, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

The effects of spaceflight on open-loop and closed-loop postural control mechanisms: human neurovestibular studies on SLS-2

NASA Technical Reports Server (NTRS)

Collins, J. J.; De Luca, C. J.; Pavlik, A. E.; Roy, S. H.; Emley, M. S.; Young, L. R. (Principal Investigator)

1995-01-01

Stabilogram-diffusion analysis was used to examine how prolonged periods in microgravity affect the open-loop and closed-loop postural control mechanisms. It was hypothesized that following spaceflight: (1) the effective stochastic activity of the open-loop postural control schemes in astronauts is increased; (2) the effective stochastic activity and uncorrelated behavior, respectively, of the closed-loop postural control mechanisms in astronauts are increased; and (3) astronauts utilized open-loop postural controls schemes for shorter time intervals and smaller displacements. Four crew members and two alternates from the 14-day Spacelab Life Sciences 2 Mission were included in the study. Each subject was tested under eyes-open, quiet-standing conditions on multiple preflight and postflight days. The subjects' center-of-pressure trajectories were measured with a force platform and analyzed according to stabilogram-diffusion analysis. It was found that the effective stochastic activity of the open-loop postural control schemes in three of the four crew members was increased following spaceflight. This result is interpreted as an indication that there may be in-flight adaptations to higher-level descending postural control pathways, e.g., a postflight increase in the tonic activation of postural muscles. This change may also be the consequence of a compensatory (e.g., "stiffening") postural control strategy that is adopted by astronauts to account for general feeling of postflight unsteadiness. The crew members, as a group, did not exhibit any consistent preflight/postflight differences in the steady-state behavior of their closed-loop postural control mechanisms or in the functional interaction of their open-loop and closed-loop postural control mechanisms. These results are interpreted as indications that although there may be in-flight adaptations to the vestibular system and/or proprioceptive system, input from the visual system can compensate for such changes during undisturbed stance.

Trajectory tracking control for underactuated stratospheric airship

NASA Astrophysics Data System (ADS)

Zheng, Zewei; Huo, Wei; Wu, Zhe

2012-10-01

Stratospheric airship is a new kind of aerospace system which has attracted worldwide developing interests for its broad application prospects. Based on the trajectory linearization control (TLC) theory, a novel trajectory tracking control method for an underactuated stratospheric airship is presented in this paper. Firstly, the TLC theory is described sketchily, and the dynamic model of the stratospheric airship is introduced with kinematics and dynamics equations. Then, the trajectory tracking control strategy is deduced in detail. The designed control system possesses a cascaded structure which consists of desired attitude calculation, position control loop and attitude control loop. Two sub-loops are designed for the position and attitude control loops, respectively, including the kinematics control loop and dynamics control loop. Stability analysis shows that the controlled closed-loop system is exponentially stable. Finally, simulation results for the stratospheric airship to track typical trajectories are illustrated to verify effectiveness of the proposed approach.

Human Y-Family DNA Polymerase κ Is More Tolerant to Changes in Its Active Site Loop than Its Ortholog Escherichia coli DinB.

PubMed

Antczak, Nicole M; Packer, Morgan R; Lu, Xueguang; Zhang, Ke; Beuning, Penny J

2017-11-20

DNA damage is a constant threat and can be bypassed in a process called translesion synthesis, which is typically carried out by Y-family DNA polymerases. Y-family DNA polymerases are conserved in all domains of life and tend to have specificity for certain types of DNA damage. Escherichia coli DinB and its human ortholog pol κ can bypass specific minor groove deoxyguanine adducts efficiently and are inhibited by major groove adducts, as Y-family DNA polymerases make contacts with the minor groove side of the DNA substrate and lack contacts with the major groove at the nascent base pair. DinB is inhibited by major groove adducts more than pol κ, and they each have active site loops of different lengths, with four additional amino acids in the DinB loop. We previously showed that the R35A active site loop mutation in DinB allows for bypass of the major groove adduct N 6 -furfuryl-dA. These observations led us to investigate the different active site loops by creating loop swap chimeras of DinB with a pol κ loop and vice versa by changing the loop residues in a stepwise fashion. We then determined their activity with undamaged DNA or DNA containing N 2 -furfuryl-dG or N 6 -furfuryl-dA. The DinB proteins with the pol kappa loop have low activity on all templates but have decreased misincorporation compared to either wild-type protein. The kappa proteins with the DinB loop retain activity on all templates and have decreased misincorporation compared to either wild-type protein. We assessed the thermal stability of the proteins and observed an increase in stability in the presence of all DNA templates and additional increases generally only in the presence of the undamaged and N 2 -furfuryl-dG adduct and dCTP, which correlates with activity. Overall we find that pol κ is more tolerant to changes in the active site loop than DinB.

Development of a Thin Film Primary Surface Heat Exchanger for Advanced Power Cycles

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

Allison, Tim; Beck, Griffin; Bennett, Jeffrey

This project objective is to develop a high-temperature design upgrade for an existing primary surface heat exchanger so that the redesigned hardware is capable of operation in CO 2 at temperatures up to 1,510°F (821°C) and pressure differentials up to 130 psi (9 bar). The heat exchanger is proposed for use as a recuperator in an advanced low-pressure oxy-fuel Brayton cycle that is predicted to achieve over 50% thermodynamic efficiency, although the heat exchanger could also be used in other high-temperature, low-differential pressure cycles. This report describes the progress to date, which includes continuing work performed to select and testmore » new candidate materials for the recuperator redesign, final mechanical and thermal performance analysis results of various redesign concepts, and the preliminary design of a test loop for the redesigned recuperator including a budgetary estimate for detailed test loop design, procurement, and test operation. A materials search was performed in order to investigate high-temperature properties of many candidate materials, including high-temperature strength and nickel content. These properties were used to rank the candidate materials, resulting in a reduced list of nine materials for corrosion testing. Multiple test rigs were considered and analyzed for short-term corrosion testing and Thermal Gravimetric Analysis (TGA) was selected as the most cost-effective option for evaluating corrosion resistance of the candidate materials. In addition, tantalum, niobium, and chromium coatings were identified as potential options for increased corrosion resistance. The test results show that many materials exhibit relatively low weight gain rates, and that niobium and tantalum coatings may improve corrosion resistance for many materials, while chromium coatings appear to oxidize and debond quickly. Metallurgical analysis of alloys was also performed, showing evidence of intergranular attack in 282 that may cause long-term reliability problems in CO 2 service at these temperatures. However, long-term testing in a flowing environment is recommended in order to understand accurately the severity of the attack. Detailed economic modeling of the existing air cycle recuperator and CO 2 cycle recuperator options was also completed, including costs for material, fabrication, fuel, maintenance, and operation. The analysis results show that the increased capital cost for high-temperature materials may be offset by higher cycle efficiencies, decreasing the overall lifetime cost of the system. The economic analysis also examines costs associated with increased pressure drop and material changes for two redesign options. These results show that, even with slightly reduced performance and/or higher material costs, the lifetime cost per energy production may still be reduced by over 12%. The existing recuperator design information was provided by Solar Turbines, Inc. via several models, drawings, and design handoff meetings. Multiple fluid/thermal and structural models were created in order to analyze critical recuperator performance and mechanical strength in critical areas throughout the redesign process. These models were analyzed for a baseline condition (consistent with current Mercury 50 operation) for validation purposes. Results are presented for heat transfer coefficients and pressure drops, matching well with the existing operational data. Simulation of higher-temperature CO 2 conditions was also performed, showing a slight expected increase in both heat transfer and pressure drop. Mechanical analysis results for critical areas on the cross-flow and counter-flow sheets have also been obtained for air and CO 2 cases. These results show similar stresses in both cases but significantly reduced safety factors for the CO 2 case due to reduced yield and creep rupture strengths of alloy 625 at the higher temperatures. A concept brainstorm session and initial down-selection were completed in order to identify promising redesign options for further analysis. Detailed analysis of all promising redesign options was performed via finite element and computational fluid dynamic simulations in order to characterize mechanical and thermal-fluid performance of each option. These options included material change, various sheet thickness configurations, pitch and phasing of cross-flow and counter-flow sheets, and separator sheets. The analysis results have identified two viable redesign options that maintain existing safety margins optimally through a material change to Haynes 282 and (A) sheet thickness increases of 40% on the counter-flow sheet and 75% on the hot side cross-flow corrugation sheet or (B) addition of a separator sheet in the counter-flow section while maintaining the original counter-flow sheet thickness and increasing the cross-flow corrugation sheet thickness by 90% to account for the increase in cell height. While both options satisfy mechanical stress constraints, the separator sheet design has a higher part count, slightly reduced heat transfer, and slightly higher pressure drop than the first option and is not preferred. Finally, several test loop concepts have been developed for different full-scale and reduced-scale recuperator testing options. For each option, various loop components, such as heat exchangers, valves, heaters, and compressors, were evaluated in an effort to maximize utilization of existing resources. All concepts utilize an existing 3-MW CO 2 compressor, heater, and loop coolers, but the concepts vary by incorporating different amounts of new equipment for achieving various flow rates (all concepts operate at design pressure and temperature). The third concept achieves a 1 kg/s test without purchasing any costly equipment (coolers, heaters, blowers, etc.). Since the stacked cell design of the recuperator results in the same flow conditions at each core cell (even for a reduced-scale test). Thus, test loop Concept #3 was selected for the preliminary design. This loop design is detailed within the report, culminating in a budgetary estimate of $1,013,000.00 for the detailed design, construction, commissioning, and operation of a high-temperature recuperator test loop.« less

Controlled-Root Approach To Digital Phase-Locked Loops

NASA Technical Reports Server (NTRS)

Stephens, Scott A.; Thomas, J. Brooks

1995-01-01

Performance tailored more flexibly and directly to satisfy design requirements. Controlled-root approach improved method for analysis and design of digital phase-locked loops (DPLLs). Developed rigorously from first principles for fully digital loops, making DPLL theory and design simpler and more straightforward (particularly for third- or fourth-order DPLL) and controlling performance more accurately in case of high gain.

Smart lighting using a liquid crystal modulator

NASA Astrophysics Data System (ADS)

Baril, Alexandre; Thibault, Simon; Galstian, Tigran

2017-08-01

Now that LEDs have massively invaded the illumination market, a clear trend has emerged for more efficient and targeted lighting. The project described here is at the leading edge of the trend and aims at developing an evaluation board to test smart lighting applications. This is made possible thanks to a new liquid crystal light modulator recently developed for broadening LED light beams. The modulator is controlled by electrical signals and is characterized by a linear working zone. This feature allows the implementation of a closed loop control with a sensor feedback. This project shows that the use of computer vision is a promising opportunity for cheap closed loop control. The developed evaluation board integrates the liquid crystal modulator, a webcam, a LED light source and all the required electronics to implement a closed loop control with a computer vision algorithm.

Closed-loop, pilot/vehicle analysis of the approach and landing task

NASA Technical Reports Server (NTRS)

Schmidt, D. K.; Anderson, M. R.

1985-01-01

Optimal-control-theoretic modeling and frequency-domain analysis is the methodology proposed to evaluate analytically the handling qualities of higher-order manually controlled dynamic systems. Fundamental to the methodology is evaluating the interplay between pilot workload and closed-loop pilot/vehicle performance and stability robustness. The model-based metric for pilot workload is the required pilot phase compensation. Pilot/vehicle performance and loop stability is then evaluated using frequency-domain techniques. When these techniques were applied to the flight-test data for thirty-two highly-augmented fighter configurations, strong correlation was obtained between the analytical and experimental results.

Study of mitochondria D-loop gene to detect the heterogeneity of gemak in Turnicidae family

NASA Astrophysics Data System (ADS)

Setiati, N.; Partaya

2018-03-01

As a part of life biodiversity, birds in Turnicidae family should be preserved from the extinction and its type heterogeneity decline. One effort for giving the strategic base of plasma nutfah conservation is through genetic heterogeneity study. The aim of the research is to analyze D-loop gen from DNA mitochondria of gemak bird in Turnicidae family molecularly. From the result of the analysis, it may be known the genetic heterogeneity of gemak bird based on the sequence of D-loop gen. The collection of both types of gemak of Turnicidae family is still easy since we can find them in ricefield area after harvest particularly for Gemakloreng (Turnix sylvatica), it means while gemak tegalan (Turnixsusciator) is getting difficult to find. Based on the above DNA quantification standard, the blood sample of Gemak in this research is mostly grouped into pure blood (ranges from 1,63 – 1,90), and it deserves to be used for PCR analysis. The sequencing analysis has not detected the sequence of nucleotide completely. However, it indicates sequence polymorphism of base as the arranger of D-loop gen. D-loop gen may identify genetic heterogeneity of gemak bird of Turnicidae family, but it is necessary to perform further sequencing analysis with PCR-RFLP technique. This complete nucleotide sequence is obtained and easy to detect after being cut restriction enzyme.

Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling

PubMed Central

MacDonald, James T.; Kelley, Lawrence A.; Freemont, Paul S.

2013-01-01

Coarse-grained (CG) methods for sampling protein conformational space have the potential to increase computational efficiency by reducing the degrees of freedom. The gain in computational efficiency of CG methods often comes at the expense of non-protein like local conformational features. This could cause problems when transitioning to full atom models in a hierarchical framework. Here, a CG potential energy function was validated by applying it to the problem of loop prediction. A novel method to sample the conformational space of backbone atoms was benchmarked using a standard test set consisting of 351 distinct loops. This method used a sequence-independent CG potential energy function representing the protein using -carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific /-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational protein design. C++ source code is available for download from http://www.sbg.bio.ic.ac.uk/phyre2/PD2/. PMID:23824634

An estimator-predictor approach to PLL loop filter design

NASA Technical Reports Server (NTRS)

Statman, J. I.; Hurd, W. J.

1986-01-01

An approach to the design of digital phase locked loops (DPLLs), using estimation theory concepts in the selection of a loop filter, is presented. The key concept is that the DPLL closed-loop transfer function is decomposed into an estimator and a predictor. The estimator provides recursive estimates of phase, frequency, and higher order derivatives, while the predictor compensates for the transport lag inherent in the loop. This decomposition results in a straightforward loop filter design procedure, enabling use of techniques from optimal and sub-optimal estimation theory. A design example for a particular choice of estimator is presented, followed by analysis of the associated bandwidth, gain margin, and steady state errors caused by unmodeled dynamics. This approach is under consideration for the design of the Deep Space Network (DSN) Advanced Receiver Carrier DPLL.

Positive And Negative Feedback Loops Coupled By Common Transcription Activator And Repressor

NASA Astrophysics Data System (ADS)

Sielewiesiuk, Jan; Łopaciuk, Agata

2015-03-01

Dynamical systems consisting of two interlocked loops with negative and positive feedback have been studied using the linear analysis of stability and numerical solutions. Conditions for saddle-node bifurcation were formulated in a general form. Conditions for Hopf bifurcations were found in a few symmetrical cases. Auto-oscillations, when they exist, are generated by the negative feedback repressive loop. This loop determines the frequency and amplitude of oscillations. The positive feedback loop of activation slightly modifies the oscillations. Oscillations are possible when the difference between Hilll's coefficients of the repression and activation is sufficiently high. The highly cooperative activation loop with a fast turnover slows down or even makes the oscillations impossible. The system under consideration can constitute a component of epigenetic or enzymatic regulation network.

An efficient algorithm for planar drawing of RNA structures with pseudoknots of any type.

PubMed

Byun, Yanga; Han, Kyungsook

2016-06-01

An RNA pseudoknot is a tertiary structural element in which bases of a loop pair with complementary bases are outside the loop. A drawing of RNA secondary structures is a tree, but a drawing of RNA pseudoknots is a graph that has an inner cycle within a pseudoknot and possibly outer cycles formed between the pseudoknot and other structural elements. Visualizing a large-scale RNA structure with pseudoknots as a planar drawing is challenging because a planar drawing of an RNA structure requires both pseudoknots and an entire structure enclosing the pseudoknots to be embedded into a plane without overlapping or crossing. This paper presents an efficient heuristic algorithm for visualizing a pseudoknotted RNA structure as a planar drawing. The algorithm consists of several parts for finding crossing stems and page mapping the stems, for the layout of stem-loops and pseudoknots, and for overlap detection between structural elements and resolving it. Unlike previous algorithms, our algorithm generates a planar drawing for a large RNA structure with pseudoknots of any type and provides a bracket view of the structure. It generates a compact and aesthetic structure graph for a large pseudoknotted RNA structure in O([Formula: see text]) time, where n is the number of stems of the RNA structure.

Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling.

PubMed

Afriat-Jurnou, Livnat; Jackson, Colin J; Tawfik, Dan S

2012-08-07

Only decades after the introduction of organophosphate pesticides, bacterial phosphotriesterases (PTEs) have evolved to catalyze their degradation with remarkable efficiency. Their closest known relatives, lactonases, with promiscuous phosphotriasterase activity, dubbed PTE-like lactonases (PLLs), share only 30% sequence identity and also differ in the configuration of their active-site loops. PTE was therefore presumed to have evolved from a yet unknown PLL whose primary activity was the hydrolysis of quorum sensing homoserine lactones (HSLs) (Afriat et al. (2006) Biochemistry 45, 13677-13686). However, how PTEs diverged from this presumed PLL remains a mystery. In this study we investigated loop remodeling as a means of reconstructing a homoserine lactonase ancestor that relates to PTE by few mutational steps. Although, in nature, loop remodeling is a common mechanism of divergence of enzymatic functions, reproducing this process in the laboratory is a challenge. Structural and phylogenetic analyses enabled us to remodel one of PTE's active-site loops into a PLL-like configuration. A deletion in loop 7, combined with an adjacent, highly epistatic, point mutation led to the emergence of an HSLase activity that is undetectable in PTE (k(cat)/K(M) values of up to 2 × 10(4)). The appearance of the HSLase activity was accompanied by only a minor decrease in PTE's paraoxonase activity. This specificity change demonstrates the potential role of bifunctional intermediates in the divergence of new enzymatic functions and highlights the critical contribution of loop remodeling to the rapid divergence of new enzyme functions.

Maximum power point tracker for photovoltaic power plants

NASA Astrophysics Data System (ADS)

Arcidiacono, V.; Corsi, S.; Lambri, L.

The paper describes two different closed-loop control criteria for the maximum power point tracking of the voltage-current characteristic of a photovoltaic generator. The two criteria are discussed and compared, inter alia, with regard to the setting-up problems that they pose. Although a detailed analysis is not embarked upon, the paper also provides some quantitative information on the energy advantages obtained by using electronic maximum power point tracking systems, as compared with the situation in which the point of operation of the photovoltaic generator is not controlled at all. Lastly, the paper presents two high-efficiency MPPT converters for experimental photovoltaic plants of the stand-alone and the grid-interconnected type.

Isotope Brayton electric power system for the 500 to 2500 watt range.

NASA Technical Reports Server (NTRS)

Macosko, R. P.; Barna, G. J.; Block, H. B.; Ingle, B. D.

1972-01-01

An extensive study was conducted at the Lewis Research Center to evaluate an isotope Brayton electric power system for use in the 500 to 2500 W power range. The study emphasized overall system simplicity in order to reduce parasitic power losses and improve system reliability. The study included detailed parametric cycle analysis, conceptual component designs, and evaluation of system packaging. The study has resulted in the selection of a single-loop system (gas) with six major components including one rotating unit. Calculated net system efficiency varies from 23 to 28% over the power range. The use of the Pu-238 heat source being developed for the Multi-Hundred-Watt Radioisotope Thermoelectric Generator program was assumed.

Chemical-Looping Combustion and Gasification of Coals and Oxygen Carrier Development: A Brief Review

DOE PAGES

Wang, Ping; Means, Nicholas; Shekhawat, Dushyant; ...

2015-09-24

Chemical-looping technology is one of the promising CO 2 capture technologies. It generates a CO 2 enriched flue gas, which will greatly benefit CO 2 capture, utilization or sequestration. Both chemical-looping combustion (CLC) and chemical-looping gasification (CLG) have the potential to be used to generate power, chemicals, and liquid fuels. Chemical-looping is an oxygen transporting process using oxygen carriers. Recently, attention has focused on solid fuels such as coal. Coal chemical-looping reactions are more complicated than gaseous fuels due to coal properties (like mineral matter) and the complex reaction pathways involving solid fuels. The mineral matter/ash and sulfur in coalmore » may affect the activity of oxygen carriers. Oxygen carriers are the key issue in chemical-looping processes. Thermogravimetric analysis (TGA) has been widely used for the development of oxygen carriers (e.g., oxide reactivity). Two proposed processes for the CLC of solid fuels are in-situ Gasification Chemical-Looping Combustion (iG-CLC) and Chemical-Looping with Oxygen Uncoupling (CLOU). The objectives of this review are to discuss various chemical-looping processes with coal, summarize TGA applications in oxygen carrier development, and outline the major challenges associated with coal chemical-looping in iG-CLC and CLOU.« less

Dislocation loops in ultra-high purity Fe(Cr) alloys after 7.2 MeV proton irradiation

NASA Astrophysics Data System (ADS)

Chen, J.; Duval, F.; Jung, P.; Schäublin, R.; Gao, N.; Barthe, M. F.

2018-05-01

Ultra-high purity Fe(Cr) alloys (from 0 wt% Cr to 14 wt% Cr) were 3D homogeneously irradiated by 0-7.2 MeV protons to 0.3 dpa at nominal temperatures from 270 °C to 500 °C. Microstructural changes were observed by transmission electron microscopy (TEM). The results showed that evolution of dislocation loops depends on the Cr content. Below 300 °C, large ½ a0 <111> loops are dominating. Above 300 °C, a0 <100> loops with a habit plane {100} appear. Loop sizes of both types are more or less the same. At temperatures from 310 °C to 400 °C, a0 <100> loops form clusters with the same {100} habit plane as the one of the loops forming them. This indicates that <100> loops of the same variant start gliding under mutual elastic interaction. At 500 °C, dislocation loops form disc shaped clusters about 1000 nm in diameter and sitting on {111} and/or {100} planes in the pure Fe samples. Based on these observations a quantitative analysis of the dislocation loops configurations and their temperature dependence is made, leading to an understanding of the basic mechanisms of formation of these loops.

On the performance of digital phase locked loops in the threshold region

NASA Technical Reports Server (NTRS)

Hurst, G. T.; Gupta, S. C.

1974-01-01

Extended Kalman filter algorithms are used to obtain a digital phase lock loop structure for demodulation of angle modulated signals. It is shown that the error variance equations obtained directly from this structure enable one to predict threshold if one retains higher frequency terms. This is in sharp contrast to the similar analysis of the analog phase lock loop, where the higher frequency terms are filtered out because of the low pass filter in the loop. Results are compared to actual simulation results and threshold region results obtained previously.

Novel design methods for magnetic flux loops in the National Compact Stellarator Experiment

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

Pomphrey, N.; Lazarus, E.; Zarnstorff, M.

2007-05-15

Magnetic pickup loops on the vacuum vessel (VV) can provide an abundance of equilibrium information for stellarators. A substantial effort has gone into designing flux loops for the National Compact Stellarator Experiment (NCSX) [Zarnstorff et al., Plasma Phys. Controlled Fusion 43, A237 (2001)], a three-field period quasi-axisymmetric stellarator under construction at the Princeton Plasma Physics Laboratory. The design philosophy, to measure all of the magnetic field distributions normal to the VV that can be measured, has necessitated the development of singular value decomposition algorithms for identifying efficient loop locations. Fields are expected to be predominantly stellarator symmetric (SS)--the symmetry ofmore » the machine design--with toroidal mode numbers per torus (n) equal to a multiple of 3 and possessing reflection symmetry in a period. However, plasma instabilities and coil imperfections will generate non-SS fields that must also be diagnosed. The measured symmetric fields will yield important information on the plasma current and pressure profile as well as on the plasma shape. All fields that obey the design symmetries could be measured by placing flux loops in a single half-period of the VV, but accurate resolution of nonsymmetric modes, quantified by the condition number of a matrix, requires repositioning loops to equivalent locations on the full torus. A subarray of loops located along the inside wall of the vertically elongated cross section was designed to detect n=3, m=5 or 6 resonant field perturbations that can cause important islands. Additional subarrays included are continuous in the toroidal and poloidal directions. Loops are also placed at symmetry points of the VV to obtain maximal sensitivity to asymmetric perturbations. Combining results from various calculations which have made extensive use of a database of 2500 free-boundary VMEC equilibria, has led to the choice of 225 flux loops for NCSX, of which 151 have distinct shapes.« less

Single nucleotide polymorphisms in the mitochondrial displacement loop and outcome of esophageal squamous cell carcinoma.

PubMed

Zhang, Ruixing; Wang, Rui; Zhang, Fengbin; Wu, Chensi; Fan, Haiyan; Li, Yan; Wang, Cuiju; Guo, Zhanjun

2010-11-26

Accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) has been described for different types of cancers and might be associated with cancer risk and disease outcome. We used a population-based series of esophageal squamous cell carcinoma (ESCC) patients for investigating the prediction power of SNPs in mitochondrial D-loop. The D-loop region of mtDNA was sequenced for 60 ESCC patients recorded in the Fourth Hospital of Hebei Medical University between 2003 and 2004. The 5 year survival curve were calculated with the Kaplan-Meier method and compared by the log-rank test at each SNP site, a multivariate survival analysis was also performed with the Cox proportional hazards method. The SNP sites of nucleotides 16274G/A, 16278C/T and 16399A/G were identified for prediction of post-operational survival by the log-rank test. In an overall multivariate analysis, the 16278 and 16399 alleles were identified as independent predictors of ESCC outcome. The length of survival of patients with the minor allele 16278T genotype was significantly shorter than that of patients with 16278C at the 16278 site (relative risk, 3.001; 95% CI, 1.029 - 8.756; p = 0.044). The length of survival of patients with the minor allele 16399G genotype was significantly shorter than that of patients with the more frequent allele 16399A at the 16399 site in ESCC patients (relative risk, 3.483; 95% CI, 1.068 - 11.359; p = 0.039). Genetic polymorphisms in the D-loop are independent prognostic markers for patients with ESCC. Accordingly, the analysis of genetic polymorphisms in the mitochondrial D-loop can help identify patient subgroups at high risk of a poor disease outcome.

Analysis of TMT primary mirror control-structure interaction

NASA Astrophysics Data System (ADS)

MacMynowski, Douglas G.; Thompson, Peter M.; Sirota, Mark J.

2008-07-01

The primary mirror control system (M1CS) keeps the 492 segments of the Thirty Meter Telescope primary mirror aligned in the presence of disturbances. A global position control loop uses feedback from inter-segment edge sensors to three actuators behind each segment that control segment piston, tip and tilt. If soft force actuators are used (e.g. voice-coil), then in addition to the global position loop there will be a local servo loop to provide stiffness. While the M1 control system at Keck compensates only for slow disturbances such as gravity and thermal variations, the M1CS for TMT will need to provide some compensation for higher frequency wind disturbances in order to meet stringent error budget targets. An analysis of expected high-wavenumber wind forces on M1 suggests that a 1Hz control bandwidth is required for the global feedback of segment edge-sensorbased position information in order to minimize high spatial frequency segment response for both seeing-limited and adaptive optics performance. A much higher bandwidth is required from the local servo loop to provide adequate stiffness to wind or acoustic disturbances. A related paper presents the control designs for the local actuator servo loops. The disturbance rejection requirements would not be difficult to achieve for a single segment, but the structural coupling between segments mounted on a flexible mirror cell results in controlstructure interaction (CSI) that limits the achievable bandwidth. Using a combination of simplified modeling to build intuition and the full telescope finite element model for verification, we present designs and analysis for both the local servo loop and global loop demonstrating sufficient bandwidth and resulting wind-disturbance rejection despite the presence of CSI.

Understanding the molecular mechanism of the broad and potent neutralization of HIV-1 by antibody VRC01 from the perspective of molecular dynamics simulation and binding free energy calculations.

PubMed

Zhang, Yan; Pan, Dabo; Shen, Yulin; Jin, Nengzhi; Liu, Huanxiang; Yao, Xiaojun

2012-09-01

VRC01 is one of the most broadly and potently neutralizing HIV-1 antibodies known-it has been shown to neutralize 91 % of the tested primary isolate Env pseudoviruses by recognizing the viral envelope glycoprotein gp120. To explore the mechanism of HIV-1 neutralization by VRC01 and thus obtain valuable information for vaccine design, we performed molecular dynamics simulations and binding free energy calculations for apo-VRC01, apo-gp120, and the gp120-VRC01 complex. For gp120, residue energy decomposition analysis showed that the hotspot residues Asn280, Lys282, Asp368, Ile371, and Asp457 are located in three primary loops, including the CD4-binding loop, loop D, and loop V5. For VRC01, the hotspot residues Trp47, Trp50, Asn58, Arg61, Gln64, Trp100, and Tyr91 mainly come from CDR2 of the heavy chain. By decomposing the binding free energy into different components, intermolecular van der Waals interactions and nonpolar solvation were found to dominate the binding process. Principal component analysis of loops D and V5, which are related to neutralization resistance, indicated that these two areas have a larger conformational space in apo-gp120 compared to bound gp120. A comparison of three representative structures from the cluster analysis of loops D and V5 indicated that changes primarily occur at the tip of loop V5, and are caused by fluctuations in the terminal Glu1 residue of the antibody. This information can be used to guide the design of vaccines and small molecule inhibitors.

Efficient H2O2/CH3COOH oxidative desulfurization/denitrification of liquid fuels in sonochemical flow-reactors.

PubMed

Calcio Gaudino, Emanuela; Carnaroglio, Diego; Boffa, Luisa; Cravotto, Giancarlo; Moreira, Elizabeth M; Nunes, Matheus A G; Dressler, Valderi L; Flores, Erico M M

2014-01-01

The oxidative desulfurization/denitrification of liquid fuels has been widely investigated as an alternative or complement to common catalytic hydrorefining. In this process, all oxidation reactions occur in the heterogeneous phase (the oil and the polar phase containing the oxidant) and therefore the optimization of mass and heat transfer is of crucial importance to enhancing the oxidation rate. This goal can be achieved by performing the reaction in suitable ultrasound (US) reactors. In fact, flow and loop US reactors stand out above classic batch US reactors thanks to their greater efficiency and flexibility as well as lower energy consumption. This paper describes an efficient sonochemical oxidation with H2O2/CH3COOH at flow rates ranging from 60 to 800 ml/min of both a model compound, dibenzotiophene (DBT), and of a mild hydro-treated diesel feedstock. Four different commercially available US loop reactors (single and multi-probe) were tested, two of which were developed in the authors' laboratory. Full DBT oxidation and efficient diesel feedstock desulfurization/denitrification were observed after the separation of the polar oxidized S/N-containing compounds (S≤5 ppmw, N≤1 ppmw). Our studies confirm that high-throughput US applications benefit greatly from flow-reactors. Copyright © 2013 Elsevier B.V. All rights reserved.

Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP

PubMed Central

Khorosheva, Eugenia M.; Karymov, Mikhail A.; Selck, David A.; Ismagilov, Rustem F.

2016-01-01

In this paper, we asked if it is possible to identify the best primers and reaction conditions based on improvements in reaction speed when optimizing isothermal reactions. We used digital single-molecule, real-time analyses of both speed and efficiency of isothermal amplification reactions, which revealed that improvements in the speed of isothermal amplification reactions did not always correlate with improvements in digital efficiency (the fraction of molecules that amplify) or with analytical sensitivity. However, we observed that the speeds of amplification for single-molecule (in a digital device) and multi-molecule (e.g. in a PCR well plate) formats always correlated for the same conditions. Also, digital efficiency correlated with the analytical sensitivity of the same reaction performed in a multi-molecule format. Our finding was supported experimentally with examples of primer design, the use or exclusion of loop primers in different combinations, and the use of different enzyme mixtures in one-step reverse-transcription loop-mediated amplification (RT-LAMP). Our results show that measuring the digital efficiency of amplification of single-template molecules allows quick, reliable comparisons of the analytical sensitivity of reactions under any two tested conditions, independent of the speeds of the isothermal amplification reactions. PMID:26358811

Catalytic Exhaust Gas Recirculation-Loop Reforming for High Efficiency in a Stoichiometric Spark-Ignited Engine through Thermochemical Recuperation and Dilution Limit Extension, Part 2: Engine Performance

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

Chang, Yan; Szybist, James P.; Pihl, Josh A.

This is the second part of a two-part investigation of on-board catalytic fuel reforming to increase the brake efficiency of a multicylinder, stoichiometric spark-ignited (SI) engine. In Part 1 of the investigation, we analytically and experimentally characterized the energetics and kinetics of a candidate reforming catalyst over a range of reforming equivalence ratios and oxygen concentration conditions to identify the best conditions for efficient reforming. In the present part of our investigation, we studied an engine strategy that combined exhaust gas recirculation (EGR)–loop reforming with dilution limit extension of the combustion. In our experiments, we found that, under an enginemore » operating condition of 2000 rpm and brake mean effective pressure (4 bar), catalytic EGR reforming made it possible to sustain stable combustion with a volumetric equivalent of 45%–55% EGR. Under this same operating condition with stoichiometric engine exhaust (and no reforming), we were only able to sustain stable combustion with EGR under 25%. In conclusion, these results indicate that multicylinder gasoline engine efficiency can be increased substantially with catalytic reforming combined with and higher EGR operation, resulting in a decrease of more than 8% in fuel consumption, compared to baseline operation.« less

Catalytic Exhaust Gas Recirculation-Loop Reforming for High Efficiency in a Stoichiometric Spark-Ignited Engine through Thermochemical Recuperation and Dilution Limit Extension, Part 2: Engine Performance

DOE PAGES

Chang, Yan; Szybist, James P.; Pihl, Josh A.; ...

2018-01-17

This is the second part of a two-part investigation of on-board catalytic fuel reforming to increase the brake efficiency of a multicylinder, stoichiometric spark-ignited (SI) engine. In Part 1 of the investigation, we analytically and experimentally characterized the energetics and kinetics of a candidate reforming catalyst over a range of reforming equivalence ratios and oxygen concentration conditions to identify the best conditions for efficient reforming. In the present part of our investigation, we studied an engine strategy that combined exhaust gas recirculation (EGR)–loop reforming with dilution limit extension of the combustion. In our experiments, we found that, under an enginemore » operating condition of 2000 rpm and brake mean effective pressure (4 bar), catalytic EGR reforming made it possible to sustain stable combustion with a volumetric equivalent of 45%–55% EGR. Under this same operating condition with stoichiometric engine exhaust (and no reforming), we were only able to sustain stable combustion with EGR under 25%. In conclusion, these results indicate that multicylinder gasoline engine efficiency can be increased substantially with catalytic reforming combined with and higher EGR operation, resulting in a decrease of more than 8% in fuel consumption, compared to baseline operation.« less

Loop-Mediated Isothermal Amplification (LAMP) Signature Identification Software

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

Torres, C.

2009-03-17

This is an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs.

Elongation of Flare Ribbons

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

Qiu, Jiong; Longcope, Dana W.; Cassak, Paul A.

2017-03-20

We present an analysis of the apparent elongation motion of flare ribbons along the polarity inversion line (PIL), as well as the shear of flare loops in several two-ribbon flares. Flare ribbons and loops spread along the PIL at a speed ranging from a few to a hundred km s{sup −1}. The shear measured from conjugate footpoints is consistent with the measurement from flare loops, and both show the decrease of shear toward a potential field as a flare evolves and ribbons and loops spread along the PIL. Flares exhibiting fast bidirectional elongation appear to have a strong shear, whichmore » may indicate a large magnetic guide field relative to the reconnection field in the coronal current sheet. We discuss how the analysis of ribbon motion could help infer properties in the corona where reconnection takes place.« less

A Bayesian Approach to Period Searching in Solar Coronal Loops

NASA Astrophysics Data System (ADS)

Scherrer, Bryan; McKenzie, David

2017-03-01

We have applied a Bayesian generalized Lomb-Scargle period searching algorithm to movies of coronal loop images obtained with the Hinode X-ray Telescope (XRT) to search for evidence of periodicities that would indicate resonant heating of the loops. The algorithm makes as its only assumption that there is a single sinusoidal signal within each light curve of the data. Both the amplitudes and noise are taken as free parameters. It is argued that this procedure should be used alongside Fourier and wavelet analyses to more accurately extract periodic intensity modulations in coronal loops. The data analyzed are from XRT Observation Program #129C: “MHD Wave Heating (Thin Filters),” which occurred during 2006 November 13 and focused on active region 10293, which included coronal loops. The first data set spans approximately 10 min with an average cadence of 2 s, 2″ per pixel resolution, and used the Al-mesh analysis filter. The second data set spans approximately 4 min with a 3 s average cadence, 1″ per pixel resolution, and used the Al-poly analysis filter. The final data set spans approximately 22 min at a 6 s average cadence, and used the Al-poly analysis filter. In total, 55 periods of sinusoidal coronal loop oscillations between 5.5 and 59.6 s are discussed, supporting proposals in the literature that resonant absorption of magnetic waves is a viable mechanism for depositing energy in the corona.

A Bayesian Approach to Period Searching in Solar Coronal Loops

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

Scherrer, Bryan; McKenzie, David

2017-03-01

We have applied a Bayesian generalized Lomb–Scargle period searching algorithm to movies of coronal loop images obtained with the Hinode X-ray Telescope (XRT) to search for evidence of periodicities that would indicate resonant heating of the loops. The algorithm makes as its only assumption that there is a single sinusoidal signal within each light curve of the data. Both the amplitudes and noise are taken as free parameters. It is argued that this procedure should be used alongside Fourier and wavelet analyses to more accurately extract periodic intensity modulations in coronal loops. The data analyzed are from XRT Observation Programmore » 129C: “MHD Wave Heating (Thin Filters),” which occurred during 2006 November 13 and focused on active region 10293, which included coronal loops. The first data set spans approximately 10 min with an average cadence of 2 s, 2″ per pixel resolution, and used the Al-mesh analysis filter. The second data set spans approximately 4 min with a 3 s average cadence, 1″ per pixel resolution, and used the Al-poly analysis filter. The final data set spans approximately 22 min at a 6 s average cadence, and used the Al-poly analysis filter. In total, 55 periods of sinusoidal coronal loop oscillations between 5.5 and 59.6 s are discussed, supporting proposals in the literature that resonant absorption of magnetic waves is a viable mechanism for depositing energy in the corona.« less

Decay-less kink oscillations in coronal loops

NASA Astrophysics Data System (ADS)

Anfinogentov, S.; Nisticò, G.; Nakariakov, V. M.

2013-12-01

Context. Kink oscillations of coronal loops in an off-limb active region are detected with the Imaging Assembly Array (AIA) instruments of the Solar Dynamics Observatory (SDO) at 171 Å. Aims: We aim to measure periods and amplitudes of kink oscillations of different loops and to determinate the evolution of the oscillation phase along the oscillating loop. Methods: Oscillating coronal loops were visually identified in the field of view of SDO/AIA and STEREO/EUVI-A: the loop length was derived by three-dimensional analysis. Several slits were taken along the loops to assemble time-distance maps. We identified oscillatory patterns and retrieved periods and amplitudes of the oscillations. We applied the cross-correlation technique to estimate the phase shift between oscillations at different segments of oscillating loops. Results: We found that all analysed loops show low-amplitude undamped transverse oscillations. Oscillation periods of loops in the same active region range from 2.5 to 11 min, and are different for different loops. The displacement amplitude is lower than 1 Mm. The oscillation phase is constant along each analysed loop. The spatial structure of the phase of the oscillations corresponds to the fundamental standing kink mode. We conclude that the observed behaviour is consistent with the empirical model in terms of a damped harmonic resonator affected by a non-resonant continuously operating external force. A movie is available in electronic form at http://www.aanda.org

In-Silico Identification Of Micro-Loops In Myelodysplastic Syndromes

NASA Astrophysics Data System (ADS)

Beck, Dominik; Brandl, Miriam; Pham, Tuan D.; Chang, Chung-Che; Zhou, Xiaobo

2011-06-01

Micro-loops are regulatory network motifs that leverage transcriptional and posttranscriptional control to effectively regulate the transcriptome. In this paper a regulatory network for Myelodysplastic Syndromes (MDSs) was constructed from the literature and publicly available data sources. The network was filtered using data from deep-sequencing of small RNAs, exon and microarrays. Motif discovery showed that micro-loops might exist in MDS. We further used the identified micro-loops and performed basic network analysis to identify the known disease gene RUNX1/AML, as well as miRNA family hsa-mir-181. This suggested that the concept of micro-loops can be applied to enhance disease gene identification and biomarker discovery.

Benchmarking and Hardware-In-The-Loop Operation of a ...

EPA Pesticide Factsheets

Engine Performance evaluation in support of LD MTE. EPA used elements of its ALPHA model to apply hardware-in-the-loop (HIL) controls to the SKYACTIV engine test setup to better understand how the engine would operate in a chassis test after combined with future leading edge technologies, advanced high-efficiency transmission, reduced mass, and reduced roadload. Predict future vehicle performance with Atkinson engine. As part of its technology assessment for the upcoming midterm evaluation of the 2017-2025 LD vehicle GHG emissions regulation, EPA has been benchmarking engines and transmissions to generate inputs for use in its ALPHA model

Ceramic heat pipe wick

NASA Technical Reports Server (NTRS)

Seidenberg, Benjamin (Inventor); Swanson, Theodore (Inventor)

1989-01-01

A wick for use in a capillary loop pump heat pipe is disclosed. The wick material is an essentially uniformly porous, permeable, open-cell, silicon dioxide/aluminum oxide inorganic ceramic foam having a silica fiber ratio, by weight, of about 78 to 22, respectively, a density of 6 lbs/cu ft, and an average pore size of less than 5 microns. A representative material having these characteristics is Lockheed Missile and Space Company, Inc.'s HTP 6-22. This material is fully compatible with the freons and anhydrous ammonia and allows for the use of these very efficient working fluids, and others, in capillary loops.

MHD thermal instabilities in cool inhomogeneous atmospheres

NASA Technical Reports Server (NTRS)

Bodo, G.; Ferrari, A.; Massaglia, S.; Rosner, R.

1983-01-01

The formation of a coronal state in a stellar atmosphere is investigated. A numerical code is used to study the effects of atmospheric gradients and finite loop dimension on the scale of unstable perturbations, solving for oscillatory perturbations as eigenfunctions of a boundary value problem. The atmosphere is considered as initially isothermal, with density and pressure having scale heights fixed by the hydrostatic equations. Joule mode instability is found to be an efficient mechanism for current filamentation and subsequent heating in initially cool atmospheres. This instability is mainly effective at the top of magnetic loops and is not suppressed by thermal conduction.

Closed-Loop Neuropharmacology For Epilepsy: Distant Dream Or Future Reality?

PubMed

Aicua-Rapun, Irene; Andre, Pascal; Novy, Jan

2018-03-08

Epilepsy is considered the most frequent severe neurological condition but most patients treated with medication become seizure free. The management of treatment however is highly empirical, mainly relying on observation. A closed-loop therapy for epilepsy would be very valuable for more efficient treatment regimens. Here we discuss monitoring treatment (therapeutic drug monitoring) and the potential developments in this field, as well as providing a review of potential biomarkers that could be used to monitor the disease activity. Finally, we consider the pharmacogenetic input in epilepsy treatment. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Testing flight software on the ground: Introducing the hardware-in-the-loop simulation method to the Alpha Magnetic Spectrometer on the International Space Station

NASA Astrophysics Data System (ADS)

Sun, Wenhao; Cai, Xudong; Meng, Qiao

2016-04-01

Complex automatic protection functions are being added to the onboard software of the Alpha Magnetic Spectrometer. A hardware-in-the-loop simulation method has been introduced to overcome the difficulties of ground testing that are brought by hardware and environmental limitations. We invented a time-saving approach by reusing the flight data as the data source of the simulation system instead of mathematical models. This is easy to implement and it works efficiently. This paper presents the system framework, implementation details and some application examples.

Energy-efficient regenerative liquid desiccant drying process

DOEpatents

Ko, Suk M.; Grodzka, Philomena G.; McCormick, Paul O.

1980-01-01

This invention relates to the use of desiccants in conjunction with an open oop drying cycle and a closed loop drying cycle to reclaim the energy expended in vaporizing moisture in harvested crops. In the closed loop cycle, the drying air is brought into contact with a desiccant after it exits the crop drying bin. Water vapor in the moist air is absorbed by the desiccant, thus reducing the relative humidity of the air. The air is then heated by the used desiccant and returned to the crop bin. During the open loop drying cycle the used desiccant is heated (either fossil or solar energy heat sources may be used) and regenerated at high temperature, driving water vapor from the desiccant. This water vapor is condensed and used to preheat the dilute (wet) desiccant before heat is added from the external source (fossil or solar). The latent heat of vaporization of the moisture removed from the desiccant is reclaimed in this manner. The sensible heat of the regenerated desiccant is utilized in the open loop drying cycle. Also, closed cycle operation implies that no net energy is expended in heating drying air.

A new design approach to innovative spectrometers. Case study: TROPOLITE

NASA Astrophysics Data System (ADS)

Volatier, Jean-Baptiste; Baümer, Stefan; Kruizinga, Bob; Vink, Rob

2014-05-01

Designing a novel optical system is a nested iterative process. The optimization loop, from a starting point to final system is already mostly automated. However this loop is part of a wider loop which is not. This wider loop starts with an optical specification and ends with a manufacturability assessment. When designing a new spectrometer with emphasis on weight and cost, numerous iterations between the optical- and mechanical designer are inevitable. The optical designer must then be able to reliably produce optical designs based on new input gained from multidisciplinary studies. This paper presents a procedure that can automatically generate new starting points based on any kind of input or new constraint that might arise. These starting points can then be handed over to a generic optimization routine to make the design tasks extremely efficient. The optical designer job is then not to design optical systems, but to meta-design a procedure that produces optical systems paving the way for system level optimization. We present here this procedure and its application to the design of TROPOLITE a lightweight push broom imaging spectrometer.

“A New Reconstructive Method after Pancreaticoduodenectomy: the Triple Roux on a “P” Loop. Rationale and Radionuclide Scanning Evaluatlon.”

PubMed Central

Cariati, Erminio

1996-01-01

We propose a method of reconstruction after pancreaticoduodenectomy consisting of a double Roux en Y on the same jejunal loop without interruption of the mesentery and a third anatomical Roux en Y to reconstitute the alimentary tract. The construction of the double Roux en Y draining pancreas and bile ducts separately, requires a linear Stapler 3-4 centimeters from the biliary anastomosis. In this way, by employing the same loop without mesenteric interruption, two functional excluded loops will be ’obtained. The rationale of the suggested model is based on the separation of biliary and pancreatic secretions. This makes it possible to avoid a stagnant cul-de-sac coinciding with the pancreaticojejunal anastomosis and to obtain in the case of leakage, a pure biliary and/or pancreatic fistula as far as is possible. 99mTc HIDA scans demonstrated the efficiency, of the biliopancreatic limbs of the reconstruction, showing normal emptying time for the gastric remnant and the absence of radionuclide stagnation or any alkaline enterogastric reflux. PMID:8809583

Experimental investigation of an alternating evaporator duty refrigerator/freezer

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

Lavanis, M.; Haider, I.; Radermacher, R.

1998-12-31

A bistable solenoid valve has been used to build an alternating evaporator duty (AED) domestic refrigerator/freezer. This refrigerator has two vapor compression refrigeration loops that share a common compressor, condenser, and suction line heat exchanger. Each of the refrigeration loops has an expansion device and evaporator. One evaporator is located in the fresh food compartment and the other is located in the freezer compartment. The bistable solenoid valve directs the flow of the refrigerant through one loop at a time. Only one of the two compartments is cooled at any given time. With this configuration, the food compartment is cooledmore » at a higher evaporator temperature than the freezer. Due to this, the energy efficiency of the refrigerator is improved by 8.5% over a conventional domestic refrigerator/freezer. Also, this cycle allows for completely independent temperature control of the freezer and fresh food compartments. There may be a penalty because this cycle does not allow for both loops to be simultaneously optimized. Isobutane was the only refrigerant used in this investigation.« less

Eigenvalue sensitivity of sampled time systems operating in closed loop

NASA Astrophysics Data System (ADS)

Bernal, Dionisio

2018-05-01

The use of feedback to create closed-loop eigenstructures with high sensitivity has received some attention in the Structural Health Monitoring field. Although practical implementation is necessarily digital, and thus in sampled time, work thus far has center on the continuous time framework, both in design and in checking performance. It is shown in this paper that the performance in discrete time, at typical sampling rates, can differ notably from that anticipated in the continuous time formulation and that discrepancies can be particularly large on the real part of the eigenvalue sensitivities; a consequence being important error on the (linear estimate) of the level of damage at which closed-loop stability is lost. As one anticipates, explicit consideration of the sampling rate poses no special difficulties in the closed-loop eigenstructure design and the relevant expressions are developed in the paper, including a formula for the efficient evaluation of the derivative of the matrix exponential based on the theory of complex perturbations. The paper presents an easily reproduced numerical example showing the level of error that can result when the discrete time implementation of the controller is not considered.

RTEL1 dismantles T loops and counteracts telomeric G4-DNA to maintain telomere integrity.

PubMed

Vannier, Jean-Baptiste; Pavicic-Kaltenbrunner, Visnja; Petalcorin, Mark I R; Ding, Hao; Boulton, Simon J

2012-05-11

T loops and telomeric G-quadruplex (G4) DNA structures pose a potential threat to genome stability and must be dismantled to permit efficient telomere replication. Here we implicate the helicase RTEL1 in the removal of telomeric DNA secondary structures, which is essential for preventing telomere fragility and loss. In the absence of RTEL1, T loops are inappropriately resolved by the SLX4 nuclease complex, resulting in loss of the telomere as a circle. Depleting SLX4 or blocking DNA replication abolished telomere circles (TCs) and rescued telomere loss in RTEL1(-/-) cells but failed to suppress telomere fragility. Conversely, stabilization of telomeric G4-DNA or loss of BLM dramatically enhanced telomere fragility in RTEL1-deficient cells but had no impact on TC formation or telomere loss. We propose that RTEL1 performs two distinct functions at telomeres: it disassembles T loops and also counteracts telomeric G4-DNA structures, which together ensure the dynamics and stability of the telomere. Copyright © 2012 Elsevier Inc. All rights reserved.

Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants.

PubMed

Mohanta, Tapan Kumar; Arora, Pankaj Kumar; Mohanta, Nibedita; Parida, Pratap; Bae, Hanhong

2015-02-06

Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses. The MAPKs are constitute the most downstream module of the three tier MAPK cascade and are phosphorylated by upstream MAP kinase kinases (MAPKK), which are in turn are phosphorylated by MAP kinase kinase kinase (MAPKKK). The MAPKs play pivotal roles in regulation of many cytoplasmic and nuclear substrates, thus regulating several biological processes. A total of 589 MAPKs genes were identified from the genome wide analysis of 40 species. The sequence analysis has revealed the presence of several N- and C-terminal conserved domains. The MAPKs were previously believed to be characterized by the presence of TEY/TDY activation loop motifs. The present study showed that, in addition to presence of activation loop TEY/TDY motifs, MAPKs are also contain MEY, TEM, TQM, TRM, TVY, TSY, TEC and TQY activation loop motifs. Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with Arabidopsis or Oryza MAPKs. We conducted global analysis of the MAPK gene family of plants from lower eukaryotes to higher eukaryotes and analyzed their genomic and evolutionary aspects. Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs. Advance study of newly identified activation loop motifs can provide further information regarding the downstream signaling cascade activated in response to a wide array of stress conditions, as well as plant growth and development.

Comprehensive Aeroelastic Analysis of Helicopter Rotor with Trailing-Edge Flap for Primary Control and Vibration Control

DTIC Science & Technology

2003-01-01

183 3.34 5/rev fixed system hub normal force with 4/rev open loop trailing-edge flap input...184 3.35 5/rev fixed system hub normal force with 5/rev open loop trailing-edge flap input...185 3.36 5/rev fixed system hub normal force with 6/rev open loop trailing-edge flap

Performance Analysis of a De-correlated Modified Code Tracking Loop for Synchronous DS-CDMA System under Multiuser Environment

NASA Astrophysics Data System (ADS)

Wu, Ya-Ting; Wong, Wai-Ki; Leung, Shu-Hung; Zhu, Yue-Sheng

This paper presents the performance analysis of a De-correlated Modified Code Tracking Loop (D-MCTL) for synchronous direct-sequence code-division multiple-access (DS-CDMA) systems under multiuser environment. Previous studies have shown that the imbalance of multiple access interference (MAI) in the time lead and time lag portions of the signal causes tracking bias or instability problem in the traditional correlating tracking loop like delay lock loop (DLL) or modified code tracking loop (MCTL). In this paper, we exploit the de-correlating technique to combat the MAI at the on-time code position of the MCTL. Unlike applying the same technique to DLL which requires an extensive search algorithm to compensate the noise imbalance which may introduce small tracking bias under low signal-to-noise ratio (SNR), the proposed D-MCTL has much lower computational complexity and exhibits zero tracking bias for the whole range of SNR, regardless of the number of interfering users. Furthermore, performance analysis and simulations based on Gold codes show that the proposed scheme has better mean square tracking error, mean-time-to-lose-lock and near-far resistance than the other tracking schemes, including traditional DLL (T-DLL), traditional MCTL (T-MCTL) and modified de-correlated DLL (MD-DLL).

A causal loop analysis of the sustainability of integrated community case management in Rwanda.

PubMed

Sarriot, Eric; Morrow, Melanie; Langston, Anne; Weiss, Jennifer; Landegger, Justine; Tsuma, Laban

2015-04-01

Expansion of community health services in Rwanda has come with the national scale up of integrated Community Case Management (iCCM) of malaria, pneumonia and diarrhea. We used a sustainability assessment framework as part of a large-scale project evaluation to identify factors affecting iCCM sustainability (2011). We then (2012) used causal-loop analysis to identify systems determinants of iCCM sustainability from a national systems perspective. This allows us to develop three high-probability future scenarios putting the achievements of community health at risk, and to recommend mitigating strategies. Our causal loop diagram highlights both balancing and reinforcing loops of cause and effect in the national iCCM system. Financial, political and technical scenarios carry high probability for threatening the sustainability through: (1) reduction in performance-based financing resources, (2) political shocks and erosion of political commitment for community health, and (3) insufficient progress in resolving district health systems--"building blocks"--performance gaps. In a complex health system, the consequences of choices may be delayed and hard to predict precisely. Causal loop analysis and scenario mapping make explicit complex cause-and-effects relationships and high probability risks, which need to be anticipated and mitigated. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Combinatorial invariants and covariants as tools for conical intersections.

PubMed

Ryb, Itai; Baer, Roi

2004-12-01

The combinatorial invariant and covariant are introduced as practical tools for analysis of conical intersections in molecules. The combinatorial invariant is a quantity depending on adiabatic electronic states taken at discrete nuclear configuration points. It is invariant to the phase choice (gauge) of these states. In the limit that the points trace a loop in nuclear configuration space, the value of the invariant approaches the corresponding Berry phase factor. The Berry phase indicates the presence of an odd or even number of conical intersections on surfaces bounded by these loops. Based on the combinatorial invariant, we develop a computationally simple and efficient method for locating conical intersections. The method is robust due to its use of gauge invariant nature. It does not rely on the landscape of intersecting potential energy surfaces nor does it require the computation of nonadiabatic couplings. We generalize the concept to open paths and combinatorial covariants for higher dimensions obtaining a technique for the construction of the gauge-covariant adiabatic-diabatic transformation matrix. This too does not make use of nonadiabatic couplings. The importance of using gauge-covariant expressions is underlined throughout. These techniques can be readily implemented by standard quantum chemistry codes. (c) 2004 American Institute of Physics.

[Principle of LAMP method--a simple and rapid gene amplification method].

PubMed

Ushikubo, Hiroshi

2004-06-01

So far nucleic acid test (NAT) has been employed in various fields, including infectious disease diagnoses. However, due to its complicated procedures and relatively high cost, it has not been widely utilized in many actual diagnostic applications. We have therefore developed a simple and rapid gene amplification technology, Loop-mediated Isothermal Amplification (LAMP) method, which has shown prominent results of surpassing the performance of the conventional gene amplification methods. LAMP method acquires three main features: (1) all reaction can be carried out under isothermal conditions; (2) the amplification efficiency is extremely high and tremendous amount of amplification products can be obtained; and (3) the reaction is highly specific. Furthermore, developed from the standard LAMP method, a rapid LAMP method, by adding in the loop primers, can reduce the amplification time from the previous 1 hour to less than 30 minutes. Enormous amount of white precipitate of magnesium pyrophosphate is produced as a by-product of the amplification, therefore, direct visual detection is possible without using any reaction indicators and detection equipments. We believe LAMP technology, with the integration of these features, can rightly apply to clinical genetic testing, food and environmental analysis, as well as NAT in different fields.

New Technique of AC drive in Tokamak using Permanent Magnets

NASA Astrophysics Data System (ADS)

Matteucci, Jackson; Zolfaghari, Ali

2013-10-01

This study investigates a new technique of capturing the rotational energy of alternating permanent magnets in order to inductively drive an alternating current in tokamak devices. The use of rotational motion bypasses many of the pitfalls seen in typical inductive and non-inductive current drives. Three specific designs are presented and assessed in the following criteria: the profile of the current generated, the RMS loop voltage generated as compared to the RMS power required to maintain it, the system's feasibility from an engineering perspective. All of the analysis has been done under ideal E&M conditions using the Maxwell 3D program. Preliminary results indicate that it is possible to produce an over 99% purely toroidal current with a RMS d Φ/dt of over 150 Tm2/s, driven by 20 MW or less of rotational power. The proposed mechanism demonstrates several key advantages including an efficient mechanical drive system, the generation of pure toroidal currents, and the potential for a quasi-steady state fusion reactor. The following quantities are presented for various driving frequencies and magnet strengths: plasma current generated, loop voltage, torque and power required. This project has been supported by DOE Funding under the SULI program.

Analysis on the Spatial Difference of Bacterial Community Structure in Micro-pressure Air-lift Loop Reactor

NASA Astrophysics Data System (ADS)

Wan, L. G.; Lin, Q.; Bian, D. J.; Ren, Q. K.; Xiao, Y. B.; Lu, W. X.

2018-02-01

In order to reveal the spatial difference of the bacterial community structure in the Micro-pressure Air-lift Loop Reactor, the activated sludge bacterial at five different representative sites in the reactor were studied by denaturing gradient gel electrophoresis (DGGE). The results of DGGE showed that the difference of environmental conditions (such as substrate concentration, dissolved oxygen and PH, etc.) resulted in different diversity and similarity of microbial flora in different spatial locations. The Shannon-Wiener diversity index of the total bacterial samples from five sludge samples varied from 0.92 to 1.28, the biodiversity index was the smallest at point 5, and the biodiversity index was the highest at point 2. The similarity of the flora between the point 2, 3 and 4 was 80% or more, respectively. The similarity of the flora between the point 5 and the other samples was below 70%, and the similarity of point 2 was only 59.2%. Due to the different contribution of different strains to the removal of pollutants, it can give full play to the synergistic effect of bacterial degradation of pollutants, and further improve the efficiency of sewage treatment.

Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression.

PubMed

Aze, Antoine; Sannino, Vincenzo; Soffientini, Paolo; Bachi, Angela; Costanzo, Vincenzo

2016-06-01

Half of the human genome is made up of repetitive DNA. However, mechanisms underlying replication of chromosome regions containing repetitive DNA are poorly understood. We reconstituted replication of defined human chromosome segments using bacterial artificial chromosomes in Xenopus laevis egg extract. Using this approach we characterized the chromatin assembly and replication dynamics of centromeric alpha-satellite DNA. Proteomic analysis of centromeric chromatin revealed replication-dependent enrichment of a network of DNA repair factors including the MSH2-6 complex, which was required for efficient centromeric DNA replication. However, contrary to expectations, the ATR-dependent checkpoint monitoring DNA replication fork arrest could not be activated on highly repetitive DNA due to the inability of the single-stranded DNA binding protein RPA to accumulate on chromatin. Electron microscopy of centromeric DNA and supercoil mapping revealed the presence of topoisomerase I-dependent DNA loops embedded in a protein matrix enriched for SMC2-4 proteins. This arrangement suppressed ATR signalling by preventing RPA hyper-loading, facilitating replication of centromeric DNA. These findings have important implications for our understanding of repetitive DNA metabolism and centromere organization under normal and stressful conditions.

Loop-Mediated Isothermal Amplification of Specific Endoglucanase Gene Sequence for Detection of the Bacterial Wilt Pathogen Ralstonia solanacearum

PubMed Central

Pirc, Manca; Llop, Pablo; Ravnikar, Maja; Dreo, Tanja

2014-01-01

The increased globalization of crops production and processing industries also promotes the side-effects of more rapid and efficient spread of plant pathogens. To prevent the associated economic losses, and particularly those related to bacterial diseases where their management relies on removal of the infected material from production, simple, easy-to-perform, rapid and cost-effective tests are needed. Loop-mediated isothermal amplification (LAMP) assays that target 16S rRNA, fliC and egl genes were compared and evaluated as on-site applications. The assay with the best performance was that targeted to the egl gene, which shows high analytical specificity for diverse strains of the betaproteobacterium Ralstonia solanacearum, including its non-European and non-race 3 biovar 2 strains. The additional melting curve analysis provides confirmation of the test results. According to our extensive assessment, the egl LAMP assay requires minimum sample preparation (a few minutes of boiling) for the identification of pure cultures and ooze from symptomatic material, and it can also be used in a high-throughput format in the laboratory. This provides sensitive and reliable detection of R. solanacearum strains of different phylotypes. PMID:24763488

Estimating power capability of aged lithium-ion batteries in presence of communication delays

NASA Astrophysics Data System (ADS)

Fridholm, Björn; Wik, Torsten; Kuusisto, Hannes; Klintberg, Anton

2018-04-01

Efficient control of electrified powertrains requires accurate estimation of the power capability of the battery for the next few seconds into the future. When implemented in a vehicle, the power estimation is part of a control loop that may contain several networked controllers which introduces time delays that may jeopardize stability. In this article, we present and evaluate an adaptive power estimation method that robustly can handle uncertain health status and time delays. A theoretical analysis shows that stability of the closed loop system can be lost if the resistance of the model is under-estimated. Stability can, however, be restored by filtering the estimated power at the expense of slightly reduced bandwidth of the signal. The adaptive algorithm is experimentally validated in lab tests using an aged lithium-ion cell subject to a high power load profile in temperatures from -20 to +25 °C. The upper voltage limit was set to 4.15 V and the lower voltage limit to 2.6 V, where significant non-linearities are occurring and the validity of the model is limited. After an initial transient when the model parameters are adapted, the prediction accuracy is within ± 2 % of the actually available power.

Thermal Analysis of of Near-Isothermal Compressed Gas Energy Storage System

DOE PAGES

Odukomaiya, Adewale; Abu-Heiba, Ahmad; Gluesenkamp, Kyle R.; ...

2016-01-01

In this paper, alternative system configurations for a novel Ground-Level Integrated Diverse Energy Storage (GLIDES) system, which can store energy via input of electricity and heat and deliver dispatchable electricity, is presented. The proposed system is low-cost and hybridizes compressed air and pumped hydro storage approaches that will allow for the off-peak storage of intermittent renewable energy for use during peak times. This study reveals that implementing direct-contact low grade heat exchange via sprayed falling droplets to cool the gas during charging (compression) and warm the gas during discharging (expansion) can be achieved through a secondary recirculating loop of liquid.more » This study shows that if the recirculating liquid loop is pre-conditioned with waste-heat prior to spraying during gas expansion and considering all the round trip conversion losses from standard 120 V 60 HZ electricity input and output with utilization of low grade heat at 90 C the alternative system design leads to a 16% boost in round trip efficiency of the electricity storage to elec = 82% with an energy density of ED = 3.59 MJ/m3.« less

Widely tunable gas laser for remote sensing

NASA Technical Reports Server (NTRS)

Rothe, D. E.

1988-01-01

An advanced, highly efficient and reliable Rare-Gas Halide laser was developed. It employs the following: (1) novel prepulse techniques and impedance matching for efficient energy transfer; (2) magnetic switches for high reliability; (3) x-ray preionization for discharge uniformity and beam quality; and (4) an integrated gas flow loop for compactness. When operated as a XeCl laser, the unit produces 2 J per pulse with good beam uniformity. Optical pulse duration is 100 ns. Pulse repetition rate was tested up to 25 Hz. Efficiency is 3 percent.

Connected Traveler

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

2016-06-01

The Connected Traveler framework seeks to boost the energy efficiency of personal travel and the overall transportation system by maximizing the accuracy of predicted traveler behavior in response to real-time feedback and incentives. It is anticipated that this approach will establish a feedback loop that 'learns' traveler preferences and customizes incentives to meet or exceed energy efficiency targets by empowering individual travelers with information needed to make energy-efficient choices and reducing the complexity required to validate transportation system energy savings. This handout provides an overview of NREL's Connected Traveler project, including graphics, milestones, and contact information.

Electrochemical studies of aluminium 7075 reinforced with Al2O3/SiCp hybrid composites in acid chloride medium

NASA Astrophysics Data System (ADS)

Ravikumar, M.; Reddappa, H. N.; Suresh, R.

2018-04-01

The study of corrosion rate and the inhibition efficiency of inhibitor for Al 7075 and Al 7075/Al2O3/SiCp corrosion in 1 M hydrochloride acid solution under Laboratory temperature by electrochemical measurements process. The efficiency increases by increasing of wt. % of reinforcement. The premier efficiency 99.1% is observed in the presence of reinforcement. The Electrochemical Impedance spectroscopic (EIS) method exhibit the capacitive loop representing the corrosion effect was controlled by the charge transfer method.

Measuring the magnetic field of a trans-equatorial loop system using coronal seismology

NASA Astrophysics Data System (ADS)

Long, D. M.; Valori, G.; Pérez-Suárez, D.; Morton, R. J.; Vásquez, A. M.

2017-07-01

Context. EIT waves are freely-propagating global pulses in the low corona which are strongly associated with the initial evolution of coronal mass ejections (CMEs). They are thought to be large-amplitude, fast-mode magnetohydrodynamic waves initially driven by the rapid expansion of a CME in the low corona. Aims: An EIT wave was observed on 6 July 2012 to impact an adjacent trans-equatorial loop system which then exhibited a decaying oscillation as it returned to rest. Observations of the loop oscillations were used to estimate the magnetic field strength of the loop system by studying the decaying oscillation of the loop, measuring the propagation of ubiquitous transverse waves in the loop and extrapolating the magnetic field from observed magnetograms. Methods: Observations from the Atmospheric Imaging Assembly onboard the Solar Dynamics Observatory (SDO/AIA) and the Coronal Multi-channel Polarimeter (CoMP) were used to study the event. An Empirical Mode Decomposition analysis was used to characterise the oscillation of the loop system in CoMP Doppler velocity and line width and in AIA intensity. Results: The loop system was shown to oscillate in the 2nd harmonic mode rather than at the fundamental frequency, with the seismological analysis returning an estimated magnetic field strength of ≈ 5.5 ± 1.5 G. This compares to the magnetic field strength estimates of ≈1-9 G and ≈3-9 G found using the measurements of transverse wave propagation and magnetic field extrapolation respectively. A movie associated to Figs. 1 and 2 is available at http://www.aanda.org

Molecular insights into the mechanism of thermal stability of actinomycete mannanase.

PubMed

Kumagai, Yuya; Uraji, Misugi; Wan, Kun; Okuyama, Masayuki; Kimura, Atsuo; Hatanaka, Tadashi

2016-09-01

Streptomyces thermolilacinus mannanase (StMan), which requires Ca(2+) for its enhanced thermal stability and hydrolysis activity, possesses two Ca(2+) -binding sites in loop6 and loop7. We evaluated the function of the Ca(2+) -binding site in loop7 and the hydrogen bond between residues Ser247 in loop6 and Asp279 in loop7. The Ca(2+) -binding in loop7 was involved only in thermal stability. Mutations of Ser247 or Asp279 retained the Ca(2+) -binding ability; however, mutants showed less thermal stability than StMan. Phylogenetic analysis indicated that most glycoside hydrolase family 5 subfamily 8 mannanases could be stabilized by Ca(2+) ; however, the mechanism of StMan thermal stability was found to be quite specific in some actinomycete mannanases. © 2016 Federation of European Biochemical Societies.

Analysis of dead zone sources in a closed-loop fiber optic gyroscope.

PubMed

Chong, Kyoung-Ho; Choi, Woo-Seok; Chong, Kil-To

2016-01-01

Analysis of the dead zone is among the intensive studies in a closed-loop fiber optic gyroscope. In a dead zone, a gyroscope cannot detect any rotation and produces a zero bias. In this study, an analysis of dead zone sources is performed in simulation and experiments. In general, the problem is mainly due to electrical cross coupling and phase modulation drift. Electrical cross coupling is caused by interference between modulation voltage and the photodetector. The cross-coupled signal produces spurious gyro bias and leads to a dead zone if it is larger than the input rate. Phase modulation drift as another dead zone source is due to the electrode contamination, the piezoelectric effect of the LiNbO3 substrate, or to organic fouling. This modulation drift lasts for a short or long period of time like a lead-lag filter response and produces gyro bias error, noise spikes, or dead zone. For a more detailed analysis, the cross-coupling effect and modulation phase drift are modeled as a filter and are simulated in both the open-loop and closed-loop modes. The sources of dead zone are more clearly analyzed in the simulation and experimental results.

Premeasured neochordae loop maker: a new technology in mitral valve repair.

PubMed

Ghavidel, Alireza Alizadeh; Samiei, Niloofar; Javadikasgari, Hoda; Bashirpour, Kamiar

2013-01-01

The exact length of neochordae loops plays the major role in the success of mitral valve repair. The Neochordae Loop Maker is a novel device that models the left ventricular structure in an individual patient. Preoperative transthoracic echocardiography is used to identify the geometry of each papillary muscle and set up the device for the patient. All required neochordae loops are made in the operating room before initiating the cardiopulmonary bypass. In the calibration phase, seven consecutive patients who were candidates for mitral valve replacement underwent transthoracic echocardiography. The device was set up for each patient, and the length of their normal chordae and their respective neochordae was compared by the Bland-Altman analysis. From seven excised mitral valves, 21 chordae were considered normal (gold standard). The length of these gold standards (1.92 ± 0.67 cm) and their respective neochordae (1.93 ± 0.69 cm) showed agreement by the Bland-Altman analysis. The proposed technology showed satisfactory preliminary results in creating the premeasured neochorda loops inasmuch as it reduced the complexity of minimally invasive surgeries.

Damage-tolerant nanotwinned metals with nanovoids under radiation environments

PubMed Central

Chen, Y.; Yu, K Y.; Liu, Y.; Shao, S.; Wang, H.; Kirk, M. A.; Wang, J.; Zhang, X.

2015-01-01

Material performance in extreme radiation environments is central to the design of future nuclear reactors. Radiation induces significant damage in the form of dislocation loops and voids in irradiated materials, and continuous radiation often leads to void growth and subsequent void swelling in metals with low stacking fault energy. Here we show that by using in situ heavy ion irradiation in a transmission electron microscope, pre-introduced nanovoids in nanotwinned Cu efficiently absorb radiation-induced defects accompanied by gradual elimination of nanovoids, enhancing radiation tolerance of Cu. In situ studies and atomistic simulations reveal that such remarkable self-healing capability stems from high density of coherent and incoherent twin boundaries that rapidly capture and transport point defects and dislocation loops to nanovoids, which act as storage bins for interstitial loops. This study describes a counterintuitive yet significant concept: deliberate introduction of nanovoids in conjunction with nanotwins enables unprecedented damage tolerance in metallic materials. PMID:25906997

Damage-tolerant nanotwinned metals with nanovoids under radiation environments.

PubMed

Chen, Y; Yu, K Y; Liu, Y; Shao, S; Wang, H; Kirk, M A; Wang, J; Zhang, X

2015-04-24

Material performance in extreme radiation environments is central to the design of future nuclear reactors. Radiation induces significant damage in the form of dislocation loops and voids in irradiated materials, and continuous radiation often leads to void growth and subsequent void swelling in metals with low stacking fault energy. Here we show that by using in situ heavy ion irradiation in a transmission electron microscope, pre-introduced nanovoids in nanotwinned Cu efficiently absorb radiation-induced defects accompanied by gradual elimination of nanovoids, enhancing radiation tolerance of Cu. In situ studies and atomistic simulations reveal that such remarkable self-healing capability stems from high density of coherent and incoherent twin boundaries that rapidly capture and transport point defects and dislocation loops to nanovoids, which act as storage bins for interstitial loops. This study describes a counterintuitive yet significant concept: deliberate introduction of nanovoids in conjunction with nanotwins enables unprecedented damage tolerance in metallic materials.

Damage-tolerant nanotwinned metals with nanovoids under radiation environments

DOE PAGES

Chen, Y.; Yu, K. Y.; Liu, Y.; ...

2015-04-24

Material performance in extreme radiation environments is central to the design of future nuclear reactors. Radiation induces significant damage in the form of dislocation loops and voids in irradiated materials, and continuous radiation often leads to void growth and subsequent void swelling in metals with low stacking fault energy. Here we show that by using in situ heavy ion irradiation in a transmission electron microscope, pre-introduced nanovoids in nanotwinned Cu efficiently absorb radiation-induced defects accompanied by gradual elimination of nanovoids, enhancing radiation tolerance of Cu. In situ studies and atomistic simulations reveal that such remarkable self-healing capability stems from highmore » density of coherent and incoherent twin boundaries that rapidly capture and transport point defects and dislocation loops to nanovoids, which act as storage bins for interstitial loops. This study describes a counterintuitive yet significant concept: deliberate introduction of nanovoids in conjunction with nanotwins enables unprecedented damage tolerance in metallic materials.« less

The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops.

PubMed

Papp, Diána; Lenti, Katalin; Módos, Dezső; Fazekas, Dávid; Dúl, Zoltán; Türei, Dénes; Földvári-Nagy, László; Nussinov, Ruth; Csermely, Péter; Korcsmáros, Tamás

2012-06-21

NRF2 is a well-known, master transcription factor (TF) of oxidative and xenobiotic stress responses. Recent studies uncovered an even wider regulatory role of NRF2 influencing carcinogenesis, inflammation and neurodegeneration. Prompted by these advances here we present a systems-level resource for NRF2 interactome and regulome that includes 289 protein-protein, 7469 TF-DNA and 85 miRNA interactions. As systems-level examples of NRF2-related signaling we identified regulatory loops of NRF2 interacting proteins (e.g., JNK1 and CBP) and a fine-tuned regulatory system, where 35 TFs regulated by NRF2 influence 63 miRNAs that down-regulate NRF2. The presented network and the uncovered regulatory loops may facilitate the development of efficient, NRF2-based therapeutic agents. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Towards the use of Structural Loop Analysis to Study System Behaviour of Socio-Ecological Systems.

NASA Astrophysics Data System (ADS)

Abram, Joseph; Dyke, James

2016-04-01

Maintaining socio-ecological systems in desirable states is key to developing a growing economy, alleviating poverty and achieving a sustainable future. While the driving forces of an environmental system are often well known, the dynamics impacting these drivers can be hidden within a tangled structure of causal chains and feedback loops. A lack of understanding of a system's dynamic structure and its influence on a system's behaviour can cause unforeseen side-effects during model scenario testing and policy implementation. Structural Loop analysis of socio-ecological system models identifies dominant feedback structures during times of behavioural shift, allowing the user to monitor key influential drivers during model simulation. This work carries out Loop Eigenvalue Elasticity Analysis (LEEA) on three system dynamic models, exploring tipping points in lake systems undergoing eutrophication. The purpose is to explore the potential benefits and limitations of the technique in the field of socio-ecology. The LEEA technique shows promise for socio-ecological systems which undergo regime shifts or express oscillatory trends, but shows limited usefulness with large models. The results of this work highlight changes in feedback loop dominance, years prior to eutrophic tipping events in lake systems. LEEA could be used as an early warning signal to impending system changes, complementary to other known early warning signals. This approach could improve our understanding during critical times of a system's behaviour, changing how we approach model analysis and the way scenario testing and policy implementation are addressed in socio-ecological system models.

Mitochondrial D-loop sequence of domesticated waterfowl in Central Java: goose and muscovy duck

NASA Astrophysics Data System (ADS)

Susanti, R.; Iswari, R. S.

2018-03-01

This study aims to determine the genetic characterization of domesticated waterfowl (goose and Muscovy duck) in Central Java based on a D-loop mtDNA gene. The D-loop gene was amplified using PCR technique by specific primer and sequenced using dideoxy termination method. Multiple alignments of D-loop gene obtained were 710 nucleotides at position 74 to 783 at the 5’ end (for goose) and 712 nucleotides at position 48 to 759 at the 5’ end (for Muscovy duck). The results of the polymorphism analysis on D-loop sequences of muscovy duck produced 3 haplotypes. In the D-loop gene of goose does not show polymorphism, with substitution at G117A. Phylogenetic trees reconstructions of goose and Muscovy duck, which was collected during this research compared with another species from Anser, Chairina and Anas was generated 2 forms of clusters. The first group consists of all kind of Muscovy duck together with Chairina moschata and Anas, while the second group consists of all geese and Anser cygnoides the other. The determination of Muscovy duck and geese identity can be distinguished from the genetic marker information. Based on the phylogenetic analysis, it can be concluded that the Muscovy duck is closely related to Chairina moschata, while geese is closely related to Anser cygnoides.

Genome-Wide Identification of Mitogen-Activated Protein Kinase Gene Family across Fungal Lineage Shows Presence of Novel and Diverse Activation Loop Motifs

PubMed Central

Mohanta, Tapan Kumar; Mohanta, Nibedita; Parida, Pratap; Panda, Sujogya Kumar; Ponpandian, Lakshmi Narayanan; Bae, Hanhong

2016-01-01

The mitogen-activated protein kinase (MAPK) is characterized by the presence of the T-E-Y, T-D-Y, and T-G-Y motifs in its activation loop region and plays a significant role in regulating diverse cellular responses in eukaryotic organisms. Availability of large-scale genome data in the fungal kingdom encouraged us to identify and analyse the fungal MAPK gene family consisting of 173 fungal species. The analysis of the MAPK gene family resulted in the discovery of several novel activation loop motifs (T-T-Y, T-I-Y, T-N-Y, T-H-Y, T-S-Y, K-G-Y, T-Q-Y, S-E-Y and S-D-Y) in fungal MAPKs. The phylogenetic analysis suggests that fungal MAPKs are non-polymorphic, had evolved from their common ancestors around 1500 million years ago, and are distantly related to plant MAPKs. We are the first to report the presence of nine novel activation loop motifs in fungal MAPKs. The specificity of the activation loop motif plays a significant role in controlling different growth and stress related pathways in fungi. Hence, the presences of these nine novel activation loop motifs in fungi are of special interest. PMID:26918378

Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase.

PubMed

Kellici, Tahsin F; Mavromoustakos, Thomas; Jendrossek, Dieter; Papageorgiou, Anastassios C

2017-07-01

An open and a closed conformation of a surface loop in PhaZ7 extracellular poly(3-hydroxybutyrate) depolymerase were identified in two high-resolution crystal structures of a PhaZ7 Y105E mutant. Molecular dynamics (MD) simulations revealed high root mean square fluctuations (RMSF) of the 281-295 loop, in particular at residue Asp289 (RMSF 7.62 Å). Covalent docking between a 3-hydroxybutyric acid trimer and the catalytic residue Ser136 showed that the binding energy of the substrate is significantly more favorable in the open loop conformation compared to that in the closed loop conformation. MD simulations with the substrate covalently bound depicted 1 Å RMSF higher values for the residues 281-295 in comparison to the apo (substrate-free) form. In addition, the presence of the substrate in the active site enhanced the ability of the loop to adopt a closed form. Taken together, the analysis suggests that the flexible loop 281-295 of PhaZ7 depolymerase can act as a lid domain to control substrate access to the active site of the enzyme. Proteins 2017; 85:1351-1361. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.