Improving Simulated Annealing by Replacing Its Variables with Game-Theoretic Utility Maximizers

NASA Technical Reports Server (NTRS)

Wolpert, David H.; Bandari, Esfandiar; Tumer, Kagan

2001-01-01

The game-theory field of Collective INtelligence (COIN) concerns the design of computer-based players engaged in a non-cooperative game so that as those players pursue their self-interests, a pre-specified global goal for the collective computational system is achieved as a side-effect. Previous implementations of COIN algorithms have outperformed conventional techniques by up to several orders of magnitude, on domains ranging from telecommunications control to optimization in congestion problems. Recent mathematical developments have revealed that these previously developed algorithms were based on only two of the three factors determining performance. Consideration of only the third factor would instead lead to conventional optimization techniques like simulated annealing that have little to do with non-cooperative games. In this paper we present an algorithm based on all three terms at once. This algorithm can be viewed as a way to modify simulated annealing by recasting it as a non-cooperative game, with each variable replaced by a player. This recasting allows us to leverage the intelligent behavior of the individual players to substantially improve the exploration step of the simulated annealing. Experiments are presented demonstrating that this recasting significantly improves simulated annealing for a model of an economic process run over an underlying small-worlds topology. Furthermore, these experiments reveal novel small-worlds phenomena, and highlight the shortcomings of conventional mechanism design in bounded rationality domains.

Modeling Effects of Annealing on Coal Char Reactivity to O 2 and CO 2 , Based on Preparation Conditions

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

Holland, Troy; Bhat, Sham; Marcy, Peter

Oxy-fired coal combustion is a promising potential carbon capture technology. Predictive computational fluid dynamics (CFD) simulations are valuable tools in evaluating and deploying oxyfuel and other carbon capture technologies, either as retrofit technologies or for new construction. However, accurate predictive combustor simulations require physically realistic submodels with low computational requirements. A recent sensitivity analysis of a detailed char conversion model (Char Conversion Kinetics (CCK)) found thermal annealing to be an extremely sensitive submodel. In the present work, further analysis of the previous annealing model revealed significant disagreement with numerous datasets from experiments performed after that annealing model was developed. Themore » annealing model was accordingly extended to reflect experimentally observed reactivity loss, because of the thermal annealing of a variety of coals under diverse char preparation conditions. The model extension was informed by a Bayesian calibration analysis. In addition, since oxyfuel conditions include extraordinarily high levels of CO 2, the development of a first-ever CO 2 reactivity loss model due to annealing is presented.« less

Modeling Effects of Annealing on Coal Char Reactivity to O 2 and CO 2 , Based on Preparation Conditions

DOE PAGES

Holland, Troy; Bhat, Sham; Marcy, Peter; ...

2017-08-25

Oxy-fired coal combustion is a promising potential carbon capture technology. Predictive computational fluid dynamics (CFD) simulations are valuable tools in evaluating and deploying oxyfuel and other carbon capture technologies, either as retrofit technologies or for new construction. However, accurate predictive combustor simulations require physically realistic submodels with low computational requirements. A recent sensitivity analysis of a detailed char conversion model (Char Conversion Kinetics (CCK)) found thermal annealing to be an extremely sensitive submodel. In the present work, further analysis of the previous annealing model revealed significant disagreement with numerous datasets from experiments performed after that annealing model was developed. Themore » annealing model was accordingly extended to reflect experimentally observed reactivity loss, because of the thermal annealing of a variety of coals under diverse char preparation conditions. The model extension was informed by a Bayesian calibration analysis. In addition, since oxyfuel conditions include extraordinarily high levels of CO 2, the development of a first-ever CO 2 reactivity loss model due to annealing is presented.« less

Exploring first-order phase transitions with population annealing

NASA Astrophysics Data System (ADS)

Barash, Lev Yu.; Weigel, Martin; Shchur, Lev N.; Janke, Wolfhard

2017-03-01

Population annealing is a hybrid of sequential and Markov chain Monte Carlo methods geared towards the efficient parallel simulation of systems with complex free-energy landscapes. Systems with first-order phase transitions are among the problems in computational physics that are difficult to tackle with standard methods such as local-update simulations in the canonical ensemble, for example with the Metropolis algorithm. It is hence interesting to see whether such transitions can be more easily studied using population annealing. We report here our preliminary observations from population annealing runs for the two-dimensional Potts model with q > 4, where it undergoes a first-order transition.

Quantum annealing versus classical machine learning applied to a simplified computational biology problem

NASA Astrophysics Data System (ADS)

Li, Richard Y.; Di Felice, Rosa; Rohs, Remo; Lidar, Daniel A.

2018-03-01

Transcription factors regulate gene expression, but how these proteins recognize and specifically bind to their DNA targets is still debated. Machine learning models are effective means to reveal interaction mechanisms. Here we studied the ability of a quantum machine learning approach to classify and rank binding affinities. Using simplified data sets of a small number of DNA sequences derived from actual binding affinity experiments, we trained a commercially available quantum annealer to classify and rank transcription factor binding. The results were compared to state-of-the-art classical approaches for the same simplified data sets, including simulated annealing, simulated quantum annealing, multiple linear regression, LASSO, and extreme gradient boosting. Despite technological limitations, we find a slight advantage in classification performance and nearly equal ranking performance using the quantum annealer for these fairly small training data sets. Thus, we propose that quantum annealing might be an effective method to implement machine learning for certain computational biology problems.

Simulated parallel annealing within a neighborhood for optimization of biomechanical systems.

PubMed

Higginson, J S; Neptune, R R; Anderson, F C

2005-09-01

Optimization problems for biomechanical systems have become extremely complex. Simulated annealing (SA) algorithms have performed well in a variety of test problems and biomechanical applications; however, despite advances in computer speed, convergence to optimal solutions for systems of even moderate complexity has remained prohibitive. The objective of this study was to develop a portable parallel version of a SA algorithm for solving optimization problems in biomechanics. The algorithm for simulated parallel annealing within a neighborhood (SPAN) was designed to minimize interprocessor communication time and closely retain the heuristics of the serial SA algorithm. The computational speed of the SPAN algorithm scaled linearly with the number of processors on different computer platforms for a simple quadratic test problem and for a more complex forward dynamic simulation of human pedaling.

High-temperature annealing of graphite: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Petersen, Andrew; Gillette, Victor

2018-05-01

A modified AIREBO potential was developed to simulate the effects of thermal annealing on the structure and physical properties of damaged graphite. AIREBO parameter modifications were made to reproduce Density Functional Theory interstitial results. These changes to the potential resulted in high-temperature annealing of the model, as measured by stored-energy reduction. These results show some resemblance to experimental high-temperature annealing results, and show promise that annealing effects in graphite are accessible with molecular dynamics and reactive potentials.

A theoretical comparison of evolutionary algorithms and simulated annealing

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

Hart, W.E.

1995-08-28

This paper theoretically compares the performance of simulated annealing and evolutionary algorithms. Our main result is that under mild conditions a wide variety of evolutionary algorithms can be shown to have greater performance than simulated annealing after a sufficiently large number of function evaluations. This class of EAs includes variants of evolutionary strategie and evolutionary programming, the canonical genetic algorithm, as well as a variety of genetic algorithms that have been applied to combinatorial optimization problems. The proof of this result is based on a performance analysis of a very general class of stochastic optimization algorithms, which has implications formore » the performance of a variety of other optimization algorithm.« less

Accessing Forbidden Glass Regimes through High-Pressure Sub-Tg Annealing

PubMed Central

Svenson, Mouritz N.; Mauro, John C.; Rzoska, Sylwester J.; Bockowski, Michal; Smedskjaer, Morten M.

2017-01-01

Density and hardness of glasses are known to increase upon both compression at the glass transition temperature (Tg) and ambient pressure sub-Tg annealing. However, a serial combination of the two methods does not result in higher density and hardness, since the effect of compression is countered by subsequent annealing and vice versa. In this study, we circumvent this by introducing a novel treatment protocol that enables the preparation of high-density, high-hardness bulk aluminosilicate glasses. This is done by first compressing a sodium-magnesium aluminosilicate glass at 1 GPa at Tg, followed by sub-Tg annealing in-situ at 1 GPa. Through density, hardness, and heat capacity measurements, we demonstrate that the effects of hot compression and sub-Tg annealing can be combined to access a “forbidden glass” regime that is inaccessible through thermal history or pressure history variation alone. We also study the relaxation behavior of the densified samples during subsequent ambient pressure sub-Tg annealing. Density and hardness are found to relax and approach their ambient condition values upon annealing, but the difference in relaxation time of density and hardness, which is usually observed for hot compressed glasses, vanishes for samples previously subjected to high-pressure sub-Tg annealing. This confirms the unique configurational state of these glasses. PMID:28418017

An Improved Simulated Annealing Technique for Enhanced Mobility in Smart Cities.

PubMed

Amer, Hayder; Salman, Naveed; Hawes, Matthew; Chaqfeh, Moumena; Mihaylova, Lyudmila; Mayfield, Martin

2016-06-30

Vehicular traffic congestion is a significant problem that arises in many cities. This is due to the increasing number of vehicles that are driving on city roads of limited capacity. The vehicular congestion significantly impacts travel distance, travel time, fuel consumption and air pollution. Avoidance of traffic congestion and providing drivers with optimal paths are not trivial tasks. The key contribution of this work consists of the developed approach for dynamic calculation of optimal traffic routes. Two attributes (the average travel speed of the traffic and the roads' length) are utilized by the proposed method to find the optimal paths. The average travel speed values can be obtained from the sensors deployed in smart cities and communicated to vehicles via the Internet of Vehicles and roadside communication units. The performance of the proposed algorithm is compared to three other algorithms: the simulated annealing weighted sum, the simulated annealing technique for order preference by similarity to the ideal solution and the Dijkstra algorithm. The weighted sum and technique for order preference by similarity to the ideal solution methods are used to formulate different attributes in the simulated annealing cost function. According to the Sheffield scenario, simulation results show that the improved simulated annealing technique for order preference by similarity to the ideal solution method improves the traffic performance in the presence of congestion by an overall average of 19.22% in terms of travel time, fuel consumption and CO₂ emissions as compared to other algorithms; also, similar performance patterns were achieved for the Birmingham test scenario.

An Improved Simulated Annealing Technique for Enhanced Mobility in Smart Cities

PubMed Central

Amer, Hayder; Salman, Naveed; Hawes, Matthew; Chaqfeh, Moumena; Mihaylova, Lyudmila; Mayfield, Martin

2016-01-01

Vehicular traffic congestion is a significant problem that arises in many cities. This is due to the increasing number of vehicles that are driving on city roads of limited capacity. The vehicular congestion significantly impacts travel distance, travel time, fuel consumption and air pollution. Avoidance of traffic congestion and providing drivers with optimal paths are not trivial tasks. The key contribution of this work consists of the developed approach for dynamic calculation of optimal traffic routes. Two attributes (the average travel speed of the traffic and the roads’ length) are utilized by the proposed method to find the optimal paths. The average travel speed values can be obtained from the sensors deployed in smart cities and communicated to vehicles via the Internet of Vehicles and roadside communication units. The performance of the proposed algorithm is compared to three other algorithms: the simulated annealing weighted sum, the simulated annealing technique for order preference by similarity to the ideal solution and the Dijkstra algorithm. The weighted sum and technique for order preference by similarity to the ideal solution methods are used to formulate different attributes in the simulated annealing cost function. According to the Sheffield scenario, simulation results show that the improved simulated annealing technique for order preference by similarity to the ideal solution method improves the traffic performance in the presence of congestion by an overall average of 19.22% in terms of travel time, fuel consumption and CO2 emissions as compared to other algorithms; also, similar performance patterns were achieved for the Birmingham test scenario. PMID:27376289

Computer-Assisted Scheduling of Army Unit Training: An Application of Simulated Annealing.

ERIC Educational Resources Information Center

Hart, Roland J.; Goehring, Dwight J.

This report of an ongoing research project intended to provide computer assistance to Army units for the scheduling of training focuses on the feasibility of simulated annealing, a heuristic approach for solving scheduling problems. Following an executive summary and brief introduction, the document is divided into three sections. First, the Army…

Re'class'ification of 'quant'ified classical simulated annealing

NASA Astrophysics Data System (ADS)

Tanaka, Toshiyuki

2009-12-01

We discuss a classical reinterpretation of quantum-mechanics-based analysis of classical Markov chains with detailed balance, that is based on the quantum-classical correspondence. The classical reinterpretation is then used to demonstrate that it successfully reproduces a sufficient condition for cooling schedule in classical simulated annealing, which has the inverse-logarithmic scaling.

An Improved SoC Test Scheduling Method Based on Simulated Annealing Algorithm

NASA Astrophysics Data System (ADS)

Zheng, Jingjing; Shen, Zhihang; Gao, Huaien; Chen, Bianna; Zheng, Weida; Xiong, Xiaoming

2017-02-01

In this paper, we propose an improved SoC test scheduling method based on simulated annealing algorithm (SA). It is our first to disorganize IP core assignment for each TAM to produce a new solution for SA, allocate TAM width for each TAM using greedy algorithm and calculate corresponding testing time. And accepting the core assignment according to the principle of simulated annealing algorithm and finally attain the optimum solution. Simultaneously, we run the test scheduling experiment with the international reference circuits provided by International Test Conference 2002(ITC’02) and the result shows that our algorithm is superior to the conventional integer linear programming algorithm (ILP), simulated annealing algorithm (SA) and genetic algorithm(GA). When TAM width reaches to 48,56 and 64, the testing time based on our algorithm is lesser than the classic methods and the optimization rates are 30.74%, 3.32%, 16.13% respectively. Moreover, the testing time based on our algorithm is very close to that of improved genetic algorithm (IGA), which is state-of-the-art at present.

Integration of electromagnetic induction sensor data in soil sampling scheme optimization using simulated annealing.

PubMed

Barca, E; Castrignanò, A; Buttafuoco, G; De Benedetto, D; Passarella, G

2015-07-01

Soil survey is generally time-consuming, labor-intensive, and costly. Optimization of sampling scheme allows one to reduce the number of sampling points without decreasing or even increasing the accuracy of investigated attribute. Maps of bulk soil electrical conductivity (EC a ) recorded with electromagnetic induction (EMI) sensors could be effectively used to direct soil sampling design for assessing spatial variability of soil moisture. A protocol, using a field-scale bulk EC a survey, has been applied in an agricultural field in Apulia region (southeastern Italy). Spatial simulated annealing was used as a method to optimize spatial soil sampling scheme taking into account sampling constraints, field boundaries, and preliminary observations. Three optimization criteria were used. the first criterion (minimization of mean of the shortest distances, MMSD) optimizes the spreading of the point observations over the entire field by minimizing the expectation of the distance between an arbitrarily chosen point and its nearest observation; the second criterion (minimization of weighted mean of the shortest distances, MWMSD) is a weighted version of the MMSD, which uses the digital gradient of the grid EC a data as weighting function; and the third criterion (mean of average ordinary kriging variance, MAOKV) minimizes mean kriging estimation variance of the target variable. The last criterion utilizes the variogram model of soil water content estimated in a previous trial. The procedures, or a combination of them, were tested and compared in a real case. Simulated annealing was implemented by the software MSANOS able to define or redesign any sampling scheme by increasing or decreasing the original sampling locations. The output consists of the computed sampling scheme, the convergence time, and the cooling law, which can be an invaluable support to the process of sampling design. The proposed approach has found the optimal solution in a reasonable computation time. The use of bulk EC a gradient as an exhaustive variable, known at any node of an interpolation grid, has allowed the optimization of the sampling scheme, distinguishing among areas with different priority levels.

Effect of excimer laser annealing on a-InGaZnO thin-film transistors passivated by solution-processed hybrid passivation layers

NASA Astrophysics Data System (ADS)

Bermundo, Juan Paolo; Ishikawa, Yasuaki; Fujii, Mami N.; Nonaka, Toshiaki; Ishihara, Ryoichi; Ikenoue, Hiroshi; Uraoka, Yukiharu

2016-01-01

We demonstrate the use of excimer laser annealing (ELA) as a low temperature annealing alternative to anneal amorphous InGaZnO (a-IGZO) thin-film transistors (TFTs) passivated by a solution-processed hybrid passivation layer. Usually, a-IGZO is annealed using thermal annealing at high temperatures of up to 400 °C. As an alternative to high temperature thermal annealing, two types of ELA, XeCl (308 nm) and KrF (248 nm) ELA, are introduced. Both ELA types enhanced the electrical characteristics of a-IGZO TFTs leading to a mobility improvement of ~13 cm2 V-1 s-1 and small threshold voltage which varied from ~0-3 V. Furthermore, two-dimensional heat simulation using COMSOL Multiphysics was used to identify possible degradation sites, analyse laser heat localization, and confirm that the substrate temperature is below 50 °C. The two-dimensional heat simulation showed that the substrate temperature remained at very low temperatures, less than 30 °C, during ELA. This implies that any flexible material can be used as the substrate. These results demonstrate the large potential of ELA as a low temperature annealing alternative for already-passivated a-IGZO TFTs.

Temperature Scaling Law for Quantum Annealing Optimizers.

PubMed

Albash, Tameem; Martin-Mayor, Victor; Hen, Itay

2017-09-15

Physical implementations of quantum annealing unavoidably operate at finite temperatures. We point to a fundamental limitation of fixed finite temperature quantum annealers that prevents them from functioning as competitive scalable optimizers and show that to serve as optimizers annealer temperatures must be appropriately scaled down with problem size. We derive a temperature scaling law dictating that temperature must drop at the very least in a logarithmic manner but also possibly as a power law with problem size. We corroborate our results by experiment and simulations and discuss the implications of these to practical annealers.

Population annealing with weighted averages: A Monte Carlo method for rough free-energy landscapes

NASA Astrophysics Data System (ADS)

Machta, J.

2010-08-01

The population annealing algorithm introduced by Hukushima and Iba is described. Population annealing combines simulated annealing and Boltzmann weighted differential reproduction within a population of replicas to sample equilibrium states. Population annealing gives direct access to the free energy. It is shown that unbiased measurements of observables can be obtained by weighted averages over many runs with weight factors related to the free-energy estimate from the run. Population annealing is well suited to parallelization and may be a useful alternative to parallel tempering for systems with rough free-energy landscapes such as spin glasses. The method is demonstrated for spin glasses.

Displacement cascades and defect annealing in tungsten, Part III: The sensitivity of cascade annealing in tungsten to the values of kinetic parameters

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

Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

2015-07-01

Object kinetic Monte Carlo (OKMC) simulations have been performed to investigate various aspects of cascade aging in bulk tungsten and to determine the sensitivity of the results to the kinetic parameters. The primary focus is on how the kinetic parameters affect the initial recombination of defects in the first few ns of a simulation. The simulations were carried out using the object kinetic Monte Carlo (OKMC) code KSOME (kinetic simulations of microstructure evolution), using a database of cascades obtained from results of molecular dynamics (MD) simulations at various primary knock-on atom (PKA) energies and directions at temperatures of 300, 1025more » and 2050 K. The OKMC model was parameterized using defect migration barriers and binding energies from ab initio calculations. Results indicate that, due to the disparate mobilities of SIA and vacancy clusters in tungsten, annealing is dominated by SIA migration even at temperatures as high as 2050 K. For 100 keV cascades initiated at 300 K recombination is dominated by annihilation of large defect clusters. But for all other PKA energies and temperatures most of the recombination is due to the migration and rotation of small SIA clusters, while all the large SIA clusters escape the cubic simulation cell. The inverse U-shape behavior exhibited by the annealing efficiency as a function of temperature curve, especially for cascades of large PKA energies, is due to asymmetry in SIA and vacancy clustering assisted by the large difference in mobilities of SIAs and vacancies. This annealing behavior is unaffected by the dimensionality of SIA migration persists over a broad range of relative mobilities of SIAs and vacancies.« less

Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations

PubMed Central

Bell, David R.; Cheng, Sara Y.; Salazar, Heber; Ren, Pengyu

2017-01-01

We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R2 = 0.93). Using RACER, we identified hydrogen-bonding (or base pairing), base stacking, and electrostatic interactions as essential driving forces for RNA folding. Also, we found that separating pairing vs. stacking interactions allowed RACER to distinguish folded vs. unfolded states. In RACER, base pairing and stacking interactions each provide an approximate stability of 3–4 kcal/mol for an A-form helix. RACER was developed based on PDB structural statistics and experimental thermodynamic data. In contrast with previous work, RACER implements a novel effective vdW potential energy function, which led us to re-parameterize hydrogen bond and electrostatic potential energy functions. Further, RACER is validated and optimized using a simulated annealing protocol to generate potential energy vs. RMSD landscapes. Finally, RACER is tested using extensive equilibrium pulling simulations (0.86 ms total) on eleven RNA sequences (hairpins and duplexes). PMID:28393861

Medical image diagnoses by artificial neural networks with image correlation, wavelet transform, simulated annealing

NASA Astrophysics Data System (ADS)

Szu, Harold H.

1993-09-01

Classical artificial neural networks (ANN) and neurocomputing are reviewed for implementing a real time medical image diagnosis. An algorithm known as the self-reference matched filter that emulates the spatio-temporal integration ability of the human visual system might be utilized for multi-frame processing of medical imaging data. A Cauchy machine, implementing a fast simulated annealing schedule, can determine the degree of abnormality by the degree of orthogonality between the patient imagery and the class of features of healthy persons. An automatic inspection process based on multiple modality image sequences is simulated by incorporating the following new developments: (1) 1-D space-filling Peano curves to preserve the 2-D neighborhood pixels' relationship; (2) fast simulated Cauchy annealing for the global optimization of self-feature extraction; and (3) a mini-max energy function for the intra-inter cluster-segregation respectively useful for top-down ANN designs.

Comparative study of post-growth annealing of Cu(hfac)2, Co2(CO)8 and Me2Au(acac) metal precursors deposited by FEBID.

PubMed

Puydinger Dos Santos, Marcos Vinicius; Szkudlarek, Aleksandra; Rydosz, Artur; Guerra-Nuñez, Carlos; Béron, Fanny; Pirota, Kleber Roberto; Moshkalev, Stanislav; Diniz, José Alexandre; Utke, Ivo

2018-01-01

Non-noble metals, such as Cu and Co, as well as noble metals, such as Au, can be used in a number modern technological applications, which include advanced scanning-probe systems, magnetic memory and storage, ferroelectric tunnel junction memristors, metal interconnects for high performance integrated circuits in microelectronics and nano-optics applications, especially in the areas of plasmonics and metamaterials. Focused-electron-beam-induced deposition (FEBID) is a maskless direct-write tool capable of defining 3-dimensional metal deposits at nanometre scale for above applications. However, codeposition of organic ligands when using organometallic precursors is a typical problem that limits FEBID of pure metal nanostructures. In this work, we present a comparative study using a post-growth annealing protocol at 100, 200, and 300 °C under high vacuum on deposits obtained from Co 2 (CO) 8 , Cu(II)(hfac) 2 , and Me 2 Au(acac) to study improvements on composition and electrical conductivity. Although the as-deposited material was similar for all precursors, metal grains embedded in a carbonaceous matrix, the post-growth annealing results differed. Cu-containing deposits showed the formation of pure Cu nanocrystals at the outer surface of the initial deposit for temperatures above 100 °C, due to the migration of Cu atoms from the carbonaceous matrix containing carbon, oxygen, and fluorine atoms. The average size of the Cu crystals doubles between 100 and 300 °C of annealing temperature, while the composition remains constant. In contrast, for Co-containing deposits oxygen release was observed upon annealing, while the carbon content remained approximately constant; the cobalt atoms coalesced to form a metallic film. The as-deposited Au-containing material shows subnanometric grains that coalesce at 100 °C, maintaining the same average size at annealing temperatures up to 300 °C. Raman analysis suggests that the amorphous carbonaceous matrix of the as-written Co, Cu and Au deposits turned into nanocrystalline graphite with comparable crystal sizes of 12-14 nm at 300 °C annealing temperature. However, we observed a more effective formation of graphite clusters in Co- than in Cu- and Au-containing deposits. The graphitisation has a minor influence on the electrical conductivity improvements of Co-C deposits, which is attributed to the high as-deposited Co content and the related metal grain percolation. On the contrary, electrical conductivity improvements by factors of 30 and 12 for, respectively, Cu-C and Au-C deposits with low metal content are mainly attributed to the graphitisation. This relatively simple vacuum-based post-growth annealing protocol may be useful for other precursors as it proved to be efficient in reliably tuning the electrical properties of as-deposited FEBID materials. Finally, a H 2 -assisted gold purification protocol is demonstrated at temperatures around 300 °C by fully removing the carbon matrix and drastically reducing the electrical resistance of the deposit.

On the effects of thermal history on the development and relaxation of thermo-mechanical stress in cryopreservation

NASA Astrophysics Data System (ADS)

Eisenberg, David P.; Steif, Paul S.; Rabin, Yoed

2014-11-01

This study investigates the effects of the thermal protocol on the development and relaxation of thermo-mechanical stress in cryopreservation by means of glass formation, also known as vitrification. The cryopreserved medium is modeled as a homogeneous viscoelastic domain, constrained within either a stiff cylindrical container or a highly compliant bag. Annealing effects during the cooling phase of the cryopreservation protocol are analyzed. Results demonstrate that an intermediate temperature-hold period can significantly reduce the maximum tensile stress, thereby decreasing the potential for structural damage. It is also demonstrated that annealing at temperatures close to glass transition significantly weakens the dependency of thermo-mechanical stress on the cooling rate. Furthermore, a slower initial rewarming rate after cryogenic storage may drastically reduce the maximum tensile stress in the material, which supports previous experimental observations on the likelihood of fracture at this stage. This study discusses the dependency of the various stress components on the storage temperature. Finally, it is demonstrated that the stiffness of the container wall can affect the location of maximum stress, with implications on the development of cryopreservation protocols.

Quantum annealing of the traveling-salesman problem.

PubMed

Martonák, Roman; Santoro, Giuseppe E; Tosatti, Erio

2004-11-01

We propose a path-integral Monte Carlo quantum annealing scheme for the symmetric traveling-salesman problem, based on a highly constrained Ising-like representation, and we compare its performance against standard thermal simulated annealing. The Monte Carlo moves implemented are standard, and consist in restructuring a tour by exchanging two links (two-opt moves). The quantum annealing scheme, even with a drastically simple form of kinetic energy, appears definitely superior to the classical one, when tested on a 1002-city instance of the standard TSPLIB.

Solving Set Cover with Pairs Problem using Quantum Annealing

NASA Astrophysics Data System (ADS)

Cao, Yudong; Jiang, Shuxian; Perouli, Debbie; Kais, Sabre

2016-09-01

Here we consider using quantum annealing to solve Set Cover with Pairs (SCP), an NP-hard combinatorial optimization problem that plays an important role in networking, computational biology, and biochemistry. We show an explicit construction of Ising Hamiltonians whose ground states encode the solution of SCP instances. We numerically simulate the time-dependent Schrödinger equation in order to test the performance of quantum annealing for random instances and compare with that of simulated annealing. We also discuss explicit embedding strategies for realizing our Hamiltonian construction on the D-wave type restricted Ising Hamiltonian based on Chimera graphs. Our embedding on the Chimera graph preserves the structure of the original SCP instance and in particular, the embedding for general complete bipartite graphs and logical disjunctions may be of broader use than that the specific problem we deal with.

Parallel computing of physical maps--a comparative study in SIMD and MIMD parallelism.

PubMed

Bhandarkar, S M; Chirravuri, S; Arnold, J

1996-01-01

Ordering clones from a genomic library into physical maps of whole chromosomes presents a central computational problem in genetics. Chromosome reconstruction via clone ordering is usually isomorphic to the NP-complete Optimal Linear Arrangement problem. Parallel SIMD and MIMD algorithms for simulated annealing based on Markov chain distribution are proposed and applied to the problem of chromosome reconstruction via clone ordering. Perturbation methods and problem-specific annealing heuristics are proposed and described. The SIMD algorithms are implemented on a 2048 processor MasPar MP-2 system which is an SIMD 2-D toroidal mesh architecture whereas the MIMD algorithms are implemented on an 8 processor Intel iPSC/860 which is an MIMD hypercube architecture. A comparative analysis of the various SIMD and MIMD algorithms is presented in which the convergence, speedup, and scalability characteristics of the various algorithms are analyzed and discussed. On a fine-grained, massively parallel SIMD architecture with a low synchronization overhead such as the MasPar MP-2, a parallel simulated annealing algorithm based on multiple periodically interacting searches performs the best. For a coarse-grained MIMD architecture with high synchronization overhead such as the Intel iPSC/860, a parallel simulated annealing algorithm based on multiple independent searches yields the best results. In either case, distribution of clonal data across multiple processors is shown to exacerbate the tendency of the parallel simulated annealing algorithm to get trapped in a local optimum.

Accelerated In Vitro Degradation of Optically Clear Low β-Sheet Silk Films by Enzyme-Mediated Pretreatment

PubMed Central

Shang, Ke; Rnjak-Kovacina, Jelena; Lin, Yinan; Hayden, Rebecca S.; Tao, Hu; Kaplan, David L.

2013-01-01

Purpose: To design patterned, transparent silk films with fast degradation rates for the purpose of tissue engineering corneal stroma. Methods: β-sheet (crystalline) content of silk films was decreased significantly by using a short water annealing time. Additionally, a protocol combining short water annealing time with enzymatic pretreatment of silk films with protease XIV was developed. Results: Low β-sheet content (17%–18%) and enzymatic pretreatment provided film stability in aqueous environments and accelerated degradation of the silk films in the presence of human corneal fibroblasts in vitro. The results demonstrate a direct relationship between reduced β-sheet content and enzymatic pretreatment, and overall degradation rate of the protein films. Conclusions: The novel protocol developed here provides new approaches to modulate the regeneration rate of silk biomaterials for corneal tissue regeneration needs. Translational Relevance: Patterned silk protein films possess desirable characteristics for corneal tissue engineering, including optical transparency, biocompatibility, cell alignment, and tunable mechanical properties, but current fabrication protocols do not provide adequate degradation rates to match the regeneration properties of the human cornea. This novel processing protocol makes silk films more suitable for the construction of human corneal stroma tissue and a promising way to tune silk film degradation properties to match corneal tissue regeneration. PMID:24049717

Accelerated in vitro Degradation of Optically Clear Low β-sheet Silk Films by Enzyme-Mediated Pretreatment

PubMed Central

Shang, Ke; Rnjak-Kovacina, Jelena; Lin, Yinan; Hayden, Rebecca S.; Hu, Tao; Kaplan, David L.

2013-01-01

Purpose To design patterned, transparent silk films with fast degradation rates for the purpose of tissue engineering corneal stroma, Methods β-sheet (crystalline) content of silk films was decreased significantly by using a short water annealing time. Additionally, a protocol combining short water annealing time with enzymatic pretreatment of silk films with protease XIV was developed. Results Low β-sheet content (17–18%) and enzymatic pre-treatment provided film stability in aqueous environments and accelerated degradation of the silk films in the presence of human corneal fibroblasts in vitro. The results demonstrate a direct relationship between reduced β-sheet content and enzymatic pre-treatment and overall degradation rate of the protein films. Conclusions The novel protocol developed here provides new approaches to modulate the regeneration rate of silk biomaterials for corneal tissue regeneration needs. Translational relevance Patterned silk protein films possess desirable characteristics for corneal tissue engineering, including optical transparency, biocompatibility, cell alignment and tunable mechanical properties, but current fabrication protocols do not provide adequate degradation rates to match the regeneration properties of the human cornea. This novel processing protocol makes silk films more suitable for the construction of human corneal stroma tissue and a promising way to tune silk film degradation properties to match corneal tissue regeneration. PMID:23579493

FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A.

PubMed

Michino, Mayako; Chen, Jianhan; Stevens, Raymond C; Brooks, Charles L

2010-08-01

Building reliable structural models of G protein-coupled receptors (GPCRs) is a difficult task because of the paucity of suitable templates, low sequence identity, and the wide variety of ligand specificities within the superfamily. Template-based modeling is known to be the most successful method for protein structure prediction. However, refinement of homology models within 1-3 A C alpha RMSD of the native structure remains a major challenge. Here, we address this problem by developing a novel protocol (foldGPCR) for modeling the transmembrane (TM) region of GPCRs in complex with a ligand, aimed to accurately model the structural divergence between the template and target in the TM helices. The protocol is based on predicted conserved inter-residue contacts between the template and target, and exploits an all-atom implicit membrane force field. The placement of the ligand in the binding pocket is guided by biochemical data. The foldGPCR protocol is implemented by a stepwise hierarchical approach, in which the TM helical bundle and the ligand are assembled by simulated annealing trials in the first step, and the receptor-ligand complex is refined with replica exchange sampling in the second step. The protocol is applied to model the human beta(2)-adrenergic receptor (beta(2)AR) bound to carazolol, using contacts derived from the template structure of bovine rhodopsin. Comparison with the X-ray crystal structure of the beta(2)AR shows that our protocol is particularly successful in accurately capturing helix backbone irregularities and helix-helix packing interactions that distinguish rhodopsin from beta(2)AR. (c) 2010 Wiley-Liss, Inc.

AnchorDock for Blind Flexible Docking of Peptides to Proteins.

PubMed

Slutzki, Michal; Ben-Shimon, Avraham; Niv, Masha Y

2017-01-01

Due to increasing interest in peptides as signaling modulators and drug candidates, several methods for peptide docking to their target proteins are under active development. The "blind" docking problem, where the peptide-binding site on the protein surface is unknown, presents one of the current challenges in the field. AnchorDock protocol was developed by Ben-Shimon and Niv to address this challenge.This protocol narrows the docking search to the most relevant parts of the conformational space. This is achieved by pre-folding the free peptide and by computationally detecting anchoring spots on the surface of the unbound protein. Multiple flexible simulated annealing molecular dynamics (SAMD) simulations are subsequently carried out, starting from pre-folded peptide conformations, constrained to the various precomputed anchoring spots.Here, AnchorDock is demonstrated using two known protein-peptide complexes. A PDZ-peptide complex provides a relatively easy case due to the relatively small size of the protein, and a typical peptide conformation and binding region; a more challenging example is a complex between USP7 N-term and a p53-derived peptide, where the protein is larger, and the peptide conformation and a binding site are generally assumed to be unknown. AnchorDock returned native-like solutions ranked first and third for the PDZ and USP7 complexes, respectively. We describe the procedure step by step and discuss possible modifications where applicable.

Pre-Steady-State Kinetic Analysis of Single-Nucleotide Incorporation by DNA Polymerases

PubMed Central

Su, Yan; Guengerich, F. Peter

2016-01-01

Pre-steady-state kinetic analysis is a powerful and widely used method to obtain multiple kinetic parameters. This protocol provides a step-by-step procedure for pre-steady-state kinetic analysis of single-nucleotide incorporation by a DNA polymerase. It describes the experimental details of DNA substrate annealing, reaction mixture preparation, handling of the RQF-3 rapid quench-flow instrument, denaturing polyacrylamide DNA gel preparation, electrophoresis, quantitation, and data analysis. The core and unique part of this protocol is the rationale for preparation of the reaction mixture (the ratio of the polymerase to the DNA substrate) and methods for conducting pre-steady-state assays on an RQF-3 rapid quench-flow instrument, as well as data interpretation after analysis. In addition, the methods for the DNA substrate annealing and DNA polyacrylamide gel preparation, electrophoresis, quantitation and analysis are suitable for use in other studies. PMID:27248785

Unidirectional self-assembly of soft templated mesoporous carbons by zone annealing

NASA Astrophysics Data System (ADS)

Xue, Jiachen; Singh, Gurpreet; Qiang, Zhe; Karim, Alamgir; Vogt, Bryan D.

2013-08-01

Surfactant or block copolymer-templated mesoporous films have been extensively explored, but achieving mesostructure coherence and unidirectional orientation over macroscopic dimensions has remained quite challenging for these self-assembled systems. Here, we extend the concepts associated with zone refinement of crystalline materials to soft templated mesoporous carbon films based on the cooperative assembly of commercial non-ionic surfactants (block copolymers) and phenolic resin oligomers (resol) to provide macroscopic alignment of both cubic (FDU-16) and hexagonal (FDU-15) mesostructures. The average orientation of these mesophases is determined from rotation grazing incidence small angle X-ray scattering (GISAXS) measurements. For FDU-15 templated by Pluronic P123, the orientation factor for the zone-annealed film is 0.98 based on the average of the second Legendre polynomial, but this orientation deteriorates significantly during carbonization. Notably, a thermal stabilization step following zone annealing preserves the orientation of the mesostructure during carbonization. The orientation factor for an isotropic cubic structure (FDU-16 templated by Pluronic F127) is only 0.48 (based on the 111 reflection with incident angle 0.15°) for the same zone annealing protocol, but this illustrates the versatility of zone annealing to different mesostructures. Unexpectedly, zone annealing of FDU-15 templated by Pluronic F127 leads to stabilization of the mesostructure through carbonization, whereas this structure collapses fully during carbonization even after extended oven annealing; despite no clear macroscopic orientation of the cylindrical mesostructure from zone annealing. Thermal zone annealing provides a simple methodology to produce highly ordered and macroscopically oriented stable mesoporous carbon films, but the efficacy is strongly tied to the mobility of the template during the zone annealing.Surfactant or block copolymer-templated mesoporous films have been extensively explored, but achieving mesostructure coherence and unidirectional orientation over macroscopic dimensions has remained quite challenging for these self-assembled systems. Here, we extend the concepts associated with zone refinement of crystalline materials to soft templated mesoporous carbon films based on the cooperative assembly of commercial non-ionic surfactants (block copolymers) and phenolic resin oligomers (resol) to provide macroscopic alignment of both cubic (FDU-16) and hexagonal (FDU-15) mesostructures. The average orientation of these mesophases is determined from rotation grazing incidence small angle X-ray scattering (GISAXS) measurements. For FDU-15 templated by Pluronic P123, the orientation factor for the zone-annealed film is 0.98 based on the average of the second Legendre polynomial, but this orientation deteriorates significantly during carbonization. Notably, a thermal stabilization step following zone annealing preserves the orientation of the mesostructure during carbonization. The orientation factor for an isotropic cubic structure (FDU-16 templated by Pluronic F127) is only 0.48 (based on the 111 reflection with incident angle 0.15°) for the same zone annealing protocol, but this illustrates the versatility of zone annealing to different mesostructures. Unexpectedly, zone annealing of FDU-15 templated by Pluronic F127 leads to stabilization of the mesostructure through carbonization, whereas this structure collapses fully during carbonization even after extended oven annealing; despite no clear macroscopic orientation of the cylindrical mesostructure from zone annealing. Thermal zone annealing provides a simple methodology to produce highly ordered and macroscopically oriented stable mesoporous carbon films, but the efficacy is strongly tied to the mobility of the template during the zone annealing. Electronic supplementary information (ESI) available: GISAXS profiles for the FDU-15-F127 at φ = 0° and φ = 90° is included along with 2D GISAXS data for all azimuthal data associated with FDU-15-P123 to illustrate the azimuthal dependence on the diffraction patterns. See DOI: 10.1039/c3nr02821f

Parameter estimation for chaotic systems using a hybrid adaptive cuckoo search with simulated annealing algorithm

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

Sheng, Zheng, E-mail: 19994035@sina.com; Wang, Jun; Zhou, Bihua

2014-03-15

This paper introduces a novel hybrid optimization algorithm to establish the parameters of chaotic systems. In order to deal with the weaknesses of the traditional cuckoo search algorithm, the proposed adaptive cuckoo search with simulated annealing algorithm is presented, which incorporates the adaptive parameters adjusting operation and the simulated annealing operation in the cuckoo search algorithm. Normally, the parameters of the cuckoo search algorithm are kept constant that may result in decreasing the efficiency of the algorithm. For the purpose of balancing and enhancing the accuracy and convergence rate of the cuckoo search algorithm, the adaptive operation is presented tomore » tune the parameters properly. Besides, the local search capability of cuckoo search algorithm is relatively weak that may decrease the quality of optimization. So the simulated annealing operation is merged into the cuckoo search algorithm to enhance the local search ability and improve the accuracy and reliability of the results. The functionality of the proposed hybrid algorithm is investigated through the Lorenz chaotic system under the noiseless and noise condition, respectively. The numerical results demonstrate that the method can estimate parameters efficiently and accurately in the noiseless and noise condition. Finally, the results are compared with the traditional cuckoo search algorithm, genetic algorithm, and particle swarm optimization algorithm. Simulation results demonstrate the effectiveness and superior performance of the proposed algorithm.« less

The effects of self-interstitial clusters on cascade defect evolution beyond the primary damage state

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

Heinisch, H.L.

1997-04-01

The intracascade evolution of the defect distributions of cascades in copper is investigated using stochastic annealing simulations applied to cascades generated with molecular dynamics (MD). The temperature and energy dependencies of annihilation, clustering and free defect production are determined for individual cascades. The annealing simulation results illustrate the strong influence on intracascade evolution of the defect configuration existing in the primary damage state. Another factor significantly affecting the evolution of the defect distribution is the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades. This phenomenon introduces a cascade energy dependence of defect evolution that is apparentmore » only beyond the primary damage state, amplifying the need for further study of the annealing phase of cascade evolution and for performing many more MD cascade simulations at higher energies.« less

Scheduling of hybrid types of machines with two-machine flowshop as the first type and a single machine as the second type

NASA Astrophysics Data System (ADS)

Hsiao, Ming-Chih; Su, Ling-Huey

2018-02-01

This research addresses the problem of scheduling hybrid machine types, in which one type is a two-machine flowshop and another type is a single machine. A job is either processed on the two-machine flowshop or on the single machine. The objective is to determine a production schedule for all jobs so as to minimize the makespan. The problem is NP-hard since the two parallel machines problem was proved to be NP-hard. Simulated annealing algorithms are developed to solve the problem optimally. A mixed integer programming (MIP) is developed and used to evaluate the performance for two SAs. Computational experiments demonstrate the efficiency of the simulated annealing algorithms, the quality of the simulated annealing algorithms will also be reported.

Analysis of optimisation method for a two-stroke piston ring using the Finite Element Method and the Simulated Annealing Method

NASA Astrophysics Data System (ADS)

Kaliszewski, M.; Mazuro, P.

2016-09-01

Simulated Annealing Method of optimisation for the sealing piston ring geometry is tested. The aim of optimisation is to develop ring geometry which would exert demanded pressure on a cylinder just while being bended to fit the cylinder. Method of FEM analysis of an arbitrary piston ring geometry is applied in an ANSYS software. The demanded pressure function (basing on formulae presented by A. Iskra) as well as objective function are introduced. Geometry definition constructed by polynomials in radial coordinate system is delivered and discussed. Possible application of Simulated Annealing Method in a piston ring optimisation task is proposed and visualised. Difficulties leading to possible lack of convergence of optimisation are presented. An example of an unsuccessful optimisation performed in APDL is discussed. Possible line of further optimisation improvement is proposed.

Simulated annealing in orbital flight planning

NASA Technical Reports Server (NTRS)

Soller, Jeffrey

1990-01-01

Simulated annealing is used to solve a minimum fuel trajectory problem in the space station environment. The environment is unique because the space station will define the first true multivehicle environment in space. The optimization yields surfaces which are potentially complex, with multiple local minima. Because of the likelihood of these local minima, descent techniques are unable to offer robust solutions. Other deterministic optimization techniques were explored without success. The simulated annealing optimization is capable of identifying a minimum-fuel, two-burn trajectory subject to four constraints. Furthermore, the computational efforts involved in the optimization are such that missions could be planned on board the space station. Potential applications could include the on-site planning of rendezvous with a target craft of the emergency rescue of an astronaut. Future research will include multiwaypoint maneuvers, using a knowledge base to guide the optimization.

Microprocessor-based integration of microfluidic control for the implementation of automated sensor monitoring and multithreaded optimization algorithms.

PubMed

Ezra, Elishai; Maor, Idan; Bavli, Danny; Shalom, Itai; Levy, Gahl; Prill, Sebastian; Jaeger, Magnus S; Nahmias, Yaakov

2015-08-01

Microfluidic applications range from combinatorial synthesis to high throughput screening, with platforms integrating analog perfusion components, digitally controlled micro-valves and a range of sensors that demand a variety of communication protocols. Currently, discrete control units are used to regulate and monitor each component, resulting in scattered control interfaces that limit data integration and synchronization. Here, we present a microprocessor-based control unit, utilizing the MS Gadgeteer open framework that integrates all aspects of microfluidics through a high-current electronic circuit that supports and synchronizes digital and analog signals for perfusion components, pressure elements, and arbitrary sensor communication protocols using a plug-and-play interface. The control unit supports an integrated touch screen and TCP/IP interface that provides local and remote control of flow and data acquisition. To establish the ability of our control unit to integrate and synchronize complex microfluidic circuits we developed an equi-pressure combinatorial mixer. We demonstrate the generation of complex perfusion sequences, allowing the automated sampling, washing, and calibrating of an electrochemical lactate sensor continuously monitoring hepatocyte viability following exposure to the pesticide rotenone. Importantly, integration of an optical sensor allowed us to implement automated optimization protocols that require different computational challenges including: prioritized data structures in a genetic algorithm, distributed computational efforts in multiple-hill climbing searches and real-time realization of probabilistic models in simulated annealing. Our system offers a comprehensive solution for establishing optimization protocols and perfusion sequences in complex microfluidic circuits.

Efficiency of quantum vs. classical annealing in nonconvex learning problems

PubMed Central

Zecchina, Riccardo

2018-01-01

Quantum annealers aim at solving nonconvex optimization problems by exploiting cooperative tunneling effects to escape local minima. The underlying idea consists of designing a classical energy function whose ground states are the sought optimal solutions of the original optimization problem and add a controllable quantum transverse field to generate tunneling processes. A key challenge is to identify classes of nonconvex optimization problems for which quantum annealing remains efficient while thermal annealing fails. We show that this happens for a wide class of problems which are central to machine learning. Their energy landscapes are dominated by local minima that cause exponential slowdown of classical thermal annealers while simulated quantum annealing converges efficiently to rare dense regions of optimal solutions. PMID:29382764

Improve earthquake hypocenter using adaptive simulated annealing inversion in regional tectonic, volcano tectonic, and geothermal observation

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

Ry, Rexha Verdhora, E-mail: rexha.vry@gmail.com; Nugraha, Andri Dian, E-mail: nugraha@gf.itb.ac.id

Observation of earthquakes is routinely used widely in tectonic activity observation, and also in local scale such as volcano tectonic and geothermal activity observation. It is necessary for determining the location of precise hypocenter which the process involves finding a hypocenter location that has minimum error between the observed and the calculated travel times. When solving this nonlinear inverse problem, simulated annealing inversion method can be applied to such global optimization problems, which the convergence of its solution is independent of the initial model. In this study, we developed own program codeby applying adaptive simulated annealing inversion in Matlab environment.more » We applied this method to determine earthquake hypocenter using several data cases which are regional tectonic, volcano tectonic, and geothermal field. The travel times were calculated using ray tracing shooting method. We then compared its results with the results using Geiger’s method to analyze its reliability. Our results show hypocenter location has smaller RMS error compared to the Geiger’s result that can be statistically associated with better solution. The hypocenter of earthquakes also well correlated with geological structure in the study area. Werecommend using adaptive simulated annealing inversion to relocate hypocenter location in purpose to get precise and accurate earthquake location.« less

Advantages of Unfair Quantum Ground-State Sampling.

PubMed

Zhang, Brian Hu; Wagenbreth, Gene; Martin-Mayor, Victor; Hen, Itay

2017-04-21

The debate around the potential superiority of quantum annealers over their classical counterparts has been ongoing since the inception of the field. Recent technological breakthroughs, which have led to the manufacture of experimental prototypes of quantum annealing optimizers with sizes approaching the practical regime, have reignited this discussion. However, the demonstration of quantum annealing speedups remains to this day an elusive albeit coveted goal. We examine the power of quantum annealers to provide a different type of quantum enhancement of practical relevance, namely, their ability to serve as useful samplers from the ground-state manifolds of combinatorial optimization problems. We study, both numerically by simulating stoquastic and non-stoquastic quantum annealing processes, and experimentally, using a prototypical quantum annealing processor, the ability of quantum annealers to sample the ground-states of spin glasses differently than thermal samplers. We demonstrate that (i) quantum annealers sample the ground-state manifolds of spin glasses very differently than thermal optimizers (ii) the nature of the quantum fluctuations driving the annealing process has a decisive effect on the final distribution, and (iii) the experimental quantum annealer samples ground-state manifolds significantly differently than thermal and ideal quantum annealers. We illustrate how quantum annealers may serve as powerful tools when complementing standard sampling algorithms.

Three-dimensional Stochastic Estimation of Porosity Distribution: Benefits of Using Ground-penetrating Radar Velocity Tomograms in Simulated-annealing-based or Bayesian Sequential Simulation Approaches

DTIC Science & Technology

2012-05-30

annealing-based or Bayesian sequential simulation approaches B. Dafflon1,2 and W. Barrash1 Received 13 May 2011; revised 12 March 2012; accepted 17 April 2012...the withheld porosity log are also withheld for this estimation process. For both cases we do this for two wells having locally variable stratigraphy ...borehole location is given at the bottom of each log comparison panel. For comparison with stratigraphy at the BHRS, contacts between Units 1 to 4

Modified Backtracking Search Optimization Algorithm Inspired by Simulated Annealing for Constrained Engineering Optimization Problems

PubMed Central

Wang, Hailong; Sun, Yuqiu; Su, Qinghua; Xia, Xuewen

2018-01-01

The backtracking search optimization algorithm (BSA) is a population-based evolutionary algorithm for numerical optimization problems. BSA has a powerful global exploration capacity while its local exploitation capability is relatively poor. This affects the convergence speed of the algorithm. In this paper, we propose a modified BSA inspired by simulated annealing (BSAISA) to overcome the deficiency of BSA. In the BSAISA, the amplitude control factor (F) is modified based on the Metropolis criterion in simulated annealing. The redesigned F could be adaptively decreased as the number of iterations increases and it does not introduce extra parameters. A self-adaptive ε-constrained method is used to handle the strict constraints. We compared the performance of the proposed BSAISA with BSA and other well-known algorithms when solving thirteen constrained benchmarks and five engineering design problems. The simulation results demonstrated that BSAISA is more effective than BSA and more competitive with other well-known algorithms in terms of convergence speed. PMID:29666635

Hybrid General Pattern Search and Simulated Annealing for Industrail Production Planning Problems

NASA Astrophysics Data System (ADS)

Vasant, P.; Barsoum, N.

2010-06-01

In this paper, the hybridization of GPS (General Pattern Search) method and SA (Simulated Annealing) incorporated in the optimization process in order to look for the global optimal solution for the fitness function and decision variables as well as minimum computational CPU time. The real strength of SA approach been tested in this case study problem of industrial production planning. This is due to the great advantage of SA for being easily escaping from trapped in local minima by accepting up-hill move through a probabilistic procedure in the final stages of optimization process. Vasant [1] in his Ph. D thesis has provided 16 different techniques of heuristic and meta-heuristic in solving industrial production problems with non-linear cubic objective functions, eight decision variables and 29 constraints. In this paper, fuzzy technological problems have been solved using hybrid techniques of general pattern search and simulated annealing. The simulated and computational results are compared to other various evolutionary techniques.

Composition dependent thermal annealing behaviour of ion tracks in apatite

NASA Astrophysics Data System (ADS)

Nadzri, A.; Schauries, D.; Mota-Santiago, P.; Muradoglu, S.; Trautmann, C.; Gleadow, A. J. W.; Hawley, A.; Kluth, P.

2016-07-01

Natural apatite samples with different F/Cl content from a variety of geological locations (Durango, Mexico; Mud Tank, Australia; and Snarum, Norway) were irradiated with swift heavy ions to simulate fission tracks. The annealing kinetics of the resulting ion tracks was investigated using synchrotron-based small-angle X-ray scattering (SAXS) combined with ex situ annealing. The activation energies for track recrystallization were extracted and consistent with previous studies using track-etching, tracks in the chlorine-rich Snarum apatite are more resistant to annealing than in the other compositions.

High-Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of Extraction Procedure, Primer Length and Annealing Temperature

PubMed Central

Sergeant, Martin J.; Constantinidou, Chrystala; Cogan, Tristan; Penn, Charles W.; Pallen, Mark J.

2012-01-01

The analysis of 16S-rDNA sequences to assess the bacterial community composition of a sample is a widely used technique that has increased with the advent of high throughput sequencing. Although considerable effort has been devoted to identifying the most informative region of the 16S gene and the optimal informatics procedures to process the data, little attention has been paid to the PCR step, in particular annealing temperature and primer length. To address this, amplicons derived from 16S-rDNA were generated from chicken caecal content DNA using different annealing temperatures, primers and different DNA extraction procedures. The amplicons were pyrosequenced to determine the optimal protocols for capture of maximum bacterial diversity from a chicken caecal sample. Even at very low annealing temperatures there was little effect on the community structure, although the abundance of some OTUs such as Bifidobacterium increased. Using shorter primers did not reveal any novel OTUs but did change the community profile obtained. Mechanical disruption of the sample by bead beating had a significant effect on the results obtained, as did repeated freezing and thawing. In conclusion, existing primers and standard annealing temperatures captured as much diversity as lower annealing temperatures and shorter primers. PMID:22666455

High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature.

PubMed

Sergeant, Martin J; Constantinidou, Chrystala; Cogan, Tristan; Penn, Charles W; Pallen, Mark J

2012-01-01

The analysis of 16S-rDNA sequences to assess the bacterial community composition of a sample is a widely used technique that has increased with the advent of high throughput sequencing. Although considerable effort has been devoted to identifying the most informative region of the 16S gene and the optimal informatics procedures to process the data, little attention has been paid to the PCR step, in particular annealing temperature and primer length. To address this, amplicons derived from 16S-rDNA were generated from chicken caecal content DNA using different annealing temperatures, primers and different DNA extraction procedures. The amplicons were pyrosequenced to determine the optimal protocols for capture of maximum bacterial diversity from a chicken caecal sample. Even at very low annealing temperatures there was little effect on the community structure, although the abundance of some OTUs such as Bifidobacterium increased. Using shorter primers did not reveal any novel OTUs but did change the community profile obtained. Mechanical disruption of the sample by bead beating had a significant effect on the results obtained, as did repeated freezing and thawing. In conclusion, existing primers and standard annealing temperatures captured as much diversity as lower annealing temperatures and shorter primers.

An adaptive approach to the physical annealing strategy for simulated annealing

NASA Astrophysics Data System (ADS)

Hasegawa, M.

2013-02-01

A new and reasonable method for adaptive implementation of simulated annealing (SA) is studied on two types of random traveling salesman problems. The idea is based on the previous finding on the search characteristics of the threshold algorithms, that is, the primary role of the relaxation dynamics in their finite-time optimization process. It is shown that the effective temperature for optimization can be predicted from the system's behavior analogous to the stabilization phenomenon occurring in the heating process starting from a quenched solution. The subsequent slow cooling near the predicted point draws out the inherent optimizing ability of finite-time SA in more straightforward manner than the conventional adaptive approach.

Compiling Planning into Quantum Optimization Problems: A Comparative Study

DTIC Science & Technology

2015-06-07

and Sipser, M. 2000. Quantum computation by adiabatic evolution. arXiv:quant- ph/0001106. Fikes, R. E., and Nilsson, N. J. 1972. STRIPS: A new...become available: quantum annealing. Quantum annealing is one of the most accessible quantum algorithms for a computer sci- ence audience not versed...in quantum computing because of its close ties to classical optimization algorithms such as simulated annealing. While large-scale universal quantum

Improved mapping of the travelling salesman problem for quantum annealing

NASA Astrophysics Data System (ADS)

Troyer, Matthias; Heim, Bettina; Brown, Ethan; Wecker, David

2015-03-01

We consider the quantum adiabatic algorithm as applied to the travelling salesman problem (TSP). We introduce a novel mapping of TSP to an Ising spin glass Hamiltonian and compare it to previous known mappings. Through direct perturbative analysis, unitary evolution, and simulated quantum annealing, we show this new mapping to be significantly superior. We discuss how this advantage can translate to actual physical implementations of TSP on quantum annealers.

Automatic Clustering Using Multi-objective Particle Swarm and Simulated Annealing

PubMed Central

Abubaker, Ahmad; Baharum, Adam; Alrefaei, Mahmoud

2015-01-01

This paper puts forward a new automatic clustering algorithm based on Multi-Objective Particle Swarm Optimization and Simulated Annealing, “MOPSOSA”. The proposed algorithm is capable of automatic clustering which is appropriate for partitioning datasets to a suitable number of clusters. MOPSOSA combines the features of the multi-objective based particle swarm optimization (PSO) and the Multi-Objective Simulated Annealing (MOSA). Three cluster validity indices were optimized simultaneously to establish the suitable number of clusters and the appropriate clustering for a dataset. The first cluster validity index is centred on Euclidean distance, the second on the point symmetry distance, and the last cluster validity index is based on short distance. A number of algorithms have been compared with the MOPSOSA algorithm in resolving clustering problems by determining the actual number of clusters and optimal clustering. Computational experiments were carried out to study fourteen artificial and five real life datasets. PMID:26132309

List-Based Simulated Annealing Algorithm for Traveling Salesman Problem.

PubMed

Zhan, Shi-hua; Lin, Juan; Zhang, Ze-jun; Zhong, Yi-wen

2016-01-01

Simulated annealing (SA) algorithm is a popular intelligent optimization algorithm which has been successfully applied in many fields. Parameters' setting is a key factor for its performance, but it is also a tedious work. To simplify parameters setting, we present a list-based simulated annealing (LBSA) algorithm to solve traveling salesman problem (TSP). LBSA algorithm uses a novel list-based cooling schedule to control the decrease of temperature. Specifically, a list of temperatures is created first, and then the maximum temperature in list is used by Metropolis acceptance criterion to decide whether to accept a candidate solution. The temperature list is adapted iteratively according to the topology of the solution space of the problem. The effectiveness and the parameter sensitivity of the list-based cooling schedule are illustrated through benchmark TSP problems. The LBSA algorithm, whose performance is robust on a wide range of parameter values, shows competitive performance compared with some other state-of-the-art algorithms.

An Introduction to Simulated Annealing

ERIC Educational Resources Information Center

Albright, Brian

2007-01-01

An attempt to model the physical process of annealing lead to the development of a type of combinatorial optimization algorithm that takes on the problem of getting trapped in a local minimum. The author presents a Microsoft Excel spreadsheet that illustrates how this works.

OBJECT KINETIC MONTE CARLO SIMULATIONS OF CASCADE ANNEALING IN TUNGSTEN

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

Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

2014-03-31

The objective of this work is to study the annealing of primary cascade damage created by primary knock-on atoms (PKAs) of various energies, at various temperatures in bulk tungsten using the object kinetic Monte Carlo (OKMC) method.

Experimental and Numerical Simulations of Phase Transformations Occurring During Continuous Annealing of DP Steel Strips

NASA Astrophysics Data System (ADS)

Wrożyna, Andrzej; Pernach, Monika; Kuziak, Roman; Pietrzyk, Maciej

2016-04-01

Due to their exceptional strength properties combined with good workability the Advanced High-Strength Steels (AHSS) are commonly used in automotive industry. Manufacturing of these steels is a complex process which requires precise control of technological parameters during thermo-mechanical treatment. Design of these processes can be significantly improved by the numerical models of phase transformations. Evaluation of predictive capabilities of models, as far as their applicability in simulation of thermal cycles thermal cycles for AHSS is considered, was the objective of the paper. Two models were considered. The former was upgrade of the JMAK equation while the latter was an upgrade of the Leblond model. The models can be applied to any AHSS though the examples quoted in the paper refer to the Dual Phase (DP) steel. Three series of experimental simulations were performed. The first included various thermal cycles going beyond limitations of the continuous annealing lines. The objective was to validate models behavior in more complex cooling conditions. The second set of tests included experimental simulations of the thermal cycle characteristic for the continuous annealing lines. Capability of the models to describe properly phase transformations in this process was evaluated. The third set included data from the industrial continuous annealing line. Validation and verification of models confirmed their good predictive capabilities. Since it does not require application of the additivity rule, the upgrade of the Leblond model was selected as the better one for simulation of industrial processes in AHSS production.

Enhanced sampling techniques in molecular dynamics simulations of biological systems.

PubMed

Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

2015-05-01

Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

Thermal decomposition of solid phase nitromethane under various heating rates and target temperatures based on ab initio molecular dynamics simulations.

PubMed

Xu, Kai; Wei, Dong-Qing; Chen, Xiang-Rong; Ji, Guang-Fu

2014-10-01

The Car-Parrinello molecular dynamics simulation was applied to study the thermal decomposition of solid phase nitromethane under gradual heating and fast annealing conditions. In gradual heating simulations, we found that, rather than C-N bond cleavage, intermolecular proton transfer is more likely to be the first reaction in the decomposition process. At high temperature, the first reaction in fast annealing simulation is intermolecular proton transfer leading to CH3NOOH and CH2NO2, whereas the initial chemical event at low temperature tends to be a unimolecular C-N bond cleavage, producing CH3 and NO2 fragments. It is the first time to date that the direct rupture of a C-N bond has been reported as the first reaction in solid phase nitromethane. In addition, the fast annealing simulations on a supercell at different temperatures are conducted to validate the effect of simulation cell size on initial reaction mechanisms. The results are in qualitative agreement with the simulations on a unit cell. By analyzing the time evolution of some molecules, we also found that the time of first water molecule formation is clearly sensitive to heating rates and target temperatures when the first reaction is an intermolecular proton transfer.

Efficient Monte Carlo Methods for Biomolecular Simulations.

NASA Astrophysics Data System (ADS)

Bouzida, Djamal

A new approach to efficient Monte Carlo simulations of biological molecules is presented. By relaxing the usual restriction to Markov processes, we are able to optimize performance while dealing directly with the inhomogeneity and anisotropy inherent in these systems. The advantage of this approach is that we can introduce a wide variety of Monte Carlo moves to deal with complicated motions of the molecule, while maintaining full optimization at every step. This enables the use of a variety of collective rotational moves that relax long-wavelength modes. We were able to show by explicit simulations that the resulting algorithms substantially increase the speed of the simulation while reproducing the correct equilibrium behavior. This approach is particularly intended for simulations of macromolecules, although we expect it to be useful in other situations. The dynamic optimization of the new Monte Carlo methods makes them very suitable for simulated annealing experiments on all systems whose state space is continuous in general, and to the protein folding problem in particular. We introduce an efficient annealing schedule using preferential bias moves. Our simulated annealing experiments yield structures whose free energies were lower than the equilibrated X-ray structure, which leads us to believe that the empirical energy function used does not fully represent the interatomic interactions. Furthermore, we believe that the largest discrepancies involve the solvent effects in particular.

Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein

PubMed Central

Hao, Ge-Fei; Xu, Wei-Fang; Yang, Sheng-Gang; Yang, Guang-Fu

2015-01-01

Protein and peptide structure predictions are of paramount importance for understanding their functions, as well as the interactions with other molecules. However, the use of molecular simulation techniques to directly predict the peptide structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale. We developed here a new strategy, named Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) to identify the native states of a peptide and miniprotein. A cluster of near native structures could be obtained by using the MSA-MD method, which turned out to be significantly more efficient in reaching the native structure compared to continuous MD and conventional SA-MD simulation. PMID:26492886

Quantum approach to classical statistical mechanics.

PubMed

Somma, R D; Batista, C D; Ortiz, G

2007-07-20

We present a new approach to study the thermodynamic properties of d-dimensional classical systems by reducing the problem to the computation of ground state properties of a d-dimensional quantum model. This classical-to-quantum mapping allows us to extend the scope of standard optimization methods by unifying them under a general framework. The quantum annealing method is naturally extended to simulate classical systems at finite temperatures. We derive the rates to assure convergence to the optimal thermodynamic state using the adiabatic theorem of quantum mechanics. For simulated and quantum annealing, we obtain the asymptotic rates of T(t) approximately (pN)/(k(B)logt) and gamma(t) approximately (Nt)(-c/N), for the temperature and magnetic field, respectively. Other annealing strategies are also discussed.

EIT image regularization by a new Multi-Objective Simulated Annealing algorithm.

PubMed

Castro Martins, Thiago; Sales Guerra Tsuzuki, Marcos

2015-01-01

Multi-Objective Optimization can be used to produce regularized Electrical Impedance Tomography (EIT) images where the weight of the regularization term is not known a priori. This paper proposes a novel Multi-Objective Optimization algorithm based on Simulated Annealing tailored for EIT image reconstruction. Images are reconstructed from experimental data and compared with images from other Multi and Single Objective optimization methods. A significant performance enhancement from traditional techniques can be inferred from the results.

Recursive Branching Simulated Annealing Algorithm

NASA Technical Reports Server (NTRS)

Bolcar, Matthew; Smith, J. Scott; Aronstein, David

2012-01-01

This innovation is a variation of a simulated-annealing optimization algorithm that uses a recursive-branching structure to parallelize the search of a parameter space for the globally optimal solution to an objective. The algorithm has been demonstrated to be more effective at searching a parameter space than traditional simulated-annealing methods for a particular problem of interest, and it can readily be applied to a wide variety of optimization problems, including those with a parameter space having both discrete-value parameters (combinatorial) and continuous-variable parameters. It can take the place of a conventional simulated- annealing, Monte-Carlo, or random- walk algorithm. In a conventional simulated-annealing (SA) algorithm, a starting configuration is randomly selected within the parameter space. The algorithm randomly selects another configuration from the parameter space and evaluates the objective function for that configuration. If the objective function value is better than the previous value, the new configuration is adopted as the new point of interest in the parameter space. If the objective function value is worse than the previous value, the new configuration may be adopted, with a probability determined by a temperature parameter, used in analogy to annealing in metals. As the optimization continues, the region of the parameter space from which new configurations can be selected shrinks, and in conjunction with lowering the annealing temperature (and thus lowering the probability for adopting configurations in parameter space with worse objective functions), the algorithm can converge on the globally optimal configuration. The Recursive Branching Simulated Annealing (RBSA) algorithm shares some features with the SA algorithm, notably including the basic principles that a starting configuration is randomly selected from within the parameter space, the algorithm tests other configurations with the goal of finding the globally optimal solution, and the region from which new configurations can be selected shrinks as the search continues. The key difference between these algorithms is that in the SA algorithm, a single path, or trajectory, is taken in parameter space, from the starting point to the globally optimal solution, while in the RBSA algorithm, many trajectories are taken; by exploring multiple regions of the parameter space simultaneously, the algorithm has been shown to converge on the globally optimal solution about an order of magnitude faster than when using conventional algorithms. Novel features of the RBSA algorithm include: 1. More efficient searching of the parameter space due to the branching structure, in which multiple random configurations are generated and multiple promising regions of the parameter space are explored; 2. The implementation of a trust region for each parameter in the parameter space, which provides a natural way of enforcing upper- and lower-bound constraints on the parameters; and 3. The optional use of a constrained gradient- search optimization, performed on the continuous variables around each branch s configuration in parameter space to improve search efficiency by allowing for fast fine-tuning of the continuous variables within the trust region at that configuration point.

Assessment of MARMOT Grain Growth Model

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

Fromm, B.; Zhang, Y.; Schwen, D.

2015-12-01

This report assesses the MARMOT grain growth model by comparing modeling predictions with experimental results from thermal annealing. The purpose here is threefold: (1) to demonstrate the validation approach of using thermal annealing experiments with non-destructive characterization, (2) to test the reconstruction capability and computation efficiency in MOOSE, and (3) to validate the grain growth model and the associated parameters that are implemented in MARMOT for UO 2. To assure a rigorous comparison, the 2D and 3D initial experimental microstructures of UO 2 samples were characterized using non-destructive Synchrotron x-ray. The same samples were then annealed at 2273K for grainmore » growth, and their initial microstructures were used as initial conditions for simulated annealing at the same temperature using MARMOT. After annealing, the final experimental microstructures were characterized again to compare with the results from simulations. So far, comparison between modeling and experiments has been done for 2D microstructures, and 3D comparison is underway. The preliminary results demonstrated the usefulness of the non-destructive characterization method for MARMOT grain growth model validation. A detailed analysis of the 3D microstructures is in progress to fully validate the current model in MARMOT.« less

Advances in Integrated Computational Materials Engineering "ICME"

NASA Astrophysics Data System (ADS)

Hirsch, Jürgen

The methods of Integrated Computational Materials Engineering that were developed and successfully applied for Aluminium have been constantly improved. The main aspects and recent advances of integrated material and process modeling are simulations of material properties like strength and forming properties and for the specific microstructure evolution during processing (rolling, extrusion, annealing) under the influence of material constitution and process variations through the production process down to the final application. Examples are discussed for the through-process simulation of microstructures and related properties of Aluminium sheet, including DC ingot casting, pre-heating and homogenization, hot and cold rolling, final annealing. New results are included of simulation solution annealing and age hardening of 6xxx alloys for automotive applications. Physically based quantitative descriptions and computer assisted evaluation methods are new ICME methods of integrating new simulation tools also for customer applications, like heat affected zones in welding of age hardening alloys. The aspects of estimating the effect of specific elements due to growing recycling volumes requested also for high end Aluminium products are also discussed, being of special interest in the Aluminium producing industries.

Field development planning using simulated annealing - optimal economic well scheduling and placement

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

Beckner, B.L.; Xong, X.

1995-12-31

A method for optimizing the net present value of a full field development by varying the placement and sequence of production wells is presented. This approach is automated and combines an economics package and Mobil`s in-house simulator, PEGASUS, within a simulated annealing optimization engine. A novel framing of the well placement and scheduling problem as a classic {open_quotes}travelling salesman problem{close_quotes} is required before optimization via simulated annealing can be applied practically. An example of a full field development using this technique shows that non-uniform well spacings are optimal (from an NPV standpoint) when the effects of well interference and variablemore » reservoir properties are considered. Examples of optimizing field NPV with variable well costs also show that non-uniform wells spacings are optimal. Project NPV increases of 25 to 30 million dollars were shown using the optimal, nonuniform development versus reasonable, uniform developments. The ability of this technology to deduce these non-uniform well spacings opens up many potential applications that should materially impact the economic performance of field developments.« less

Stamping an AA5754 Train Window Panel with High Dent Resistance Using Locally Annealed Blanks

NASA Astrophysics Data System (ADS)

Piccininni, A.; Guglielmi, P.; Lo Franco, A.; Palumbo, G.

2017-09-01

The warm stamping of an AA5754-H32 window panel for railway vehicles applications has been proposed in the present work. The adoption of increased working temperatures can be surely considered the most effective solution for this alloy to overcome the limited material formability at room temperature [Palumbo et al. “Warm Forming of an AA5754 Component for Railway Vehicle Applications”, Procedia Engineering, Vol. 183, 2017, Pages 351-356] but, in order to improve the overall dent resistance of the component, the initial wrought conditions have been chosen in the present work. The manufacturing of the window panel was thus subdivided into a preliminary local heat treatment (assumed to be performed by laser) to anneal the material and a subsequent warm stamping step using heated tools. The best combination of temperature and holding time able to produce the annealing of the investigated alloy was determined using the physical simulator Gleeble 3180. On the contrary, the warm forming step was designed by means of thermo-mechanical simulations: in order to model the AA5754-H32 blank with annealed regions, an extensive experimental campaign (tensile and formability tests) was conducted using specimens in the annealed (H111) and in the wrought (H32) conditions. Through the numerical approach it was thus possible define: (i) the extent of the annealed regions; (ii) the punch speed to get a sound component.

A Simulated Annealing Algorithm for the Optimization of Multistage Depressed Collector Efficiency

NASA Technical Reports Server (NTRS)

Vaden, Karl R.; Wilson, Jeffrey D.; Bulson, Brian A.

2002-01-01

The microwave traveling wave tube amplifier (TWTA) is widely used as a high-power transmitting source for space and airborne communications. One critical factor in designing a TWTA is the overall efficiency. However, overall efficiency is highly dependent upon collector efficiency; so collector design is critical to the performance of a TWTA. Therefore, NASA Glenn Research Center has developed an optimization algorithm based on Simulated Annealing to quickly design highly efficient multi-stage depressed collectors (MDC).

Minimizing distortion and internal forces in truss structures by simulated annealing

NASA Technical Reports Server (NTRS)

Kincaid, Rex K.; Padula, Sharon L.

1990-01-01

Inaccuracies in the length of members and the diameters of joints of large space structures may produce unacceptable levels of surface distortion and internal forces. Here, two discrete optimization problems are formulated, one to minimize surface distortion (DSQRMS) and the other to minimize internal forces (FSQRMS). Both of these problems are based on the influence matrices generated by a small-deformation linear analysis. Good solutions are obtained for DSQRMS and FSQRMS through the use of a simulated annealing heuristic.

Iterative repair for scheduling and rescheduling

NASA Technical Reports Server (NTRS)

Zweben, Monte; Davis, Eugene; Deale, Michael

1991-01-01

An iterative repair search method is described called constraint based simulated annealing. Simulated annealing is a hill climbing search technique capable of escaping local minima. The utility of the constraint based framework is shown by comparing search performance with and without the constraint framework on a suite of randomly generated problems. Results are also shown of applying the technique to the NASA Space Shuttle ground processing problem. These experiments show that the search methods scales to complex, real world problems and reflects interesting anytime behavior.

Design of continuous surface-relief phase plates by surface-based simulated annealing to achieve control of focal-plane irradiance

NASA Astrophysics Data System (ADS)

Lin, Y.; Kessler, T. J.; Lawrence, G. N.

1996-10-01

High-performance phase plates are of vital concern for controlling the far-field irradiance of laser-fusion systems. Several designs for solving this difficult problem have been reported in Optics Letters [e. g., S. N. Dixit et al., Opt. Lett. 19, 417 (1994)]. We report a surface-based form of simulated annealing that significantly improves the irradiance control while eliminating the high-scatter problems that have plagued other methods.

Optimal protocols for slowly driven quantum systems.

PubMed

Zulkowski, Patrick R; DeWeese, Michael R

2015-09-01

The design of efficient quantum information processing will rely on optimal nonequilibrium transitions of driven quantum systems. Building on a recently developed geometric framework for computing optimal protocols for classical systems driven in finite time, we construct a general framework for optimizing the average information entropy for driven quantum systems. Geodesics on the parameter manifold endowed with a positive semidefinite metric correspond to protocols that minimize the average information entropy production in finite time. We use this framework to explicitly compute the optimal entropy production for a simple two-state quantum system coupled to a heat bath of bosonic oscillators, which has applications to quantum annealing.

Design of a composite filter realizable on practical spatial light modulators

NASA Technical Reports Server (NTRS)

Rajan, P. K.; Ramakrishnan, Ramachandran

1994-01-01

Hybrid optical correlator systems use two spatial light modulators (SLM's), one at the input plane and the other at the filter plane. Currently available SLM's such as the deformable mirror device (DMD) and liquid crystal television (LCTV) SLM's exhibit arbitrarily constrained operating characteristics. The pattern recognition filters designed with the assumption that the SLM's have ideal operating characteristic may not behave as expected when implemented on the DMD or LCTV SLM's. Therefore it is necessary to incorporate the SLM constraints in the design of the filters. In this report, an iterative method is developed for the design of an unconstrained minimum average correlation energy (MACE) filter. Then using this algorithm a new approach for the design of a SLM constrained distortion invariant filter in the presence of input SLM is developed. Two different optimization algorithms are used to maximize the objective function during filter synthesis, one based on the simplex method and the other based on the Hooke and Jeeves method. Also, the simulated annealing based filter design algorithm proposed by Khan and Rajan is refined and improved. The performance of the filter is evaluated in terms of its recognition/discrimination capabilities using computer simulations and the results are compared with a simulated annealing optimization based MACE filter. The filters are designed for different LCTV SLM's operating characteristics and the correlation responses are compared. The distortion tolerance and the false class image discrimination qualities of the filter are comparable to those of the simulated annealing based filter but the new filter design takes about 1/6 of the computer time taken by the simulated annealing filter design.

Annealing effect of the InAs dot-in-well structure grown by MBE

NASA Astrophysics Data System (ADS)

Zhao, Xuyi; Wang, Peng; Cao, Chunfang; Yan, Jinyi; Zha, Fangxing; Wang, Hailong; Gong, Qian

2017-12-01

We have demonstrated that in situ annealing effect has to be taken into account in order to realize the 1.31 μm InAs quantum dot (QD) lasers with the dot-in-well (DWELL) structure. The photoluminescence (PL) properties have been investigated for the InAs DWELL samples annealed at different temperatures in situ, simulating the annealing process during the growth of the top cladding AlGaAs layer in the laser structure. The QDs with large size in the DWELL structure are vulnerable to the annealing process at temperatures above 550 °C, revealed by the drastic change in the PL spectra. However, the DWELL structure is stable during the annealing process at 540 °C for three hours. The thermal stability of the QDs in the DWELL structure has to be considered in the growth of QD lasers for long wavelength operation.

Microstructure engineering of Pt-Al alloy thin films through Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Harris, R. A.; Terblans, J. J.; Swart, H. C.

2014-06-01

A kinetic algorithm, based on the regular solution model, was used in conjunction with the Monte Carlo method to simulate the evolution of a micro-scaled thin film system during exposure to a high temperature environment. Pt-Al thin films were prepared via electron beam physical vapor deposition (EB-PVD) with an atomic concentration ratio of Pt63:Al37. These films were heat treated at an annealing temperature of 400 °C for 16 and 49 minutes. Scanning Auger Microscopy (SAM) (PHI 700) was used to obtain elemental maps while sputtering through the thin films. Simulations were run for the same annealing temperatures and thin-film composition. From these simulations theoretical depth profiles and simulated microstructures were obtained. These were compared to the experimentally measured depth profiles and elemental maps.

Forecasting Nonlinear Chaotic Time Series with Function Expression Method Based on an Improved Genetic-Simulated Annealing Algorithm

PubMed Central

Wang, Jun; Zhou, Bi-hua; Zhou, Shu-dao; Sheng, Zheng

2015-01-01

The paper proposes a novel function expression method to forecast chaotic time series, using an improved genetic-simulated annealing (IGSA) algorithm to establish the optimum function expression that describes the behavior of time series. In order to deal with the weakness associated with the genetic algorithm, the proposed algorithm incorporates the simulated annealing operation which has the strong local search ability into the genetic algorithm to enhance the performance of optimization; besides, the fitness function and genetic operators are also improved. Finally, the method is applied to the chaotic time series of Quadratic and Rossler maps for validation. The effect of noise in the chaotic time series is also studied numerically. The numerical results verify that the method can forecast chaotic time series with high precision and effectiveness, and the forecasting precision with certain noise is also satisfactory. It can be concluded that the IGSA algorithm is energy-efficient and superior. PMID:26000011

Vehicle routing problem with time windows using natural inspired algorithms

NASA Astrophysics Data System (ADS)

Pratiwi, A. B.; Pratama, A.; Sa’diyah, I.; Suprajitno, H.

2018-03-01

Process of distribution of goods needs a strategy to make the total cost spent for operational activities minimized. But there are several constrains have to be satisfied which are the capacity of the vehicles and the service time of the customers. This Vehicle Routing Problem with Time Windows (VRPTW) gives complex constrains problem. This paper proposes natural inspired algorithms for dealing with constrains of VRPTW which involves Bat Algorithm and Cat Swarm Optimization. Bat Algorithm is being hybrid with Simulated Annealing, the worst solution of Bat Algorithm is replaced by the solution from Simulated Annealing. Algorithm which is based on behavior of cats, Cat Swarm Optimization, is improved using Crow Search Algorithm to make simplier and faster convergence. From the computational result, these algorithms give good performances in finding the minimized total distance. Higher number of population causes better computational performance. The improved Cat Swarm Optimization with Crow Search gives better performance than the hybridization of Bat Algorithm and Simulated Annealing in dealing with big data.

Forecasting nonlinear chaotic time series with function expression method based on an improved genetic-simulated annealing algorithm.

PubMed

Wang, Jun; Zhou, Bi-hua; Zhou, Shu-dao; Sheng, Zheng

2015-01-01

The paper proposes a novel function expression method to forecast chaotic time series, using an improved genetic-simulated annealing (IGSA) algorithm to establish the optimum function expression that describes the behavior of time series. In order to deal with the weakness associated with the genetic algorithm, the proposed algorithm incorporates the simulated annealing operation which has the strong local search ability into the genetic algorithm to enhance the performance of optimization; besides, the fitness function and genetic operators are also improved. Finally, the method is applied to the chaotic time series of Quadratic and Rossler maps for validation. The effect of noise in the chaotic time series is also studied numerically. The numerical results verify that the method can forecast chaotic time series with high precision and effectiveness, and the forecasting precision with certain noise is also satisfactory. It can be concluded that the IGSA algorithm is energy-efficient and superior.

List-Based Simulated Annealing Algorithm for Traveling Salesman Problem

PubMed Central

Zhan, Shi-hua; Lin, Juan; Zhang, Ze-jun

2016-01-01

Simulated annealing (SA) algorithm is a popular intelligent optimization algorithm which has been successfully applied in many fields. Parameters' setting is a key factor for its performance, but it is also a tedious work. To simplify parameters setting, we present a list-based simulated annealing (LBSA) algorithm to solve traveling salesman problem (TSP). LBSA algorithm uses a novel list-based cooling schedule to control the decrease of temperature. Specifically, a list of temperatures is created first, and then the maximum temperature in list is used by Metropolis acceptance criterion to decide whether to accept a candidate solution. The temperature list is adapted iteratively according to the topology of the solution space of the problem. The effectiveness and the parameter sensitivity of the list-based cooling schedule are illustrated through benchmark TSP problems. The LBSA algorithm, whose performance is robust on a wide range of parameter values, shows competitive performance compared with some other state-of-the-art algorithms. PMID:27034650

A trajectory planning scheme for spacecraft in the space station environment. M.S. Thesis - University of California

NASA Technical Reports Server (NTRS)

Soller, Jeffrey Alan; Grunwald, Arthur J.; Ellis, Stephen R.

1991-01-01

Simulated annealing is used to solve a minimum fuel trajectory problem in the space station environment. The environment is special because the space station will define a multivehicle environment in space. The optimization surface is a complex nonlinear function of the initial conditions of the chase and target crafts. Small permutations in the input conditions can result in abrupt changes to the optimization surface. Since no prior knowledge about the number or location of local minima on the surface is available, the optimization must be capable of functioning on a multimodal surface. It was reported in the literature that the simulated annealing algorithm is more effective on such surfaces than descent techniques using random starting points. The simulated annealing optimization was found to be capable of identifying a minimum fuel, two-burn trajectory subject to four constraints which are integrated into the optimization using a barrier method. The computations required to solve the optimization are fast enough that missions could be planned on board the space station. Potential applications for on board planning of missions are numerous. Future research topics may include optimal planning of multi-waypoint maneuvers using a knowledge base to guide the optimization, and a study aimed at developing robust annealing schedules for potential on board missions.

Experimental demonstration of a quantum annealing algorithm for the traveling salesman problem in a nuclear-magnetic-resonance quantum simulator

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

Chen Hongwei; High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031; Kong Xi

The method of quantum annealing (QA) is a promising way for solving many optimization problems in both classical and quantum information theory. The main advantage of this approach, compared with the gate model, is the robustness of the operations against errors originated from both external controls and the environment. In this work, we succeed in demonstrating experimentally an application of the method of QA to a simplified version of the traveling salesman problem by simulating the corresponding Schroedinger evolution with a NMR quantum simulator. The experimental results unambiguously yielded the optimal traveling route, in good agreement with the theoretical prediction.

Nonequilibrium thermodynamics of restricted Boltzmann machines.

PubMed

Salazar, Domingos S P

2017-08-01

In this work, we analyze the nonequilibrium thermodynamics of a class of neural networks known as restricted Boltzmann machines (RBMs) in the context of unsupervised learning. We show how the network is described as a discrete Markov process and how the detailed balance condition and the Maxwell-Boltzmann equilibrium distribution are sufficient conditions for a complete thermodynamics description, including nonequilibrium fluctuation theorems. Numerical simulations in a fully trained RBM are performed and the heat exchange fluctuation theorem is verified with excellent agreement to the theory. We observe how the contrastive divergence functional, mostly used in unsupervised learning of RBMs, is closely related to nonequilibrium thermodynamic quantities. We also use the framework to interpret the estimation of the partition function of RBMs with the annealed importance sampling method from a thermodynamics standpoint. Finally, we argue that unsupervised learning of RBMs is equivalent to a work protocol in a system driven by the laws of thermodynamics in the absence of labeled data.

Effects of a modular two-step ozone-water and annealing process on silicon carbide graphene

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

Webb, Matthew J., E-mail: matthew.webb@cantab.net; Lundstedt, Anna; Grennberg, Helena

By combining ozone and water, the effect of exposing epitaxial graphene on silicon carbide to an aggressive wet-chemical process has been evaluated after high temperature annealing in ultra high vacuum. The decomposition of ozone in water produces a number of oxidizing species, however, despite long exposure times to the aqueous-ozone environment, no graphene oxide was observed after the two-step process. The systems were comprehensively characterized before and after processing using Raman spectroscopy, core level photoemission spectroscopy, and angle resolved photoemission spectroscopy together with low energy electron diffraction, low energy electron microscopy, and atomic force microscopy. In spite of the chemicalmore » potential of the aqueous-ozone reaction environment, the graphene domains were largely unaffected raising the prospect of employing such simple chemical and annealing protocols to clean or prepare epitaxial graphene surfaces.« less

Enhanced intelligent water drops algorithm for multi-depot vehicle routing problem

PubMed Central

Akutsah, Francis; Olusanya, Micheal O.; Adewumi, Aderemi O.

2018-01-01

The intelligent water drop algorithm is a swarm-based metaheuristic algorithm, inspired by the characteristics of water drops in the river and the environmental changes resulting from the action of the flowing river. Since its appearance as an alternative stochastic optimization method, the algorithm has found applications in solving a wide range of combinatorial and functional optimization problems. This paper presents an improved intelligent water drop algorithm for solving multi-depot vehicle routing problems. A simulated annealing algorithm was introduced into the proposed algorithm as a local search metaheuristic to prevent the intelligent water drop algorithm from getting trapped into local minima and also improve its solution quality. In addition, some of the potential problematic issues associated with using simulated annealing that include high computational runtime and exponential calculation of the probability of acceptance criteria, are investigated. The exponential calculation of the probability of acceptance criteria for the simulated annealing based techniques is computationally expensive. Therefore, in order to maximize the performance of the intelligent water drop algorithm using simulated annealing, a better way of calculating the probability of acceptance criteria is considered. The performance of the proposed hybrid algorithm is evaluated by using 33 standard test problems, with the results obtained compared with the solutions offered by four well-known techniques from the subject literature. Experimental results and statistical tests show that the new method possesses outstanding performance in terms of solution quality and runtime consumed. In addition, the proposed algorithm is suitable for solving large-scale problems. PMID:29554662

Enhanced intelligent water drops algorithm for multi-depot vehicle routing problem.

PubMed

Ezugwu, Absalom E; Akutsah, Francis; Olusanya, Micheal O; Adewumi, Aderemi O

2018-01-01

The intelligent water drop algorithm is a swarm-based metaheuristic algorithm, inspired by the characteristics of water drops in the river and the environmental changes resulting from the action of the flowing river. Since its appearance as an alternative stochastic optimization method, the algorithm has found applications in solving a wide range of combinatorial and functional optimization problems. This paper presents an improved intelligent water drop algorithm for solving multi-depot vehicle routing problems. A simulated annealing algorithm was introduced into the proposed algorithm as a local search metaheuristic to prevent the intelligent water drop algorithm from getting trapped into local minima and also improve its solution quality. In addition, some of the potential problematic issues associated with using simulated annealing that include high computational runtime and exponential calculation of the probability of acceptance criteria, are investigated. The exponential calculation of the probability of acceptance criteria for the simulated annealing based techniques is computationally expensive. Therefore, in order to maximize the performance of the intelligent water drop algorithm using simulated annealing, a better way of calculating the probability of acceptance criteria is considered. The performance of the proposed hybrid algorithm is evaluated by using 33 standard test problems, with the results obtained compared with the solutions offered by four well-known techniques from the subject literature. Experimental results and statistical tests show that the new method possesses outstanding performance in terms of solution quality and runtime consumed. In addition, the proposed algorithm is suitable for solving large-scale problems.

Stochastic annealing simulations of defect interactions among subcascades

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

Heinisch, H.L.; Singh, B.N.

1997-04-01

The effects of the subcascade structure of high energy cascades on the temperature dependencies of annihilation, clustering and free defect production are investigated. The subcascade structure is simulated by closely spaced groups of lower energy MD cascades. The simulation results illustrate the strong influence of the defect configuration existing in the primary damage state on subsequent intracascade evolution. Other significant factors affecting the evolution of the defect distribution are the large differences in mobility and stability of vacancy and interstitial defects and the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades. Annealing simulations are also performedmore » on high-energy, subcascade-producing cascades generated with the binary collision approximation and calibrated to MD results.« less

Design of continuous surface-relief phase plates by surface-based simulated annealing to achieve control of focal-plane irradiance

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

Lin, Y.; Kessler, T.J.; Lawrence, G.N.

1996-10-01

High-performance phase plates are of vital concern for controlling the far-field irradiance of laser-fusion systems. Several designs for solving this difficult problem have been reported in {ital Optics} {ital Letters} [e.g., S. N. Dixit {ital et} {ital al}., Opt. Lett. {bold 19}, 417 (1994)]. We report a surface-based form of simulated annealing that significantly improves the irradiance control while eliminating the high-scatter problems that have plagued other methods. {copyright} {ital 1996 Optical Society of America.}

Functionality limit of classical simulated annealing

NASA Astrophysics Data System (ADS)

Hasegawa, M.

2015-09-01

By analyzing the system dynamics in the landscape paradigm, optimization function of classical simulated annealing is reviewed on the random traveling salesman problems. The properly functioning region of the algorithm is experimentally determined in the size-time plane and the influence of its boundary on the scalability test is examined in the standard framework of this method. From both results, an empirical choice of temperature length is plausibly explained as a minimum requirement that the algorithm maintains its scalability within its functionality limit. The study exemplifies the applicability of computational physics analysis to the optimization algorithm research.

Simulation of local ion transport in lamellar block copolymer electrolytes based on electron micrographs

DOE PAGES

Chintapalli, Mahati; Higa, Kenneth; Chen, X. Chelsea; ...

2016-12-19

A method is presented in this paper to relate local morphology and ionic conductivity in a solid, lamellar block copolymer electrolyte for lithium batteries, by simulating conductivity through transmission electron micrographs. The electrolyte consists of polystyrene-block-poly(ethylene oxide) mixed with lithium bis(trifluoromethanesulfonyl) imide salt (SEO/LiTFSI), where the polystyrene phase is structural phase and the poly(ethylene oxide)/LiTFSI phase is ionically conductive. The electric potential distribution is simulated in binarized micrographs by solving the Laplace equation with constant potential boundary conditions. A morphology factor, f, is reported for each image by calculating the effective conductivity relative to a homogenous conductor. Images from twomore » samples are examined, one annealed with large lamellar grains and one unannealed with small grains. The average value off is 0.45 ± 0.04 for the annealed sample, and 0.37 ± 0.03 for the unannealed sample, both close to the value predicted by effective medium theory, 1/2. Simulated conductivities are compared to published experimental conductivities. The value of f Unannealed/f Annealed is 0.82 for simulations and 6.2 for experiments. Simulation results correspond well to predictions by effective medium theory but do not explain the experimental measurements. Finally, observation of nanoscale morphology over length scales greater than the size of the micrographs (~1 μm) may be required to explain the experimental results.« less

Simulation of local ion transport in lamellar block copolymer electrolytes based on electron micrographs

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

Chintapalli, Mahati; Higa, Kenneth; Chen, X. Chelsea

A method is presented in this paper to relate local morphology and ionic conductivity in a solid, lamellar block copolymer electrolyte for lithium batteries, by simulating conductivity through transmission electron micrographs. The electrolyte consists of polystyrene-block-poly(ethylene oxide) mixed with lithium bis(trifluoromethanesulfonyl) imide salt (SEO/LiTFSI), where the polystyrene phase is structural phase and the poly(ethylene oxide)/LiTFSI phase is ionically conductive. The electric potential distribution is simulated in binarized micrographs by solving the Laplace equation with constant potential boundary conditions. A morphology factor, f, is reported for each image by calculating the effective conductivity relative to a homogenous conductor. Images from twomore » samples are examined, one annealed with large lamellar grains and one unannealed with small grains. The average value off is 0.45 ± 0.04 for the annealed sample, and 0.37 ± 0.03 for the unannealed sample, both close to the value predicted by effective medium theory, 1/2. Simulated conductivities are compared to published experimental conductivities. The value of f Unannealed/f Annealed is 0.82 for simulations and 6.2 for experiments. Simulation results correspond well to predictions by effective medium theory but do not explain the experimental measurements. Finally, observation of nanoscale morphology over length scales greater than the size of the micrographs (~1 μm) may be required to explain the experimental results.« less

Deterministic quantum annealing expectation-maximization algorithm

NASA Astrophysics Data System (ADS)

Miyahara, Hideyuki; Tsumura, Koji; Sughiyama, Yuki

2017-11-01

Maximum likelihood estimation (MLE) is one of the most important methods in machine learning, and the expectation-maximization (EM) algorithm is often used to obtain maximum likelihood estimates. However, EM heavily depends on initial configurations and fails to find the global optimum. On the other hand, in the field of physics, quantum annealing (QA) was proposed as a novel optimization approach. Motivated by QA, we propose a quantum annealing extension of EM, which we call the deterministic quantum annealing expectation-maximization (DQAEM) algorithm. We also discuss its advantage in terms of the path integral formulation. Furthermore, by employing numerical simulations, we illustrate how DQAEM works in MLE and show that DQAEM moderate the problem of local optima in EM.

Self-assembly of single-wall carbon nanotubes during the cooling process of hot carbon gas.

PubMed

Wen, Yushi; Zheng, Ke; Long, Xinping; Li, Ming; Xue, Xianggui; Dai, Xiaogan; Deng, Chuan

2018-04-25

In this work, self-assembly mechanism of single-wall carbon nanotube (SWCNT) during the annealing process of hot gaseous carbon is presented using reactive force field (ReaxFF)-based reactive molecular simulations. A series of simulations were performed on the evolution of reactive carbon gas. The simulation results show that the reactive carbon gas can be assembled into regular SWCNT without a catalyst. Five distinct stages of SWCNT self-assembly are proposed. For some initial configurations, the CNT was found to spin at an ultra-high rate after the nucleation. Graphical abstract Self-assembly process of single-wall carbon nanotube from the annealing of hot gaseous carbon.

Parameterization of annealing kinetics in pharmaceutical glasses.

PubMed

Hodge, Ian M

2013-07-01

Numerical simulations indicate that neglecting the canonical nonlinearity of glassy-state annealing kinetics in pharmaceutical (and other) glasses leads to good KWW fits to the dependence of enthalpy on annealing time, but with spurious KWW parameters that are affected by nonlinearity. A simplified treatment of nonlinearity that uses the Struik shift factor is found to be a useful approximation for these analyses, and can account for previously reported differences between linear and nonlinear KWW parameters (Kawakami K, Pikal MJ. 2005. J Pharm Sci 94:948-965). Copyright © 2013 Wiley Periodicals, Inc.

Non-stoquastic Hamiltonians in quantum annealing via geometric phases

NASA Astrophysics Data System (ADS)

Vinci, Walter; Lidar, Daniel A.

2017-09-01

We argue that a complete description of quantum annealing implemented with continuous variables must take into account the non-adiabatic Aharonov-Anandan geometric phase that arises when the system Hamiltonian changes during the anneal. We show that this geometric effect leads to the appearance of non-stoquasticity in the effective quantum Ising Hamiltonians that are typically used to describe quantum annealing with flux qubits. We explicitly demonstrate the effect of this geometric non-stoquasticity when quantum annealing is performed with a system of one and two coupled flux qubits. The realization of non-stoquastic Hamiltonians has important implications from a computational complexity perspective, since it is believed that in many cases quantum annealing with stoquastic Hamiltonians can be efficiently simulated via classical algorithms such as Quantum Monte Carlo. It is well known that the direct implementation of non-stoquastic Hamiltonians with flux qubits is particularly challenging. Our results suggest an alternative path for the implementation of non-stoquasticity via geometric phases that can be exploited for computational purposes.

Simulated annealing algorithm for solving chambering student-case assignment problem

NASA Astrophysics Data System (ADS)

Ghazali, Saadiah; Abdul-Rahman, Syariza

2015-12-01

The problem related to project assignment problem is one of popular practical problem that appear nowadays. The challenge of solving the problem raise whenever the complexity related to preferences, the existence of real-world constraints and problem size increased. This study focuses on solving a chambering student-case assignment problem by using a simulated annealing algorithm where this problem is classified under project assignment problem. The project assignment problem is considered as hard combinatorial optimization problem and solving it using a metaheuristic approach is an advantage because it could return a good solution in a reasonable time. The problem of assigning chambering students to cases has never been addressed in the literature before. For the proposed problem, it is essential for law graduates to peruse in chambers before they are qualified to become legal counselor. Thus, assigning the chambering students to cases is a critically needed especially when involving many preferences. Hence, this study presents a preliminary study of the proposed project assignment problem. The objective of the study is to minimize the total completion time for all students in solving the given cases. This study employed a minimum cost greedy heuristic in order to construct a feasible initial solution. The search then is preceded with a simulated annealing algorithm for further improvement of solution quality. The analysis of the obtained result has shown that the proposed simulated annealing algorithm has greatly improved the solution constructed by the minimum cost greedy heuristic. Hence, this research has demonstrated the advantages of solving project assignment problem by using metaheuristic techniques.

Determining Annealing Temperatures for Polymerase Chain Reaction

ERIC Educational Resources Information Center

Porta, Angela R.; Enners, Edward

2012-01-01

The polymerase chain reaction (PCR) is a common technique used in high school and undergraduate science teaching. Students often do not fully comprehend the underlying principles of the technique and how optimization of the protocol affects the outcome and analysis. In this molecular biology laboratory, students learn the steps of PCR with an…

Solving the patient zero inverse problem by using generalized simulated annealing

NASA Astrophysics Data System (ADS)

Menin, Olavo H.; Bauch, Chris T.

2018-01-01

Identifying patient zero - the initially infected source of a given outbreak - is an important step in epidemiological investigations of both existing and emerging infectious diseases. Here, the use of the Generalized Simulated Annealing algorithm (GSA) to solve the inverse problem of finding the source of an outbreak is studied. The classical disease natural histories susceptible-infected (SI), susceptible-infected-susceptible (SIS), susceptible-infected-recovered (SIR) and susceptible-infected-recovered-susceptible (SIRS) in a regular lattice are addressed. Both the position of patient zero and its time of infection are considered unknown. The algorithm performance with respect to the generalization parameter q˜v and the fraction ρ of infected nodes for whom infection was ascertained is assessed. Numerical experiments show the algorithm is able to retrieve the epidemic source with good accuracy, even when ρ is small, but present no evidence to support that GSA performs better than its classical version. Our results suggest that simulated annealing could be a helpful tool for identifying patient zero in an outbreak where not all cases can be ascertained.

Robust quantum optimizer with full connectivity.

PubMed

Nigg, Simon E; Lörch, Niels; Tiwari, Rakesh P

2017-04-01

Quantum phenomena have the potential to speed up the solution of hard optimization problems. For example, quantum annealing, based on the quantum tunneling effect, has recently been shown to scale exponentially better with system size than classical simulated annealing. However, current realizations of quantum annealers with superconducting qubits face two major challenges. First, the connectivity between the qubits is limited, excluding many optimization problems from a direct implementation. Second, decoherence degrades the success probability of the optimization. We address both of these shortcomings and propose an architecture in which the qubits are robustly encoded in continuous variable degrees of freedom. By leveraging the phenomenon of flux quantization, all-to-all connectivity with sufficient tunability to implement many relevant optimization problems is obtained without overhead. Furthermore, we demonstrate the robustness of this architecture by simulating the optimal solution of a small instance of the nondeterministic polynomial-time hard (NP-hard) and fully connected number partitioning problem in the presence of dissipation.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

PubMed

Bratholm, Lars A; Jensen, Jan H

2017-03-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift.

Neighbourhood generation mechanism applied in simulated annealing to job shop scheduling problems

NASA Astrophysics Data System (ADS)

Cruz-Chávez, Marco Antonio

2015-11-01

This paper presents a neighbourhood generation mechanism for the job shop scheduling problems (JSSPs). In order to obtain a feasible neighbour with the generation mechanism, it is only necessary to generate a permutation of an adjacent pair of operations in a scheduling of the JSSP. If there is no slack time between the adjacent pair of operations that is permuted, then it is proven, through theory and experimentation, that the new neighbour (schedule) generated is feasible. It is demonstrated that the neighbourhood generation mechanism is very efficient and effective in a simulated annealing.

Analytical Applications of Monte Carlo Techniques.

ERIC Educational Resources Information Center

Guell, Oscar A.; Holcombe, James A.

1990-01-01

Described are analytical applications of the theory of random processes, in particular solutions obtained by using statistical procedures known as Monte Carlo techniques. Supercomputer simulations, sampling, integration, ensemble, annealing, and explicit simulation are discussed. (CW)

Self-Tuning of Design Variables for Generalized Predictive Control

NASA Technical Reports Server (NTRS)

Lin, Chaung; Juang, Jer-Nan

2000-01-01

Three techniques are introduced to determine the order and control weighting for the design of a generalized predictive controller. These techniques are based on the application of fuzzy logic, genetic algorithms, and simulated annealing to conduct an optimal search on specific performance indexes or objective functions. Fuzzy logic is found to be feasible for real-time and on-line implementation due to its smooth and quick convergence. On the other hand, genetic algorithms and simulated annealing are applicable for initial estimation of the model order and control weighting, and final fine-tuning within a small region of the solution space, Several numerical simulations for a multiple-input and multiple-output system are given to illustrate the techniques developed in this paper.

Effect of deposition rate on melting point of copper film catalyst substrate at atomic scale

NASA Astrophysics Data System (ADS)

Marimpul, Rinaldo; Syuhada, Ibnu; Rosikhin, Ahmad; Winata, Toto

2018-03-01

Annealing process of copper film catalyst substrate was studied by molcular dynamics simulation. This copper film catalyst substrate was produced using thermal evaporation method. The annealing process was limited in nanosecond order to observe the mechanism at atomic scale. We found that deposition rate parameter affected the melting point of catalyst substrate. The change of crystalline structure of copper atoms was observed before it had been already at melting point. The optimum annealing temperature was obtained to get the highest percentage of fcc structure on copper film catalyst substrate.

Simulated annealing model of acupuncture

NASA Astrophysics Data System (ADS)

Shang, Charles; Szu, Harold

2015-05-01

The growth control singularity model suggests that acupuncture points (acupoints) originate from organizers in embryogenesis. Organizers are singular points in growth control. Acupuncture can cause perturbation of a system with effects similar to simulated annealing. In clinical trial, the goal of a treatment is to relieve certain disorder which corresponds to reaching certain local optimum in simulated annealing. The self-organizing effect of the system is limited and related to the person's general health and age. Perturbation at acupoints can lead a stronger local excitation (analogous to higher annealing temperature) compared to perturbation at non-singular points (placebo control points). Such difference diminishes as the number of perturbed points increases due to the wider distribution of the limited self-organizing activity. This model explains the following facts from systematic reviews of acupuncture trials: 1. Properly chosen single acupoint treatment for certain disorder can lead to highly repeatable efficacy above placebo 2. When multiple acupoints are used, the result can be highly repeatable if the patients are relatively healthy and young but are usually mixed if the patients are old, frail and have multiple disorders at the same time as the number of local optima or comorbidities increases. 3. As number of acupoints used increases, the efficacy difference between sham and real acupuncture often diminishes. It predicted that the efficacy of acupuncture is negatively correlated to the disease chronicity, severity and patient's age. This is the first biological - physical model of acupuncture which can predict and guide clinical acupuncture research.

Effect of Annealing Treatments on the Microstructure, Mechanical Properties and Corrosion Behavior of Direct Metal Laser Sintered Ti-6Al-4V

NASA Astrophysics Data System (ADS)

Xu, Yangzi; Lu, Yuan; Sundberg, Kristin L.; Liang, Jianyu; Sisson, Richard D.

2017-05-01

An experimental investigation on the effects of post-annealing treatments on the microstructure, mechanical properties and corrosion behavior of direct metal laser sintered Ti-6Al-4V alloys has been conducted. The microstructure and phase evolution as affected by annealing treatment temperature were examined through scanning electron microscopy and x-ray diffraction. The tensile properties and Vickers hardness were measured and compared to the commercial Grade 5 Ti-6Al-4V alloy. Corrosion behavior of the parts was analyzed electrochemically in simulated body fluid at 37 °C. It was found out that the as-printed parts mainly composed of non-equilibrium α' phase. Annealing treatment allowed the transformation from α' to α phase and the development of β phase. The tensile test results indicated that post-annealing treatment could improve the ductility and decrease the strength. The as-printed Ti-6Al-4V part exhibits inferior corrosion resistance compared to the commercial alloy, and post-annealing treatment can reduce its susceptibility to corrosion by reducing the two-phase interface area.

Prediction of the thermal annealing of thick oxide metal-oxide-semiconductor dosimeters irradiated in a harsh radiation environment

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

Ravotti, F.; Glaser, M.; Saigne, F.

Radiation-sensing metal-oxide-semiconductor field-effect transistors produced by the laboratory LAAS-CNRS were exposed to a harsh hadron field that represents the real radiation environment expected at the CERN Large Hadron Collider experiments. The long-term stability of the transistor's I{sub ds}-V{sub gs} characteristic was investigated using the isochronal annealing technique. In this work, devices exposed to high intensity hadron levels ({phi}{>=}10{sup 12} neutrons/cm{sup 2}) show evidences of displacement damages in the I{sub ds}-V{sub gs} annealing behavior. By comparing experimental and simulated results over 14 months, the isochronal annealing method, originally devoted to oxide trapped charge, is shown to enable prediction of the recoverymore » of silicon bulk defects.« less

Calibrated work function mapping by Kelvin probe force microscopy

NASA Astrophysics Data System (ADS)

Fernández Garrillo, Pablo A.; Grévin, Benjamin; Chevalier, Nicolas; Borowik, Łukasz

2018-04-01

We propose and demonstrate the implementation of an alternative work function tip calibration procedure for Kelvin probe force microscopy under ultrahigh vacuum, using monocrystalline metallic materials with known crystallographic orientation as reference samples, instead of the often used highly oriented pyrolytic graphite calibration sample. The implementation of this protocol allows the acquisition of absolute and reproducible work function values, with an improved uncertainty with respect to unprepared highly oriented pyrolytic graphite-based protocols. The developed protocol allows the local investigation of absolute work function values over nanostructured samples and can be implemented in electronic structures and devices characterization as demonstrated over a nanostructured semiconductor sample presenting Al0.7Ga0.3As and GaAs layers with variable thickness. Additionally, using our protocol we find that the work function of annealed highly oriented pyrolytic graphite is equal to 4.6 ± 0.03 eV.

Bayesian Parameter Inference and Model Selection by Population Annealing in Systems Biology

PubMed Central

Murakami, Yohei

2014-01-01

Parameter inference and model selection are very important for mathematical modeling in systems biology. Bayesian statistics can be used to conduct both parameter inference and model selection. Especially, the framework named approximate Bayesian computation is often used for parameter inference and model selection in systems biology. However, Monte Carlo methods needs to be used to compute Bayesian posterior distributions. In addition, the posterior distributions of parameters are sometimes almost uniform or very similar to their prior distributions. In such cases, it is difficult to choose one specific value of parameter with high credibility as the representative value of the distribution. To overcome the problems, we introduced one of the population Monte Carlo algorithms, population annealing. Although population annealing is usually used in statistical mechanics, we showed that population annealing can be used to compute Bayesian posterior distributions in the approximate Bayesian computation framework. To deal with un-identifiability of the representative values of parameters, we proposed to run the simulations with the parameter ensemble sampled from the posterior distribution, named “posterior parameter ensemble”. We showed that population annealing is an efficient and convenient algorithm to generate posterior parameter ensemble. We also showed that the simulations with the posterior parameter ensemble can, not only reproduce the data used for parameter inference, but also capture and predict the data which was not used for parameter inference. Lastly, we introduced the marginal likelihood in the approximate Bayesian computation framework for Bayesian model selection. We showed that population annealing enables us to compute the marginal likelihood in the approximate Bayesian computation framework and conduct model selection depending on the Bayes factor. PMID:25089832

Iterative simulated quenching for designing irregular-spot-array generators.

PubMed

Gillet, J N; Sheng, Y

2000-07-10

We propose a novel, to our knowledge, algorithm of iterative simulated quenching with temperature rescaling for designing diffractive optical elements, based on an analogy between simulated annealing and statistical thermodynamics. The temperature is iteratively rescaled at the end of each quenching process according to ensemble statistics to bring the system back from a frozen imperfect state with a local minimum of energy to a dynamic state in a Boltzmann heat bath in thermal equilibrium at the rescaled temperature. The new algorithm achieves much lower cost function and reconstruction error and higher diffraction efficiency than conventional simulated annealing with a fast exponential cooling schedule and is easy to program. The algorithm is used to design binary-phase generators of large irregular spot arrays. The diffractive phase elements have trapezoidal apertures of varying heights, which fit ideal arbitrary-shaped apertures better than do trapezoidal apertures of fixed heights.

Understanding Quantum Tunneling through Quantum Monte Carlo Simulations.

PubMed

Isakov, Sergei V; Mazzola, Guglielmo; Smelyanskiy, Vadim N; Jiang, Zhang; Boixo, Sergio; Neven, Hartmut; Troyer, Matthias

2016-10-28

The tunneling between the two ground states of an Ising ferromagnet is a typical example of many-body tunneling processes between two local minima, as they occur during quantum annealing. Performing quantum Monte Carlo (QMC) simulations we find that the QMC tunneling rate displays the same scaling with system size, as the rate of incoherent tunneling. The scaling in both cases is O(Δ^{2}), where Δ is the tunneling splitting (or equivalently the minimum spectral gap). An important consequence is that QMC simulations can be used to predict the performance of a quantum annealer for tunneling through a barrier. Furthermore, by using open instead of periodic boundary conditions in imaginary time, equivalent to a projector QMC algorithm, we obtain a quadratic speedup for QMC simulations, and achieve linear scaling in Δ. We provide a physical understanding of these results and their range of applicability based on an instanton picture.

First-order design of geodetic networks using the simulated annealing method

NASA Astrophysics Data System (ADS)

Berné, J. L.; Baselga, S.

2004-09-01

The general problem of the optimal design for a geodetic network subject to any extrinsic factors, namely the first-order design problem, can be dealt with as a numeric optimization problem. The classic theory of this problem and the optimization methods are revised. Then the innovative use of the simulated annealing method, which has been successfully applied in other fields, is presented for this classical geodetic problem. This method, belonging to iterative heuristic techniques in operational research, uses a thermodynamical analogy to crystalline networks to offer a solution that converges probabilistically to the global optimum. Basic formulation and some examples are studied.

Sparse approximation problem: how rapid simulated annealing succeeds and fails

NASA Astrophysics Data System (ADS)

Obuchi, Tomoyuki; Kabashima, Yoshiyuki

2016-03-01

Information processing techniques based on sparseness have been actively studied in several disciplines. Among them, a mathematical framework to approximately express a given dataset by a combination of a small number of basis vectors of an overcomplete basis is termed the sparse approximation. In this paper, we apply simulated annealing, a metaheuristic algorithm for general optimization problems, to sparse approximation in the situation where the given data have a planted sparse representation and noise is present. The result in the noiseless case shows that our simulated annealing works well in a reasonable parameter region: the planted solution is found fairly rapidly. This is true even in the case where a common relaxation of the sparse approximation problem, the G-relaxation, is ineffective. On the other hand, when the dimensionality of the data is close to the number of non-zero components, another metastable state emerges, and our algorithm fails to find the planted solution. This phenomenon is associated with a first-order phase transition. In the case of very strong noise, it is no longer meaningful to search for the planted solution. In this situation, our algorithm determines a solution with close-to-minimum distortion fairly quickly.

Optimization of cladding parameters for resisting corrosion on low carbon steels using simulated annealing algorithm

NASA Astrophysics Data System (ADS)

Balan, A. V.; Shivasankaran, N.; Magibalan, S.

2018-04-01

Low carbon steels used in chemical industries are frequently affected by corrosion. Cladding is a surfacing process used for depositing a thick layer of filler metal in a highly corrosive materials to achieve corrosion resistance. Flux cored arc welding (FCAW) is preferred in cladding process due to its augmented efficiency and higher deposition rate. In this cladding process, the effect of corrosion can be minimized by controlling the output responses such as minimizing dilution, penetration and maximizing bead width, reinforcement and ferrite number. This paper deals with the multi-objective optimization of flux cored arc welding responses by controlling the process parameters such as wire feed rate, welding speed, Nozzle to plate distance, welding gun angle for super duplex stainless steel material using simulated annealing technique. Regression equation has been developed and validated using ANOVA technique. The multi-objective optimization of weld bead parameters was carried out using simulated annealing to obtain optimum bead geometry for reducing corrosion. The potentiodynamic polarization test reveals the balanced formation of fine particles of ferrite and autenite content with desensitized nature of the microstructure in the optimized clad bead.

Kinetics modeling of precipitation with characteristic shape during post-implantation annealing

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

Li, Kun-Dar, E-mail: kundar@mail.nutn.edu.tw; Chen, Kwanyu

2015-11-15

In this study, we investigated the precipitation with characteristic shape in the microstructure during post-implantation annealing via a theoretical modeling approach. The processes of precipitates formation and evolution during phase separation were based on a nucleation and growth mechanism of atomic diffusion. Different stages of the precipitation, including the nucleation, growth and coalescence, were distinctly revealed in the numerical simulations. In addition, the influences of ion dose, temperature and crystallographic symmetry on the processes of faceted precipitation were also demonstrated. To comprehend the kinetic mechanism, the simulation results were further analyzed quantitatively by the Kolmogorov-Johnson-Mehl-Avrami (KJMA) equation. The Avrami exponentsmore » obtained from the regression curves varied from 1.47 to 0.52 for different conditions. With the increase of ion dose and temperature, the nucleation and growth of precipitations were expedited in accordance with the shortened incubation time and the raised coefficient of growth rate. A miscellaneous shape of precipitates in various crystallographic symmetry systems could be simulated through this anisotropic model. From the analyses of the kinetics, more fundamental information about the nucleation and growth mechanism of faceted precipitation during post-implantation annealing was acquired for future application.« less

Excess oxygen limited diffusion and precipitation of iron in amorphous silicon dioxide

NASA Astrophysics Data System (ADS)

Leveneur, J.; Langlois, M.; Kennedy, J.; Metson, James B.

2017-10-01

In micro- and nano- electronic device fabrication, and particularly 3D designs, the diffusion of a metal into sublayers during annealing needs to be minimized as it is usually detrimental to device performance. Diffusion also causes the formation and growth of nanoprecipitates in solid matrices. In this paper, the diffusion behavior of low energy, low fluence, ion implanted iron into a thermally grown silicon oxide layer on silicon is investigated. Different ion beam analysis and imaging techniques were used. Magnetization measurements were also undertaken to provide evidence of nanocrystalline ordering. While standard vacuum furnace annealing and electron beam annealing lead to fast diffusion of the implanted species towards the Si/SiO2 interface, we show that furnace annealing in an oxygen rich atmosphere prevents the diffusion of iron that, in turn, limits the growth of the nanoparticles. The diffusion and particle growth is also greatly reduced when oxygen atoms are implanted in the SiO2 prior to Fe implantation, effectively acting as a diffusion barrier. The excess oxygen is hypothesized to trap Fe atoms and reduce their mean free path during the diffusion. Monte-Carlo simulations of the diffusion process which consider the random walk of Fe, Fick's diffusion of O atoms, Fe precipitation, and desorption of the SiO2 layer under the electron beam annealing were performed. Simulation results for the three preparation conditions are found in good agreement with the experimental data.

Dissipation in adiabatic quantum computers: lessons from an exactly solvable model

NASA Astrophysics Data System (ADS)

Keck, Maximilian; Montangero, Simone; Santoro, Giuseppe E.; Fazio, Rosario; Rossini, Davide

2017-11-01

We introduce and study the adiabatic dynamics of free-fermion models subject to a local Lindblad bath and in the presence of a time-dependent Hamiltonian. The merit of these models is that they can be solved exactly, and will help us to study the interplay between nonadiabatic transitions and dissipation in many-body quantum systems. After the adiabatic evolution, we evaluate the excess energy (the average value of the Hamiltonian) as a measure of the deviation from reaching the final target ground state. We compute the excess energy in a variety of different situations, where the nature of the bath and the Hamiltonian is modified. We find robust evidence of the fact that an optimal working time for the quantum annealing protocol emerges as a result of the competition between the nonadiabatic effects and the dissipative processes. We compare these results with the matrix-product-operator simulations of an Ising system and show that the phenomenology we found also applies for this more realistic case.

Depth profiles of oxygen precipitates in nitride-coated silicon wafers subjected to rapid thermal annealing

NASA Astrophysics Data System (ADS)

Voronkov, V. V.; Falster, R.; Kim, TaeHyeong; Park, SoonSung; Torack, T.

2013-07-01

Silicon wafers, coated with a silicon nitride layer and subjected to high temperature Rapid Thermal Annealing (RTA) in Ar, show—upon a subsequent two-step precipitation anneal cycle (such as 800 °C + 1000 °C)—peculiar depth profiles of oxygen precipitate densities. Some profiles are sharply peaked near the wafer surface, sometimes with a zero bulk density. Other profiles are uniform in depth. The maximum density is always the same. These profiles are well reproduced by simulations assuming that precipitation starts from a uniformly distributed small oxide plates originated from RTA step and composed of oxygen atoms and vacancies ("VO2 plates"). During the first step of the precipitation anneal, an oxide layer propagates around this core plate by a process of oxygen attachment, meaning that an oxygen-only ring-shaped plate emerges around the original plate. These rings, depending on their size, then either dissolve or grow during the second part of the anneal leading to a rich variety of density profiles.

Rapid shear alignment of sub-10 nm cylinder-forming block copolymer films based on thermal expansion mismatch

NASA Astrophysics Data System (ADS)

Nicaise, Samuel M.; Gadelrab, Karim R.; G, Amir Tavakkoli K.; Ross, Caroline A.; Alexander-Katz, Alfredo; Berggren, Karl K.

2018-01-01

Directed self-assembly of block copolymers (BCPs) provided by shear-stress can produce aligned sub-10 nm structures over large areas for applications in integrated circuits, next-generation data storage, and plasmonic structures. In this work, we present a fast, versatile BCP shear-alignment process based on coefficient of thermal expansion mismatch of the BCP film, a rigid top coat and a substrate. Monolayer and bilayer cylindrical microdomains of poly(styrene-b-dimethylsiloxane) aligned preferentially in-plane and orthogonal to naturally-forming or engineered cracks in the top coat film, allowing for orientation control over 1 cm2 substrates. Annealing temperatures, up to 275 °C, provided low-defect alignment up to 2 mm away from cracks for rapid (<1 min) annealing times. Finite-element simulations of the stress as a function of annealing time, annealing temperature, and distance from cracks showed that shear stress during the cooling phase of the thermal annealing was critical for the observed microdomain alignment.

Quantum Monte Carlo tunneling from quantum chemistry to quantum annealing

NASA Astrophysics Data System (ADS)

Mazzola, Guglielmo; Smelyanskiy, Vadim N.; Troyer, Matthias

2017-10-01

Quantum tunneling is ubiquitous across different fields, from quantum chemical reactions and magnetic materials to quantum simulators and quantum computers. While simulating the real-time quantum dynamics of tunneling is infeasible for high-dimensional systems, quantum tunneling also shows up in quantum Monte Carlo (QMC) simulations, which aim to simulate quantum statistics with resources growing only polynomially with the system size. Here we extend the recent results obtained for quantum spin models [Phys. Rev. Lett. 117, 180402 (2016), 10.1103/PhysRevLett.117.180402], and we study continuous-variable models for proton transfer reactions. We demonstrate that QMC simulations efficiently recover the scaling of ground-state tunneling rates due to the existence of an instanton path, which always connects the reactant state with the product. We discuss the implications of our results in the context of quantum chemical reactions and quantum annealing, where quantum tunneling is expected to be a valuable resource for solving combinatorial optimization problems.

Development of a Tool for an Efficient Calibration of CORSIM Models

DOT National Transportation Integrated Search

2014-08-01

This project proposes a Memetic Algorithm (MA) for the calibration of microscopic traffic flow simulation models. The proposed MA includes a combination of genetic and simulated annealing algorithms. The genetic algorithm performs the exploration of ...

Image-Based Airborne Sensors: A Combined Approach for Spectral Signatures Classification through Deterministic Simulated Annealing

PubMed Central

Guijarro, María; Pajares, Gonzalo; Herrera, P. Javier

2009-01-01

The increasing technology of high-resolution image airborne sensors, including those on board Unmanned Aerial Vehicles, demands automatic solutions for processing, either on-line or off-line, the huge amountds of image data sensed during the flights. The classification of natural spectral signatures in images is one potential application. The actual tendency in classification is oriented towards the combination of simple classifiers. In this paper we propose a combined strategy based on the Deterministic Simulated Annealing (DSA) framework. The simple classifiers used are the well tested supervised parametric Bayesian estimator and the Fuzzy Clustering. The DSA is an optimization approach, which minimizes an energy function. The main contribution of DSA is its ability to avoid local minima during the optimization process thanks to the annealing scheme. It outperforms simple classifiers used for the combination and some combined strategies, including a scheme based on the fuzzy cognitive maps and an optimization approach based on the Hopfield neural network paradigm. PMID:22399989

Robust quantum optimizer with full connectivity

PubMed Central

Nigg, Simon E.; Lörch, Niels; Tiwari, Rakesh P.

2017-01-01

Quantum phenomena have the potential to speed up the solution of hard optimization problems. For example, quantum annealing, based on the quantum tunneling effect, has recently been shown to scale exponentially better with system size than classical simulated annealing. However, current realizations of quantum annealers with superconducting qubits face two major challenges. First, the connectivity between the qubits is limited, excluding many optimization problems from a direct implementation. Second, decoherence degrades the success probability of the optimization. We address both of these shortcomings and propose an architecture in which the qubits are robustly encoded in continuous variable degrees of freedom. By leveraging the phenomenon of flux quantization, all-to-all connectivity with sufficient tunability to implement many relevant optimization problems is obtained without overhead. Furthermore, we demonstrate the robustness of this architecture by simulating the optimal solution of a small instance of the nondeterministic polynomial-time hard (NP-hard) and fully connected number partitioning problem in the presence of dissipation. PMID:28435880

Computer simulations of melts of randomly branching polymers

NASA Astrophysics Data System (ADS)

Rosa, Angelo; Everaers, Ralf

2016-10-01

Randomly branching polymers with annealed connectivity are model systems for ring polymers and chromosomes. In this context, the branched structure represents transient folding induced by topological constraints. Here we present computer simulations of melts of annealed randomly branching polymers of 3 ≤ N ≤ 1800 segments in d = 2 and d = 3 dimensions. In all cases, we perform a detailed analysis of the observed tree connectivities and spatial conformations. Our results are in excellent agreement with an asymptotic scaling of the average tree size of R ˜ N1/d, suggesting that the trees behave as compact, territorial fractals. The observed swelling relative to the size of ideal trees, R ˜ N1/4, demonstrates that excluded volume interactions are only partially screened in melts of annealed trees. Overall, our results are in good qualitative agreement with the predictions of Flory theory. In particular, we find that the trees swell by the combination of modified branching and path stretching. However, the former effect is subdominant and difficult to detect in d = 3 dimensions.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.

PubMed Central

2017-01-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1–0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift. PMID:28451325

Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

PubMed

Smith, Colin A; Kortemme, Tanja

2011-01-01

Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface), interactions between and within parts of the structure (e.g. domains) can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

Computational Thermodynamics Characterization of 7075, 7039, and 7020 Aluminum Alloys Using JMatPro

DTIC Science & Technology

2011-09-01

parameters of temperature and time may be selected to simulate effects on microstructure during annealing , solution treating, quenching, and tempering...nucleation may be taken into account by use of a wetting angle function. Activation energy may be taken into account for rapidly quenched alloys...the stable forms of precipitates that result from solutionizing, annealing or intermediate heat treatment, and phase formation during nonequilibrium

A modular tooling set-up for incremental sheet forming (ISF) with subsequent stress-relief annealing under partial constraints

NASA Astrophysics Data System (ADS)

Maqbool, Fawad; Bambach, Markus

2017-10-01

Incremental sheet forming (ISF) is a manufacturing process most suitable for small-batch production of sheet metal parts. In ISF, a CNC-controlled tool moves over the sheet metal, following a specified contour to form a part of the desired geometry. This study focuses on one of the dominant process limitations associated with the ISF, i.e., the limited geometrical accuracy. In this regard, a case study is performed which shows that increased geometrical accuracy of the formed part can be achieved by a using stress-relief annealing before unclamping. To keep the tooling costs low, a modular die design consisting of a stiff metal frame and inserts made from inexpensive plastics (Sika®) were devised. After forming, the plastics inserts are removed. The metal frame supports the part during stress-relief annealing. Finite Element (FE) simulations of the manufacturing process are performed. Due to the residual stresses induced during the forming, the geometry of the formed part, from FE simulation and the actual manufacturing process, shows severe distortion upon unclamping the part. Stress relief annealing of the formed part under partial constraints exerted by the tool frame shows that a part with high geometrical accuracy can be obtained.

Annealing effect on thermodynamic and physical properties of mesoporous silicon: A simulation and nitrogen sorption study

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

Kumar, Pushpendra, E-mail: pkumar-iitd@yahoo.com; Huber, Patrick, E-mail: patrick.huber@tuhh.de

Discovery of porous silicon formation in silicon substrate in 1956 while electro-polishing crystalline Si in hydrofluoric acid (HF), has triggered large scale investigations of porous silicon formation and their changes in physical and chemical properties with thermal and chemical treatment. A nitrogen sorption study is used to investigate the effect of thermal annealing on electrochemically etched mesoporous silicon (PS). The PS was thermally annealed from 200°C to 800°C for 1 hr in the presence of air. It was shown that the pore diameter and porosity of PS vary with annealing temperature. The experimentally obtained adsorption / desorption isotherms show hysteresis typicalmore » for capillary condensation in porous materials. A simulation study based on Saam and Cole model was performed and compared with experimentally observed sorption isotherms to study the physics behind of hysteresis formation. We discuss the shape of the hysteresis loops in the framework of the morphology of the layers. The different behavior of adsorption and desorption of nitrogen in PS with pore diameter was discussed in terms of concave menisci formation inside the pore space, which was shown to related with the induced pressure in varying the pore diameter from 7.2 nm to 3.4 nm.« less

Differential evolution-simulated annealing for multiple sequence alignment

NASA Astrophysics Data System (ADS)

Addawe, R. C.; Addawe, J. M.; Sueño, M. R. K.; Magadia, J. C.

2017-10-01

Multiple sequence alignments (MSA) are used in the analysis of molecular evolution and sequence structure relationships. In this paper, a hybrid algorithm, Differential Evolution - Simulated Annealing (DESA) is applied in optimizing multiple sequence alignments (MSAs) based on structural information, non-gaps percentage and totally conserved columns. DESA is a robust algorithm characterized by self-organization, mutation, crossover, and SA-like selection scheme of the strategy parameters. Here, the MSA problem is treated as a multi-objective optimization problem of the hybrid evolutionary algorithm, DESA. Thus, we name the algorithm as DESA-MSA. Simulated sequences and alignments were generated to evaluate the accuracy and efficiency of DESA-MSA using different indel sizes, sequence lengths, deletion rates and insertion rates. The proposed hybrid algorithm obtained acceptable solutions particularly for the MSA problem evaluated based on the three objectives.

Simulated annealing with restart strategy for the blood pickup routing problem

NASA Astrophysics Data System (ADS)

Yu, V. F.; Iswari, T.; Normasari, N. M. E.; Asih, A. M. S.; Ting, H.

2018-04-01

This study develops a simulated annealing heuristic with restart strategy (SA_RS) for solving the blood pickup routing problem (BPRP). BPRP minimizes the total length of the routes for blood bag collection between a blood bank and a set of donation sites, each associated with a time window constraint that must be observed. The proposed SA_RS is implemented in C++ and tested on benchmark instances of the vehicle routing problem with time windows to verify its performance. The algorithm is then tested on some newly generated BPRP instances and the results are compared with those obtained by CPLEX. Experimental results show that the proposed SA_RS heuristic effectively solves BPRP.

Airport Flight Departure Delay Model on Improved BN Structure Learning

NASA Astrophysics Data System (ADS)

Cao, Weidong; Fang, Xiangnong

An high score prior genetic simulated annealing Bayesian network structure learning algorithm (HSPGSA) by combining genetic algorithm(GA) with simulated annealing algorithm(SAA) is developed. The new algorithm provides not only with strong global search capability of GA, but also with strong local hill climb search capability of SAA. The structure with the highest score is prior selected. In the mean time, structures with lower score are also could be choice. It can avoid efficiently prematurity problem by higher score individual wrong direct growing population. Algorithm is applied to flight departure delays analysis in a large hub airport. Based on the flight data a BN model is created. Experiments show that parameters learning can reflect departure delay.

Distributed genetic algorithms for the floorplan design problem

NASA Technical Reports Server (NTRS)

Cohoon, James P.; Hegde, Shailesh U.; Martin, Worthy N.; Richards, Dana S.

1991-01-01

Designing a VLSI floorplan calls for arranging a given set of modules in the plane to minimize the weighted sum of area and wire-length measures. A method of solving the floorplan design problem using distributed genetic algorithms is presented. Distributed genetic algorithms, based on the paleontological theory of punctuated equilibria, offer a conceptual modification to the traditional genetic algorithms. Experimental results on several problem instances demonstrate the efficacy of this method and indicate the advantages of this method over other methods, such as simulated annealing. The method has performed better than the simulated annealing approach, both in terms of the average cost of the solutions found and the best-found solution, in almost all the problem instances tried.

Simulated annealing in networks for computing possible arrangements for red and green cones

NASA Technical Reports Server (NTRS)

Ahumada, Albert J., Jr.

1987-01-01

Attention is given to network models in which each of the cones of the retina is given a provisional color at random, and then the cones are allowed to determine the colors of their neighbors through an iterative process. A symmetric-structure spin-glass model has allowed arrays to be generated from completely random arrangements of red and green to arrays with approximately as much disorder as the parafoveal cones. Simulated annealing has also been added to the process in an attempt to generate color arrangements with greater regularity and hence more revealing moirepatterns than than the arrangements yielded by quenched spin-glass processes. Attention is given to the perceptual implications of these results.

Radiation Resistance Studies of Amorphous Silicon Alloy Photovoltaic Materials

NASA Technical Reports Server (NTRS)

Woodyard, James R.

1994-01-01

The radiation resistance of commercial solar cells fabricated from hydrogenated amorphous silicon alloys was investigated. A number of different device structures were irradiated with 1.0 MeV protons. The cells were insensitive to proton fluences below 1E12 sq cm. The parameters of the irradiated cells were restored with annealing at 200 C. The annealing time was dependent on proton fluence. Annealing devices for one hour restores cell parameters for fluences below lE14 sq cm require longer annealing times. A parametric fitting model was used to characterize current mechanisms observed in dark I-V measurements. The current mechanisms were explored with irradiation fluence, and voltage and light soaking times. The thermal generation current density and quality factor increased with proton fluence. Device simulation shows the degradation in cell characteristics may be explained by the reduction of the electric field in the intrinsic layer.

Investigation of the stability and 1.0 MeV proton radiation resistance of commercially produced hydrogenated amorphous silicon alloy solar cells

NASA Technical Reports Server (NTRS)

Lord, Kenneth R., II; Walters, Michael R.; Woodyard, James R.

1994-01-01

The radiation resistance of commercial solar cells fabricated from hydrogenated amorphous silicon alloys is reported. A number of different device structures were irradiated with 1.0 MeV protons. The cells were annealing at 200 C. The annealing time was dependent on proton fluence. Annealing devices for one hour restores cell parameters or fluences below 1(exp 14) cm(exp -2); fluences above 1(exp 14) cm(exp -2) require longer annealing times. A parametric fitting model was used to characterize current mechanisms observed in dark I-V measurements. The current mechanisms were explored with irradiation fluence, and voltage and light soaking times. The thermal generation current density and quality factor increased with proton fluence. Device simulation shows the degradation in cell characteristics may be explained by the reduction of the electric field in the intrinsic layer.

Optimization of conditions for thermal smoothing GaAs surfaces

NASA Astrophysics Data System (ADS)

Akhundov, I. O.; Kazantsev, D. M.; Kozhuhov, A. S.; Alperovich, V. L.

2018-03-01

GaAs thermal smoothing by annealing in conditions which are close to equilibrium between the surface and vapors of As and Ga was earlier proved to be effective for the step-terraced surface formation on epi-ready substrates with a small root-mean-square roughness (Rq ≤ 0.15 nm). In the present study, this technique is further developed in order to reduce the annealing duration and to smooth GaAs samples with a larger initial roughness. To this end, we proposed a two-stage anneal with the first high-temperature stage aimed at smoothing "coarse" relief features and the second stage focused on "fine" smoothing at a lower temperature. The optimal temperatures and durations of two-stage annealing are found by Monte Carlo simulations and adjusted after experimentation. It is proved that the temperature and duration of the first high-temperature stage are restricted by the surface roughening, which occurs due to deviations from equilibrium conditions.

Investigation of the binding of a carbohydrate-mimetic peptide to its complementary anticarbohydrate antibody by STD-NMR spectroscopy and molecular-dynamics simulations.

PubMed

Szczepina, Monica G; Bleile, Dustin W; Pinto, B Mario

2011-10-04

Saturation transfer difference (STD)-NMR spectroscopy was used to probe experimentally the bioactive solution conformation of the carbohydrate mimic MDWNMHAA 1 of the O-polysaccharide of Shigella flexneri Y when bound to its complementary antibody, mAb SYA/J6. Molecular dynamics simulations using the ZymeCAD™ Molecular Dynamics platform were also undertaken to give a more accurate picture of the conformational flexibility and the possibilities for bound ligand conformations. The ligand topology, or the dynamic epitope, was mapped with the CORCEMA-ST (COmplete Relaxation and Conformational Exchange Matrix Analysis of Saturation Transfer) program that calculates a total matrix analysis of relaxation and exchange effects to generate predicted STD-NMR intensities from simulation. The comparison of these predicted STD enhancements with experimental data was used to select a representative binding mode. A protocol that employed theoretical STD effects calculated at snapshots during the entire course of a molecular dynamics (MD) trajectory of the peptide bound to the Fv portion of the antibody, and not the averaged atomic positions of receptor-ligand complexes, was also examined. In addition, the R factor was calculated on the basis of STD (fit) to avoid T1 bias, and an effective R factor, R(eff), was defined such that if the calculated STD (fit) for proton k was within error of the experimental STD (fit) for proton k, then that calculated STD (fit) for proton k was not included in the calculation of the R factor. This protocol was effective in deriving the antibody-bound solution conformation of the peptide which also differed from the bound conformation determined by X-ray crystallography; however, several discrepancies between experimental and calculated STD (fit) values were observed. The bound conformation was therefore further refined with a simulated annealing refinement protocol known as STD-NMR intensity-restrained CORCEMA optimization (SICO) to give a more accurate representation of the bound peptide epitope. Further optimization was required in this case, but a satisfactory correlation between experimental and calculated STD values was obtained. Attempts were also made to obtain STD enhancements with a synthetic pentasaccharide hapten, corresponding to the O-polysaccharide, while bound to the antibody. However, unfavorable kinetics of binding in this system prevented sufficient STD build-up, which, in turn, hindered a rigorous analysis via full STD build-up curves. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improved amplification results following episodes of failure to amplify at the Amelogenin Locus using PowerPlex® ESI 16 Fast System.

PubMed

Berlyne, Sigal; Oz, Carla; Einot, Naftaly; Avraham, Shlomit; Ram, Tanya; Goldberg, Miri D; Gafny, Ron

2017-07-01

In 2012 the Israel Police DNA Casework laboratory adopted the 16 STR PowerPlex ® ESI kit for routine use. The Promega Company updated this kit and developed the PowerPlex ® ESI 16 Fast System in which all autosomal primer pairs remained identical to the original set, except at the amelogenin site. The master mix was improved and optimized which allowed for direct, faster and more robust amplification. Prior to implementing the PowerPlex ® ESI 16 Fast System in our lab, we conducted a preliminary assay where 213 casework samples were amplified using the new kit. These samples had previously been extracted by one of two extraction kits employed by our lab. (the PrepFiler ExpressTM and PrepFiler BTATM Forensic DNA Extraction Kits). The amplification results from these samples were compared to samples amplified using the original PowerPlex ® ESI 16 kit. Multiple incidents of failure to amplify at the amelogenin locus were noted using the new system with the recommended protocol at a rate of 13% (28 of 213 samples). Experiments were performed to understand whether these amplification failures could be a result of primer binding site mutations, extraction method reagents and/or inhibitors. The conclusions reached following these experiments, in conjunction with consultation with the manufacturer, led to the trial of a modified amplification protocol where the suggested annealing temperature was reduced by 2 degrees. To evaluate the efficiency of this altered protocol, a comparison study was undertaken where 88 additional casework samples were chosen and amplified using both the modified 58°C and the recommended 60°C annealing temperatures. We concluded that the most effective method in our laboratory for achieving a consistent and balanced amplification at the amelogenin locus was to reduce the annealing temperature from the manufacturer's recommended 60°C to 58°C. This modification resulted in a reduction of the failure to amplify at the amelogenin locus from 13% (28/213) to 1.1% (1/88) without any observed changes to the autosomal STR amplification results. Copyright © 2017 Elsevier B.V. All rights reserved.

Diffusion and Stability of Hydrogen in Mg-Doped GaN: A Density Functional Study

NASA Astrophysics Data System (ADS)

Park, Ji-Sang; Chang, Kee Joo

2012-06-01

Using hybrid functional calculations, we study the diffusion and thermal stability of hydrogen in Mg-doped GaN. Compared with the generalized gradient approximation, we obtain a higher activation barrier for dissociating a Mg-H complex, which is attributed to the increase in the binding energy of Mg-H. Kinetic Monte Carlo simulations yield the annealing temperature of around 800 °C for activating Mg acceptors, close to the measured values. The results provide an insight to understanding the annealing effect such that the annealing temperature generally increases with the Mg-H concentration, and the retrapping of H is partly responsible for the low doping efficiencies at high Mg concentrations.

A Genetic Algorithm for the Generation of Packetization Masks for Robust Image Communication

PubMed Central

Zapata-Quiñones, Katherine; Duran-Faundez, Cristian; Gutiérrez, Gilberto; Lecuire, Vincent; Arredondo-Flores, Christopher; Jara-Lipán, Hugo

2017-01-01

Image interleaving has proven to be an effective solution to provide the robustness of image communication systems when resource limitations make reliable protocols unsuitable (e.g., in wireless camera sensor networks); however, the search for optimal interleaving patterns is scarcely tackled in the literature. In 2008, Rombaut et al. presented an interesting approach introducing a packetization mask generator based in Simulated Annealing (SA), including a cost function, which allows assessing the suitability of a packetization pattern, avoiding extensive simulations. In this work, we present a complementary study about the non-trivial problem of generating optimal packetization patterns. We propose a genetic algorithm, as an alternative to the cited work, adopting the mentioned cost function, then comparing it to the SA approach and a torus automorphism interleaver. In addition, we engage the validation of the cost function and provide results attempting to conclude about its implication in the quality of reconstructed images. Several scenarios based on visual sensor networks applications were tested in a computer application. Results in terms of the selected cost function and image quality metric PSNR show that our algorithm presents similar results to the other approaches. Finally, we discuss the obtained results and comment about open research challenges. PMID:28452934

Atomistic insights into the nanosecond long amorphization and crystallization cycle of nanoscale G e2S b2T e5 : An ab initio molecular dynamics study

NASA Astrophysics Data System (ADS)

Branicio, Paulo S.; Bai, Kewu; Ramanarayan, H.; Wu, David T.; Sullivan, Michael B.; Srolovitz, David J.

2018-04-01

The complete process of amorphization and crystallization of the phase-change material G e2S b2T e5 is investigated using nanosecond ab initio molecular dynamics simulations. Varying the quench rate during the amorphization phase of the cycle results in the generation of a variety of structures from entirely crystallized (-0.45 K/ps) to entirely amorphized (-16 K/ps). The 1.5-ns annealing simulations indicate that the crystallization process depends strongly on both the annealing temperature and the initial amorphous structure. The presence of crystal precursors (square rings) in the amorphous matrix enhances nucleation/crystallization kinetics. The simulation data are used to construct a combined continuous-cooling-transformation (CCT) and temperature-time-transformation (TTT) diagram. The nose of the CCT-TTT diagram corresponds to the minimum time for the onset of homogenous crystallization and is located at 600 K and 70 ps. That corresponds to a critical cooling rate for amorphization of -4.5 K/ps. The results, in excellent agreement with experimental observations, suggest that a strategy that utilizes multiple quench rates and annealing temperatures may be used to effectively optimize the reversible switching speed and enable fast and energy-efficient phase-change memories.

Designing a practical system for spectral imaging of skylight.

PubMed

López-Alvarez, Miguel A; Hernández-Andrés, Javier; Romero, Javier; Lee, Raymond L

2005-09-20

In earlier work [J. Opt. Soc. Am. A 21, 13-23 (2004)], we showed that a combination of linear models and optimum Gaussian sensors obtained by an exhaustive search can recover daylight spectra reliably from broadband sensor data. Thus our algorithm and sensors could be used to design an accurate, relatively inexpensive system for spectral imaging of daylight. Here we improve our simulation of the multispectral system by (1) considering the different kinds of noise inherent in electronic devices such as change-coupled devices (CCDs) or complementary metal-oxide semiconductors (CMOS) and (2) extending our research to a different kind of natural illumination, skylight. Because exhaustive searches are expensive computationally, here we switch to a simulated annealing algorithm to define the optimum sensors for recovering skylight spectra. The annealing algorithm requires us to minimize a single cost function, and so we develop one that calculates both the spectral and colorimetric similarity of any pair of skylight spectra. We show that the simulated annealing algorithm yields results similar to the exhaustive search but with much less computational effort. Our technique lets us study the properties of optimum sensors in the presence of noise, one side effect of which is that adding more sensors may not improve the spectral recovery.

Simulated Annealing-based Optimal Proportional-Integral-Derivative (PID) Controller Design: A Case Study on Nonlinear Quadcopter Dynamics

NASA Astrophysics Data System (ADS)

Nemirsky, Kristofer Kevin

In this thesis, the history and evolution of rotor aircraft with simulated annealing-based PID application were reviewed and quadcopter dynamics are presented. The dynamics of a quadcopter were then modeled, analyzed, and linearized. A cascaded loop architecture with PID controllers was used to stabilize the plant dynamics, which was improved upon through the application of simulated annealing (SA). A Simulink model was developed to test the controllers and verify the functionality of the proposed control system design. In addition, the data that the Simulink model provided were compared with flight data to present the validity of derived dynamics as a proper mathematical model representing the true dynamics of the quadcopter system. Then, the SA-based global optimization procedure was applied to obtain optimized PID parameters. It was observed that the tuned gains through the SA algorithm produced a better performing PID controller than the original manually tuned one. Next, we investigated the uncertain dynamics of the quadcopter setup. After adding uncertainty to the gyroscopic effects associated with pitch-and-roll rate dynamics, the controllers were shown to be robust against the added uncertainty. A discussion follows to summarize SA-based algorithm PID controller design and performance outcomes. Lastly, future work on SA application on multi-input-multi-output (MIMO) systems is briefly discussed.

Prediction of Flood Warning in Taiwan Using Nonlinear SVM with Simulated Annealing Algorithm

NASA Astrophysics Data System (ADS)

Lee, C.

2013-12-01

The issue of the floods is important in Taiwan. It is because the narrow and high topography of the island make lots of rivers steep in Taiwan. The tropical depression likes typhoon always causes rivers to flood. Prediction of river flow under the extreme rainfall circumstances is important for government to announce the warning of flood. Every time typhoon passed through Taiwan, there were always floods along some rivers. The warning is classified to three levels according to the warning water levels in Taiwan. The propose of this study is to predict the level of floods warning from the information of precipitation, rainfall duration and slope of riverbed. To classify the level of floods warning by the above-mentioned information and modeling the problems, a machine learning model, nonlinear Support vector machine (SVM), is formulated to classify the level of floods warning. In addition, simulated annealing (SA), a probabilistic heuristic algorithm, is used to determine the optimal parameter of the SVM model. A case study of flooding-trend rivers of different gradients in Taiwan is conducted. The contribution of this SVM model with simulated annealing is capable of making efficient announcement for flood warning and keeping the danger of flood from residents along the rivers.

Towards global optimization with adaptive simulated annealing

NASA Astrophysics Data System (ADS)

Forbes, Gregory W.; Jones, Andrew E.

1991-01-01

The structure of the simulated annealing algorithm is presented and its rationale is discussed. A unifying heuristic is then introduced which serves as a guide in the design of all of the sub-components of the algorithm. Simply put this heuristic principle states that at every cycle in the algorithm the occupation density should be kept as close as possible to the equilibrium distribution. This heuristic has been used as a guide to develop novel step generation and temperature control methods intended to improve the efficiency of the simulated annealing algorithm. The resulting algorithm has been used in attempts to locate good solutions for one of the lens design problems associated with this conference viz. the " monochromatic quartet" and a sample of the results is presented. 1 Global optimization in the context oflens design Whatever the context optimization algorithms relate to problems that take the following form: Given some configuration space with coordinates r (x1 . . x) and a merit function written asffr) find the point r whereftr) takes it lowest value. That is find the global minimum. In many cases there is also a set of auxiliary constraints that must be met so the problem statement becomes: Find the global minimum of the merit function within the region defined by E. (r) 0 j 1 2 . . . p and 0 j 1 2 . . . q.

Toll-Like Receptor-9-Mediated Invasion in Breast Cancer

DTIC Science & Technology

2011-07-01

Molecular Dynamics Simulations. Theoretical structural models were obtained from molecular dynamics simulations using explicit solvation by...with AMBER by MARDIGRAS. The solution structure was then derived by coupling the resulting NMR distance restraints with a molecular dynamic ...Overlay of NMR restrained structure (red) with theoretical molecular dynamic simulated annealing structure (blue). Energetic stability of the 9-mer

Quantum Optimization of Fully Connected Spin Glasses

NASA Astrophysics Data System (ADS)

Venturelli, Davide; Mandrà, Salvatore; Knysh, Sergey; O'Gorman, Bryan; Biswas, Rupak; Smelyanskiy, Vadim

2015-07-01

Many NP-hard problems can be seen as the task of finding a ground state of a disordered highly connected Ising spin glass. If solutions are sought by means of quantum annealing, it is often necessary to represent those graphs in the annealer's hardware by means of the graph-minor embedding technique, generating a final Hamiltonian consisting of coupled chains of ferromagnetically bound spins, whose binding energy is a free parameter. In order to investigate the effect of embedding on problems of interest, the fully connected Sherrington-Kirkpatrick model with random ±1 couplings is programmed on the D-Wave TwoTM annealer using up to 270 qubits interacting on a Chimera-type graph. We present the best embedding prescriptions for encoding the Sherrington-Kirkpatrick problem in the Chimera graph. The results indicate that the optimal choice of embedding parameters could be associated with the emergence of the spin-glass phase of the embedded problem, whose presence was previously uncertain. This optimal parameter setting allows the performance of the quantum annealer to compete with (and potentially outperform, in the absence of analog control errors) optimized simulated annealing algorithms.

Minimizing distortion and internal forces in truss structures by simulated annealing

NASA Technical Reports Server (NTRS)

Kincaid, Rex K.

1989-01-01

Inaccuracies in the length of members and the diameters of joints of large truss reflector backup structures may produce unacceptable levels of surface distortion and member forces. However, if the member lengths and joint diameters can be measured accurately it is possible to configure the members and joints so that root-mean-square (rms) surface error and/or rms member forces is minimized. Following Greene and Haftka (1989) it is assumed that the force vector f is linearly proportional to the member length errors e(sub M) of dimension NMEMB (the number of members) and joint errors e(sub J) of dimension NJOINT (the number of joints), and that the best-fit displacement vector d is a linear function of f. Let NNODES denote the number of positions on the surface of the truss where error influences are measured. The solution of the problem is discussed. To classify, this problem was compared to a similar combinatorial optimization problem. In particular, when only the member length errors are considered, minimizing d(sup 2)(sub rms) is equivalent to the quadratic assignment problem. The quadratic assignment problem is a well known NP-complete problem in operations research literature. Hence minimizing d(sup 2)(sub rms) is is also an NP-complete problem. The focus of the research is the development of a simulated annealing algorithm to reduce d(sup 2)(sub rms). The plausibility of this technique is its recent success on a variety of NP-complete combinatorial optimization problems including the quadratic assignment problem. A physical analogy for simulated annealing is the way liquids freeze and crystallize. All computational experiments were done on a MicroVAX. The two interchange heuristic is very fast but produces widely varying results. The two and three interchange heuristic provides less variability in the final objective function values but runs much more slowly. Simulated annealing produced the best objective function values for every starting configuration and was faster than the two and three interchange heuristic.

Minimizing losses by variational counter-diabatic driving

NASA Astrophysics Data System (ADS)

Sels, Dries; Polkovnikov, Anatoli

Despite the time-reversal symmetry of the microscopic dynamics of isolated systems, losses are ubiquitous in any process that tries to manipulate them. Whether it's the heat produced in a car engine or the decoherence of a qubit, all losses arise from our lack of control on the microscopic degrees of freedom of the system. Counter-diabatic driving protocols were proposed as a means to do fast changes in the Hamiltonian without exciting transitions. Such driving in principle allows one to realize arbitrarily fast annealing protocols or implement fast dissipationless driving, circumventing standard adiabatic limitations requiring infinitesimally slow rates. These ideas were tested and used both experimentally and theoretically in small systems, but in larger chaotic systems it is known that exact counter-diabatic protocols do not exist. Here we will present a simple variational approach allowing one to find best physical counter-diabatic protocols. We will show that, while they do not get rid of all transitions, the variational protocols are able to significantly reduce the induced fluctuations in the system. D.S. acknowledges support by the FWO.

Representing the work of medical protocols for organizational simulation.

PubMed Central

Fridsma, D. B.

1998-01-01

Developing and implementing patient care protocols within a specific organizational setting requires knowledge of the protocol, the organization, and the way in which the organization does its work. Computer-based simulation tools have been used in many industries to provide managers with prospective insight into problems of work process and organization design mismatch. Many of these simulation tools are designed for well-understood routine work processes in which there are few contingent tasks. In this paper, we describe theoretic that make it possible to simulate medical protocols using an information-processing theory framework. These simulations will allow medical administrators to test different protocol and organizational designs before actually using them within a particular clinical setting. PMID:9929231

The use of high-fidelity human patient simulation as an evaluative tool in the development of clinical research protocols and procedures.

PubMed

Wright, Melanie C; Taekman, Jeffrey M; Barber, Linda; Hobbs, Gene; Newman, Mark F; Stafford-Smith, Mark

2005-12-01

Errors in clinical research can be costly, in terms of patient safety, data integrity, and data collection. Data inaccuracy in early subjects of a clinical study may be associated with problems in the design of the protocol, procedures, and data collection tools. High-fidelity patient simulation centers provide an ideal environment to apply human-centered design to clinical trial development. A draft of a complex clinical protocol was designed, evaluated and modified using a high-fidelity human patient simulator in the Duke University Human Simulation and Patient Safety Center. The process included walk-throughs, detailed modifications of the protocol and development of procedural aids. Training of monitors and coordinators provided an opportunity for observation of performance that was used to identify further improvements to the protocol. Evaluative steps were used to design the research protocol and procedures. Iterative modifications were made to the protocol and data collection tools. The success in use of human simulation in the preparation of a complex clinical drug trial suggests the benefits of human patient simulation extend beyond training and medical equipment evaluation. Human patient simulation can provide a context for informal expert evaluation of clinical protocol design and for formal "rehearsal" to evaluate the efficacy of procedures and support tools.

Adaptive MANET multipath routing algorithm based on the simulated annealing approach.

PubMed

Kim, Sungwook

2014-01-01

Mobile ad hoc network represents a system of wireless mobile nodes that can freely and dynamically self-organize network topologies without any preexisting communication infrastructure. Due to characteristics like temporary topology and absence of centralized authority, routing is one of the major issues in ad hoc networks. In this paper, a new multipath routing scheme is proposed by employing simulated annealing approach. The proposed metaheuristic approach can achieve greater and reciprocal advantages in a hostile dynamic real world network situation. Therefore, the proposed routing scheme is a powerful method for finding an effective solution into the conflict mobile ad hoc network routing problem. Simulation results indicate that the proposed paradigm adapts best to the variation of dynamic network situations. The average remaining energy, network throughput, packet loss probability, and traffic load distribution are improved by about 10%, 10%, 5%, and 10%, respectively, more than the existing schemes.

Tree branch-shaped cupric oxide for highly effective photoelectrochemical water reduction

NASA Astrophysics Data System (ADS)

Jang, Youn Jeong; Jang, Ji-Wook; Choi, Sun Hee; Kim, Jae Young; Kim, Ju Hun; Youn, Duck Hyun; Kim, Won Yong; Han, Suenghoon; Sung Lee, Jae

2015-04-01

Highly efficient tree branch-shaped CuO photocathodes are fabricated using the hybrid microwave annealing process with a silicon susceptor within 10 minutes. The unique hierarchical, one-dimensional structure provides more facile charge transport, larger surface areas, and increased crystallinity and crystal ordering with less defects compared to irregular-shaped CuO prepared by conventional thermal annealing. As a result, the photocathode fabricated with the tree branch-shaped CuO produces an unprecedently high photocurrent density of -4.4 mA cm-2 at 0 VRHE under AM 1.5 G simulated sunlight compared to -1.44 mA cm-2 observed for a photocathode fabricated by thermal annealing. It is also confirmed that stoichiometric hydrogen and oxygen are produced from photoelectrochemical water splitting on the tree branch-shaped CuO photocathode and a platinum anode.Highly efficient tree branch-shaped CuO photocathodes are fabricated using the hybrid microwave annealing process with a silicon susceptor within 10 minutes. The unique hierarchical, one-dimensional structure provides more facile charge transport, larger surface areas, and increased crystallinity and crystal ordering with less defects compared to irregular-shaped CuO prepared by conventional thermal annealing. As a result, the photocathode fabricated with the tree branch-shaped CuO produces an unprecedently high photocurrent density of -4.4 mA cm-2 at 0 VRHE under AM 1.5 G simulated sunlight compared to -1.44 mA cm-2 observed for a photocathode fabricated by thermal annealing. It is also confirmed that stoichiometric hydrogen and oxygen are produced from photoelectrochemical water splitting on the tree branch-shaped CuO photocathode and a platinum anode. Electronic supplementary information (ESI) available: The detailed schematic diagram for the HMA process, XRD results, the temperature profile during HMA, derivative XANES results, TEM images, J-V curves, lists of previously reported copper oxide photocathode, and parameters extracted from EIS. See DOI: 10.1039/c5nr00208g

Hybrid algorithms for fuzzy reverse supply chain network design.

PubMed

Che, Z H; Chiang, Tzu-An; Kuo, Y C; Cui, Zhihua

2014-01-01

In consideration of capacity constraints, fuzzy defect ratio, and fuzzy transport loss ratio, this paper attempted to establish an optimized decision model for production planning and distribution of a multiphase, multiproduct reverse supply chain, which addresses defects returned to original manufacturers, and in addition, develops hybrid algorithms such as Particle Swarm Optimization-Genetic Algorithm (PSO-GA), Genetic Algorithm-Simulated Annealing (GA-SA), and Particle Swarm Optimization-Simulated Annealing (PSO-SA) for solving the optimized model. During a case study of a multi-phase, multi-product reverse supply chain network, this paper explained the suitability of the optimized decision model and the applicability of the algorithms. Finally, the hybrid algorithms showed excellent solving capability when compared with original GA and PSO methods.

Parameter discovery in stochastic biological models using simulated annealing and statistical model checking.

PubMed

Hussain, Faraz; Jha, Sumit K; Jha, Susmit; Langmead, Christopher J

2014-01-01

Stochastic models are increasingly used to study the behaviour of biochemical systems. While the structure of such models is often readily available from first principles, unknown quantitative features of the model are incorporated into the model as parameters. Algorithmic discovery of parameter values from experimentally observed facts remains a challenge for the computational systems biology community. We present a new parameter discovery algorithm that uses simulated annealing, sequential hypothesis testing, and statistical model checking to learn the parameters in a stochastic model. We apply our technique to a model of glucose and insulin metabolism used for in-silico validation of artificial pancreata and demonstrate its effectiveness by developing parallel CUDA-based implementation for parameter synthesis in this model.

Hybrid Algorithms for Fuzzy Reverse Supply Chain Network Design

PubMed Central

Che, Z. H.; Chiang, Tzu-An; Kuo, Y. C.

2014-01-01

In consideration of capacity constraints, fuzzy defect ratio, and fuzzy transport loss ratio, this paper attempted to establish an optimized decision model for production planning and distribution of a multiphase, multiproduct reverse supply chain, which addresses defects returned to original manufacturers, and in addition, develops hybrid algorithms such as Particle Swarm Optimization-Genetic Algorithm (PSO-GA), Genetic Algorithm-Simulated Annealing (GA-SA), and Particle Swarm Optimization-Simulated Annealing (PSO-SA) for solving the optimized model. During a case study of a multi-phase, multi-product reverse supply chain network, this paper explained the suitability of the optimized decision model and the applicability of the algorithms. Finally, the hybrid algorithms showed excellent solving capability when compared with original GA and PSO methods. PMID:24892057

High-dose-rate prostate brachytherapy inverse planning on dose-volume criteria by simulated annealing.

PubMed

Deist, T M; Gorissen, B L

2016-02-07

High-dose-rate brachytherapy is a tumor treatment method where a highly radioactive source is brought in close proximity to the tumor. In this paper we develop a simulated annealing algorithm to optimize the dwell times at preselected dwell positions to maximize tumor coverage under dose-volume constraints on the organs at risk. Compared to existing algorithms, our algorithm has advantages in terms of speed and objective value and does not require an expensive general purpose solver. Its success mainly depends on exploiting the efficiency of matrix multiplication and a careful selection of the neighboring states. In this paper we outline its details and make an in-depth comparison with existing methods using real patient data.

Genetic Algorithms and Their Application to the Protein Folding Problem

DTIC Science & Technology

1993-12-01

and symbolic methods, random methods such as Monte Carlo simulation and simulated annealing, distance geometry, and molecular dynamics. Many of these...calculated energies with those obtained using the molecular simulation software package called CHARMm. 10 9) Test both the simple and parallel simpie genetic...homology-based, and simplification techniques. 3.21 Molecular Dynamics. Perhaps the most natural approach is to actually simulate the folding process. This

OBJECT KINETIC MONTE CARLO SIMULATIONS OF MICROSTRUCTURE EVOLUTION

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

Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

2013-09-30

The objective is to report the development of the flexible object kinetic Monte Carlo (OKMC) simulation code KSOME (kinetic simulation of microstructure evolution) which can be used to simulate microstructure evolution of complex systems under irradiation. In this report we briefly describe the capabilities of KSOME and present preliminary results for short term annealing of single cascades in tungsten at various primary-knock-on atom (PKA) energies and temperatures.

A Green Protocol for Synthesis of MAl2O4, [M=Cu and Co] Spinels Under Microwave Irradiation Method

NASA Astrophysics Data System (ADS)

Yuvasravana, R.; George, P. P.

Nanosized metal aluminates MAl2O4, [M=Cu and Co] are synthesized from their nitrates solution by using pomegranate peel extract as fuel in microwave combustion. MAl2O4 [M=Cu and Co] nanoparticles are grown in microwave assisted synthesis followed by annealing at 700∘C. The nanoparticles have been characterized by powder X-ray diffraction (PXRD), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), UV-VIS spectroscopy and photoluminescence (PL) spectroscopy. The PXRD analysis has confirmed their spinel composition. The green protocol and microwave combustion route for spinel synthesis are rapid, simple, without any hazardous chemicals as reducing or stabilizing agents and economical.

Thermodynamics of a phase transition of silicon nanoparticles at the annealing and carbonization of porous silicon

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

Nagornov, Yu. S., E-mail: Nagornov.Yuri@gmail.com

2015-12-15

The formation of SiC nanocrystals of the cubic modification in the process of high-temperature carbonization of porous silicon has been analyzed. A thermodynamic model has been proposed to describe the experimental data obtained by atomic-force microscopy, Raman scattering, spectral analysis, Auger spectroscopy, and X-ray diffraction spectroscopy. It has been shown that the surface energy of silicon nanoparticles and quantum filaments is released in the process of annealing and carbonization. The Monte Carlo simulation has shown that the released energy makes it possible to overcome the nucleation barrier and to form SiC nanocrystals. The processes of laser annealing and electron irradiationmore » of carbonized porous silicon have been analyzed.« less

Effect of hydrogen adsorption on the formation and annealing of Stone-Wales defects in graphene

NASA Astrophysics Data System (ADS)

Podlivaev, A. I.; Openov, L. A.

2015-12-01

The heights of energy barriers preventing the formation and annealing of Stone-Wales defects in graphene with a hydrogen atom adsorbed on the defect or in its immediate vicinity have been calculated using the atomistic computer simulation. It has been shown that, in the presence of hydrogen, both barriers are significantly lower than those in the absence of hydrogen. Based on the analysis of the potential energy surface, the frequency factors have been calculated for two different paths of the Stone-Wales transformation, and the temperature dependences of the corresponding annealing times of the defects have been found. The results obtained have been compared with the first-principles calculations and molecular dynamics data.

Minimizing the Discrepancy between Simulated and Historical Failures in Turbine Engines: A Simulation-Based Optimization Method (Postprint)

DTIC Science & Technology

2015-01-01

Procedure. The simulated annealing (SA) algorithm is a well-known local search metaheuristic used to address discrete, continuous, and multiobjective...design of experiments (DOE) to tune the parameters of the optimiza- tion algorithm . Section 5 shows the results of the case study. Finally, concluding... metaheuristic . The proposed method is broken down into two phases. Phase I consists of a Monte Carlo simulation to obtain the simulated percentage of failure

Heavy Ion Induced Degradation in SiC Schottky Diodes: Bias and Energy Deposition Dependence

NASA Technical Reports Server (NTRS)

Javanainen, Arto; Galloway, Kenneth F.; Nicklaw, Christopher; Bosser, Alexandre L.; Ferlet-Cavrois, Veronique; Lauenstein, Jean-Marie; Pintacuda, Francesco; Reed, Robert A.; Schrimpf, Ronald D.; Weller, Robert A.;

Measured and Simulated Dark J-V Characteristics of a-Si:H Single Junction p-i-n Solar Cells Irradiated with 40 keV Electrons

NASA Technical Reports Server (NTRS)

Lord, Kenneth; Woodyard, James R.

2002-01-01

The effect of 40 keV electron irradiation on a-Si:H p-i-n single-junction solar cells was investigated using measured and simulated dark J-V characteristics. EPRI-AMPS and PC-1D simulators were explored for use in the studies. The EPRI-AMPS simulator was employed and simulator parameters selected to produce agreement with measured J-V characteristics. Three current mechanisms were evident in the measured dark J-V characteristics after electron irradiation, namely, injection, shunting and a term of the form CV(sup m). Using a single discrete defect state level at the center of the band gap, good agreement was achieved between measured and simulated J-V characteristics in the forward-bias voltage region where the dark current density was dominated by injection. The current mechanism of the form CV(sup m) was removed by annealing for two hours at 140 C. Subsequent irradiation restored the CV(sup m) current mechanism and it was removed by a second anneal. Some evidence of the CV(sup m) term is present in device simulations with a higher level of discrete density of states located at the center of the bandgap.

Surface faceting and elemental diffusion behaviour at atomic scale for alloy nanoparticles during in situ annealing

PubMed Central

Chi, Miaofang; Wang, Chao; Lei, Yinkai; Wang, Guofeng; Li, Dongguo; More, Karren L.; Lupini, Andrew; Allard, Lawrence F.; Markovic, Nenad M.; Stamenkovic, Vojislav R.

2015-01-01

The catalytic performance of nanoparticles is primarily determined by the precise nature of the surface and near-surface atomic configurations, which can be tailored by post-synthesis annealing effectively and straightforwardly. Understanding the complete dynamic response of surface structure and chemistry to thermal treatments at the atomic scale is imperative for the rational design of catalyst nanoparticles. Here, by tracking the same individual Pt3Co nanoparticles during in situ annealing in a scanning transmission electron microscope, we directly discern five distinct stages of surface elemental rearrangements in Pt3Co nanoparticles at the atomic scale: initial random (alloy) elemental distribution; surface platinum-skin-layer formation; nucleation of structurally ordered domains; ordered framework development and, finally, initiation of amorphization. Furthermore, a comprehensive interplay among phase evolution, surface faceting and elemental inter-diffusion is revealed, and supported by atomistic simulations. This work may pave the way towards designing catalysts through post-synthesis annealing for optimized catalytic performance. PMID:26576477

Surface faceting and elemental diffusion behaviour at atomic scale for alloy nanoparticles during in situ annealing

DOE PAGES

Chi, Miaofang; Wang, Chao; Lei, Yinkai; ...

2015-11-18

The catalytic performance of nanoparticles is primarily determined by the precise nature of the surface and near-surface atomic configurations, which can be tailored by post-synthesis annealing effectively and straightforwardly. Understanding the complete dynamic response of surface structure and chemistry to thermal treatments at the atomic scale is imperative for the rational design of catalyst nanoparticles. Here, by tracking the same individual Pt 3Co nanoparticles during in situ annealing in a scanning transmission electron microscope, we directly discern five distinct stages of surface elemental rearrangements in Pt 3Co nanoparticles at the atomic scale: initial random (alloy) elemental distribution; surface platinum-skin-layer formation;more » nucleation of structurally ordered domains; ordered framework development and, finally, initiation of amorphization. Furthermore, a comprehensive interplay among phase evolution, surface faceting and elemental inter-diffusion is revealed, and supported by atomistic simulations. In conlcusion, this work may pave the way towards designing catalysts through post-synthesis annealing for optimized catalytic performance.« less

Investigation of the Stability and 1.0 MeV Proton Radiation Resistance of Commercially Produced Hydrogenated Amorphous Silicon Alloy Solar Cells

NASA Technical Reports Server (NTRS)

Lord, Kenneth R., II; Walters, Michael R.; Woodyard, James R.

1994-01-01

The radiation resistance of commercial solar cells fabricated from hydrogenated amorphous silicon alloys is reported. A number of different device structures were irradiated with 1.0 MeV protons. The cells were insensitive to proton fluences below 1E12 sq cm. The parameters of the irradiated cells were restored with annealing at 200 C. The annealing time was dependent on proton fluence. Annealing devices for one hour restores cell parameters for fluences below 1E14 sq cm fluences above 1E14 sq cm require longer annealing times. A parametric fitting model was used to characterize current mechanisms observed In dark I-V measurements. The current mechanism were explored with irradiation fluence, and voltage and light soaking times. The thermal generation current density and quality factor increased with proton fluence. Device simulation shows the degradation in cell characteristics may be explained by the reduction of the electric field in the intrinsic layer.

Performance of Al2O3:C optically stimulated luminescence dosimeters for clinical radiation therapy applications.

PubMed

Hu, B; Wang, Y; Zealey, W

2009-12-01

A commercial Optical Stimulated Luminescence (OSL) dosimetry system developed by Landauer was tested to analyse the possibility of using OSL dosimetry for external beam radiotherapy planning checks. Experiments were performed to determine signal sensitivity, dose response range, beam type/energy dependency, reproducibility and linearity. Optical annealing processes to test OSL material reusability were also studied. In each case the measurements were converted into absorbed dose. The experimental results show that OSL dosimetry provides a wide dose response range, good linearity and reproducibility for the doses up to 800cGy. The OSL output is linear with dose up to 600cGy range showing a maximum deviation from linearity of 2.0% for the doses above 600cGy. The standard deviation in response of 20 dosimeters was 3.0%. After optical annealing using incandescent light, the readout intensity decreased by approximately 98% in the first 30 minutes. The readout intensity, I, decreased after repeated optical annealing as a power law, given by I infinity t (-1.3). This study concludes that OSL dosimetry can provide an alternative dosimetry technique for use in in-vivo dosimetry if rigorous measurement protocols are established.

Dynamics of open quantum systems by interpolation of von Neumann and classical master equations, and its application to quantum annealing

NASA Astrophysics Data System (ADS)

Kadowaki, Tadashi

2018-02-01

We propose a method to interpolate dynamics of von Neumann and classical master equations with an arbitrary mixing parameter to investigate the thermal effects in quantum dynamics. The two dynamics are mixed by intervening to continuously modify their solutions, thus coupling them indirectly instead of directly introducing a coupling term. This maintains the quantum system in a pure state even after the introduction of thermal effects and obtains not only a density matrix but also a state vector representation. Further, we demonstrate that the dynamics of a two-level system can be rewritten as a set of standard differential equations, resulting in quantum dynamics that includes thermal relaxation. These equations are equivalent to the optical Bloch equations at the weak coupling and asymptotic limits, implying that the dynamics cause thermal effects naturally. Numerical simulations of ferromagnetic and frustrated systems support this idea. Finally, we use this method to study thermal effects in quantum annealing, revealing nontrivial performance improvements for a spin glass model over a certain range of annealing time. This result may enable us to optimize the annealing time of real annealing machines.

ABS-SmartComAgri: An Agent-Based Simulator of Smart Communication Protocols in Wireless Sensor Networks for Debugging in Precision Agriculture.

PubMed

García-Magariño, Iván; Lacuesta, Raquel; Lloret, Jaime

2018-03-27

Smart communication protocols are becoming a key mechanism for improving communication performance in networks such as wireless sensor networks. However, the literature lacks mechanisms for simulating smart communication protocols in precision agriculture for decreasing production costs. In this context, the current work presents an agent-based simulator of smart communication protocols for efficiently managing pesticides. The simulator considers the needs of electric power, crop health, percentage of alive bugs and pesticide consumption. The current approach is illustrated with three different communication protocols respectively called (a) broadcast, (b) neighbor and (c) low-cost neighbor. The low-cost neighbor protocol obtained a statistically-significant reduction in the need of electric power over the neighbor protocol, with a very large difference according to the common interpretations about the Cohen's d effect size. The presented simulator is called ABS-SmartComAgri and is freely distributed as open-source from a public research data repository. It ensures the reproducibility of experiments and allows other researchers to extend the current approach.

ABS-SmartComAgri: An Agent-Based Simulator of Smart Communication Protocols in Wireless Sensor Networks for Debugging in Precision Agriculture

PubMed Central

2018-01-01

Smart communication protocols are becoming a key mechanism for improving communication performance in networks such as wireless sensor networks. However, the literature lacks mechanisms for simulating smart communication protocols in precision agriculture for decreasing production costs. In this context, the current work presents an agent-based simulator of smart communication protocols for efficiently managing pesticides. The simulator considers the needs of electric power, crop health, percentage of alive bugs and pesticide consumption. The current approach is illustrated with three different communication protocols respectively called (a) broadcast, (b) neighbor and (c) low-cost neighbor. The low-cost neighbor protocol obtained a statistically-significant reduction in the need of electric power over the neighbor protocol, with a very large difference according to the common interpretations about the Cohen’s d effect size. The presented simulator is called ABS-SmartComAgri and is freely distributed as open-source from a public research data repository. It ensures the reproducibility of experiments and allows other researchers to extend the current approach. PMID:29584703

Protein structure modeling and refinement by global optimization in CASP12.

PubMed

Hong, Seung Hwan; Joung, InSuk; Flores-Canales, Jose C; Manavalan, Balachandran; Cheng, Qianyi; Heo, Seungryong; Kim, Jong Yun; Lee, Sun Young; Nam, Mikyung; Joo, Keehyoung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2018-03-01

For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain re-modeling. For better template selection and model selection, we updated our model quality assessment (QA) method with the newly developed SVMQA (support vector machine for quality assessment). For 3D chain building, we updated our energy function by including restraints generated from predicted residue-residue contacts. New energy terms for the predicted secondary structure and predicted solvent accessible surface area were also introduced. For difficult targets, we proposed a new method, LEEab, where the template term played a less significant role than it did in LEE, complemented by increased contributions from other terms such as the predicted contact term. For TBM (template-based modeling) targets, LEE performed better than LEEab, but for FM targets, LEEab was better. For model refinement, we modified our CASP11 molecular dynamics (MD) based protocol by using explicit solvents and tuning down restraint weights. Refinement results from MD simulations that used a new augmented statistical energy term in the force field were quite promising. Finally, when using inaccurate information (such as the predicted contacts), it was important to use the Lorentzian function for which the maximal penalty arising from wrong information is always bounded. © 2017 Wiley Periodicals, Inc.

Optimal mapping of irregular finite element domains to parallel processors

NASA Technical Reports Server (NTRS)

Flower, J.; Otto, S.; Salama, M.

1987-01-01

Mapping the solution domain of n-finite elements into N-subdomains that may be processed in parallel by N-processors is an optimal one if the subdomain decomposition results in a well-balanced workload distribution among the processors. The problem is discussed in the context of irregular finite element domains as an important aspect of the efficient utilization of the capabilities of emerging multiprocessor computers. Finding the optimal mapping is an intractable combinatorial optimization problem, for which a satisfactory approximate solution is obtained here by analogy to a method used in statistical mechanics for simulating the annealing process in solids. The simulated annealing analogy and algorithm are described, and numerical results are given for mapping an irregular two-dimensional finite element domain containing a singularity onto the Hypercube computer.

Close packing in curved space by simulated annealing

NASA Astrophysics Data System (ADS)

Wille, L. T.

1987-12-01

The problem of packing spheres of a maximum radius on the surface of a four-dimensional hypersphere is considered. It is shown how near-optimal solutions can be obtained by packing soft spheres, modelled as classical particles interacting under an inverse power potential, followed by a subsequent hardening of the interaction. In order to avoid trapping in high-lying local minima, the simulated annealing method is used to optimise the soft-sphere packing. Several improvements over other work (based on local optimisation of random initial configurations of hard spheres) have been found. The freezing behaviour of this system is discussed as a function of particle number, softness of the potential and cooling rate. Apart from their geometric interest, these results are useful in the study of topological frustration, metallic glasses and quasicrystals.

[The utility boiler low NOx combustion optimization based on ANN and simulated annealing algorithm].

PubMed

Zhou, Hao; Qian, Xinping; Zheng, Ligang; Weng, Anxin; Cen, Kefa

2003-11-01

With the developing restrict environmental protection demand, more attention was paid on the low NOx combustion optimizing technology for its cheap and easy property. In this work, field experiments on the NOx emissions characteristics of a 600 MW coal-fired boiler were carried out, on the base of the artificial neural network (ANN) modeling, the simulated annealing (SA) algorithm was employed to optimize the boiler combustion to achieve a low NOx emissions concentration, and the combustion scheme was obtained. Two sets of SA parameters were adopted to find a better SA scheme, the result show that the parameters of T0 = 50 K, alpha = 0.6 can lead to a better optimizing process. This work can give the foundation of the boiler low NOx combustion on-line control technology.

Shape optimization of road tunnel cross-section by simulated annealing

NASA Astrophysics Data System (ADS)

Sobótka, Maciej; Pachnicz, Michał

2016-06-01

The paper concerns shape optimization of a tunnel excavation cross-section. The study incorporates optimization procedure of the simulated annealing (SA). The form of a cost function derives from the energetic optimality condition, formulated in the authors' previous papers. The utilized algorithm takes advantage of the optimization procedure already published by the authors. Unlike other approaches presented in literature, the one introduced in this paper takes into consideration a practical requirement of preserving fixed clearance gauge. Itasca Flac software is utilized in numerical examples. The optimal excavation shapes are determined for five different in situ stress ratios. This factor significantly affects the optimal topology of excavation. The resulting shapes are elongated in the direction of a principal stress greater value. Moreover, the obtained optimal shapes have smooth contours circumscribing the gauge.

Jovian vortices by simulated annealing

NASA Astrophysics Data System (ADS)

Morrison, P. J.; Flierl, G. R.; Swaminathan, R. V.

2017-11-01

We explore the conditions required for isolated vortices to exist in sheared zonal flows and the stability of the underlying zonal winds. This is done using the standard 2-layer quasigeostrophic model with the lower layer depth becoming infinite; however, this model differs from the usual layer model because the lower layer is not assumed to be motionless but has a steady configuration of alternating zonal flows. Steady state vortices are obtained by a simulated annealing computational method introduced in, generalized and applied in in fluid flow, and used in the context of magnetohydrodynamics in. Various cases of vortices with a constant potential vorticity anomaly atop zonal winds and the stability of the underlying winds are considered using a mix of computational and analytical techniques. U.S. Department of Energy Contract DE-FG05-80ET-53088.

Free Energy Minimization by Simulated Annealing with Applications to Lithospheric Slabs and Mantle Plumes

NASA Astrophysics Data System (ADS)

Bina, C. R.

An optimization algorithm based upon the method of simulated annealing is of utility in calculating equilibrium phase assemblages as functions of pressure, temperature, and chemical composi tion. Operating by analogy to the statistical mechanics of the chemical system, it is applicable both to problems of strict chemical equilibrium and to problems involving metastability. The method reproduces known phase diagrams and illustrates the expected thermal deflection of phase transitions in thermal models of subducting lithospheric slabs and buoyant mantle plumes. It reveals temperature-induced changes in phase transition sharpness and the stability of Fe-rich γ phase within an α+γ field in cold slab thermal models, and it suggests that transitions such as the possible breakdown of silicate perovskite to mixed oxides can amplify velocity anomalies.

The atomic-scale nucleation mechanism of NiTi metallic glasses upon isothermal annealing studied via molecular dynamics simulations.

PubMed

Li, Yang; Li, JiaHao; Liu, BaiXin

2015-10-28

Nucleation is one of the most essential transformation paths in phase transition and exerts a significant influence on the crystallization process. Molecular dynamics simulations were performed to investigate the atomic-scale nucleation mechanisms of NiTi metallic glasses upon devitrification at various temperatures (700 K, 750 K, 800 K, and 850 K). Our simulations reveal that at 700 K and 750 K, nucleation is polynuclear with high nucleation density, while at 800 K it is mononuclear. The underlying nucleation mechanisms have been clarified, manifesting that nucleation can be induced either by the initial ordered clusters (IOCs) or by the other precursors of nuclei evolved directly from the supercooled liquid. IOCs and other precursors stem from the thermal fluctuations of bond orientational order in supercooled liquids during the quenching process and during the annealing process, respectively. The simulation results not only elucidate the underlying nucleation mechanisms varied with temperature, but also unveil the origin of nucleation. These discoveries offer new insights into the devitrification mechanism of metallic glasses.

A comparative study of the annealing behavior of Cu(In,Ga)(S,Se){sub 2} based solar cells with an indium sulfide buffer layer, partly submitted to wet chemical treatments

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

Hönes, C., E-mail: christian.hoenes@de.bosch.com; Laboratory for Photovoltaics, University of Luxembourg, 41 rue du Brill, L-4422 Belvaux; Hackenberg, J.

2015-03-07

Indium sulfide thin films deposited via thermal evaporation from compound source material have been successfully utilized as a cadmium free buffer layer for Cu(In,Ga)Se{sub 2} based solar cells. However, high efficiencies are only reached after an additional annealing step. In this work, the annealing behavior of Cu(In,Ga)(S,Se){sub 2} based indium sulfide buffered solar cells is compared to the annealing behavior of similar cells, which were submitted to wet chemical treatments partly containing cadmium ions. Upon annealing a significant improvement of the initial solar cell characteristics is observed for the untreated cell and is related to the increase of activation energymore » for the carrier recombination process and a decrease of the ideality factor within the one diode model. It is shown here that this improvement can also be achieved by wet treatments of the absorber prior to buffer layer deposition. Upon annealing these treated cells still gain in collection length but lose open circuit voltage, which is explained here within a model including a highly p-doped absorber surface layer and supported by simulations showing that a decrease in doping density of such a surface layer would lead to the observed effects.« less

PECVD silicon-rich nitride and low stress nitride films mechanical characterization using membrane point load deflection

NASA Astrophysics Data System (ADS)

Bagolini, Alvise; Picciotto, Antonino; Crivellari, Michele; Conci, Paolo; Bellutti, Pierluigi

2016-02-01

An analysis of the mechanical properties of plasma enhanced chemical vapor (PECVD) silicon nitrides is presented, using micro fabricated silicon nitride membranes under point load deflection. The membranes are made of PECVD silicon-rich nitride and low stress nitride films. The mechanical performance of the bended membranes is examined both with analytical models and finite element simulation in order to extract the elastic modulus and residual stress values. The elastic modulus of low stress silicon nitride is calculated using stress free analytical models, while for silicon-rich silicon nitride and annealed low stress silicon nitride it is estimated with a pre-stressed model of point-load deflection. The effect of annealing both in nitrogen and hydrogen atmosphere is evaluated in terms of residual stress, refractive index and thickness variation. It is demonstrated that a hydrogen rich annealing atmosphere induces very little change in low stress silicon nitride. Nitrogen annealing effects are measured and shown to be much higher in silicon-rich nitride than in low stress silicon nitride. An estimate of PECVD silicon-rich nitride elastic modulus is obtained in the range between 240-320 GPa for deposited samples and 390 GPa for samples annealed in nitrogen atmosphere. PECVD low stress silicon nitride elastic modulus is estimated to be 88 GPa as deposited and 320 GPa after nitrogen annealing.

Monte Carlo Simulation Study of Atomic Structure of alnico Permanent Magnets

NASA Astrophysics Data System (ADS)

Nguyen, Manh Cuong; Wang, Cai-Zhuang; Ho, Kai-Ming

Lattice Monte Carlo simulation based on quinternary cluster expansion energy model is used to investigate nano-scale structure of alnico alloy, which is considered as a candidate material for rare-earth free high performance permanent magnets, especially for high or elevated temperature applications such as electric motor for vehicles. We observe phase decomposition of the master alnico alloy into FeCo-rich magnetic (α1) and NiAl-rich matrix (α2) phases. Concentrations of Fe and Co in α1 phase and Ni and Al in α2 phase are higher for lower annealing temperature. Ti is residing mostly in the α2 phase. The phase boundary between α1 and α2 phases are quite sharp with only few atomic layers. The α1 phase is in B2 ordering with Fe and Al occupying the α-site and Ni and Co occupying the β-site. The α2 phase is in L21 ordering with Al occupying the 4a-site. The phase composition profile again annealing temperature suggests that lower annealing temperature would improve the magnetism of α2 and diminish the magnetism of α2 phase, hence improve shape anisotropy of α1 phase rods and that of alnico.

Softening due to disordered grain boundaries in nanocrystalline Co.

PubMed

Yuasa, Motohiro; Hakamada, Masataka; Nakano, Hiromi; Mabuchi, Mamoru; Chino, Yasumasa

2013-08-28

Nanocrystalline Co consisting of fcc and hcp phases was processed by electrodeposition, and its mechanical properties were investigated by hardness tests. In addition, high-resolution transmission electron microscopy observations and molecular dynamics (MD) simulations were performed to investigate the grain boundary structure and dislocation nucleation from the grain boundaries. A large amount of disorders existed at the grain boundaries and stacking faults were formed from the grain boundaries in the as-deposited Co specimen. The as-deposited specimen showed a lower hardness than did the annealed specimen, although the grain size of the former was smaller than that of the latter. The activation volume of the as-deposited specimen (=1.5b(3)) was lower than that of the annealed specimen (=50b(3)), thus indicating that nucleation of dislocations from grain boundaries is more active in the as-deposited specimen than in the annealed specimens. The MD simulations showed that dislocation nucleation was closely related to a change in the defect structures at the boundary. Therefore, it is suggested that a significant amount of defects enhance changes in the defect structures at the boundary, resulting in softening of the as-deposited specimen.

Softening due to disordered grain boundaries in nanocrystalline Co

NASA Astrophysics Data System (ADS)

Yuasa, Motohiro; Hakamada, Masataka; Nakano, Hiromi; Mabuchi, Mamoru; Chino, Yasumasa

2013-08-01

Nanocrystalline Co consisting of fcc and hcp phases was processed by electrodeposition, and its mechanical properties were investigated by hardness tests. In addition, high-resolution transmission electron microscopy observations and molecular dynamics (MD) simulations were performed to investigate the grain boundary structure and dislocation nucleation from the grain boundaries. A large amount of disorders existed at the grain boundaries and stacking faults were formed from the grain boundaries in the as-deposited Co specimen. The as-deposited specimen showed a lower hardness than did the annealed specimen, although the grain size of the former was smaller than that of the latter. The activation volume of the as-deposited specimen (=1.5b3) was lower than that of the annealed specimen (=50b3), thus indicating that nucleation of dislocations from grain boundaries is more active in the as-deposited specimen than in the annealed specimens. The MD simulations showed that dislocation nucleation was closely related to a change in the defect structures at the boundary. Therefore, it is suggested that a significant amount of defects enhance changes in the defect structures at the boundary, resulting in softening of the as-deposited specimen.

Mechanical annealing under low-amplitude cyclic loading in micropillars

NASA Astrophysics Data System (ADS)

Cui, Yi-nan; Liu, Zhan-li; Wang, Zhang-jie; Zhuang, Zhuo

2016-04-01

Mechanical annealing has been demonstrated to be an effective method for decreasing the overall dislocation density in submicron single crystal. However, simultaneously significant shape change always unexpectedly happens under extremely high monotonic loading to drive the pre-existing dislocations out of the free surfaces. In the present work, through in situ TEM experiments it is found that cyclic loading with low stress amplitude can drive most dislocations out of the submicron sample with virtually little change of the shape. The underlying dislocation mechanism is revealed by carrying out discrete dislocation dynamic (DDD) simulations. The simulation results indicate that the dislocation density decreases within cycles, while the accumulated plastic strain is small. By comparing the evolution of dislocation junction under monotonic, cyclic and relaxation deformation, the cumulative irreversible slip is found to be the key factor of promoting junction destruction and dislocation annihilation at free surface under low-amplitude cyclic loading condition. By introducing this mechanics into dislocation density evolution equations, the critical conditions for mechanical annealing under cyclic and monotonic loadings are discussed. Low-amplitude cyclic loading which strengthens the single crystal without seriously disturbing the structure has the potential applications in the manufacture of defect-free nano-devices.

Tunable optical response of bowtie nanoantenna arrays on thermoplastic substrates

NASA Astrophysics Data System (ADS)

Sharac, N.; Sharma, H.; Veysi, M.; Sanderson, R. N.; Khine, M.; Capolino, F.; Ragan, R.

2016-03-01

Thermally responsive polymers present an interesting avenue for tuning the optical properties of nanomaterials on their surfaces by varying their periodicity and shape using facile processing methods. Gold bowtie nanoantenna arrays are fabricated using nanosphere lithography on prestressed polyolefin (PO), a thermoplastic polymer, and optical properties are investigated via a combination of spectroscopy and electromagnetic simulations to correlate shape evolution with optical response. Geometric features of bowtie nanoantennas evolve by annealing at temperatures between 105 °C and 135 °C by releasing the degree of prestress in PO. Due to the higher modulus of Au versus PO, compressive stress occurs on Au bowtie regions on PO, which leads to surface buckling at the two highest annealing temperatures; regions with a 5 nm gap between bowtie nanoantennas are observed and the average reduction is 75%. Reflectance spectroscopy and full-wave electromagnetic simulations both demonstrate the ability to tune the plasmon resonance wavelength with a window of approximately 90 nm in the range of annealing temperatures investigated. Surface-enhanced Raman scattering measurements demonstrate that maximum enhancement is observed as the excitation wavelength approaches the plasmon resonance of Au bowtie nanoantennas. Both the size and morphology tunability offered by PO allows for customizing optical response.

Dynamical quenching and annealing in self-organization multiagent models.

PubMed

Burgos, E; Ceva, H; Perazzo, R P

2001-07-01

We study the dynamics of a generalized minority game (GMG) and of the bar attendance model (BAM) in which a number of agents self-organize to match an attendance that is fixed externally as a control parameter. We compare the usual dynamics used for the minority game with one for the BAM that makes a better use of the available information. We study the asymptotic states reached in both frameworks. We show that states that can be assimilated to either thermodynamic equilibrium or quenched configurations can appear in both models, but with different settings. We discuss the relevance of the parameter G that measures the value of the prize for winning in units of the fine for losing. We also provide an annealing protocol by which the quenched configurations of the GMG can progressively be modified to reach an asymptotic equilibrium state that coincides with the one obtained with the BAM.

Dynamical quenching and annealing in self-organization multiagent models

NASA Astrophysics Data System (ADS)

Burgos, E.; Ceva, Horacio; Perazzo, R. P.

2001-07-01

We study the dynamics of a generalized minority game (GMG) and of the bar attendance model (BAM) in which a number of agents self-organize to match an attendance that is fixed externally as a control parameter. We compare the usual dynamics used for the minority game with one for the BAM that makes a better use of the available information. We study the asymptotic states reached in both frameworks. We show that states that can be assimilated to either thermodynamic equilibrium or quenched configurations can appear in both models, but with different settings. We discuss the relevance of the parameter G that measures the value of the prize for winning in units of the fine for losing. We also provide an annealing protocol by which the quenched configurations of the GMG can progressively be modified to reach an asymptotic equilibrium state that coincides with the one obtained with the BAM.

Production of intergranular attack of alloy 600, alloy 690, and alloy 800 tubing in tubesheet crevices: Topical report

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

Scott, D.B.; Glaves, C.L.,

1987-07-01

Three model boilers, manufactured to simulate full-size tube sheet crevices, were tested with various secondary side environments. The first was faulted with organics representative of the decomposition of humic acid. The second was faulted with sodium carbonate and sodium hydroxide, while the third was faulted with sodium sulfate and sodium hydroxide. Each model contained seven tubes, which included Alloy 600 in the mill-annealed (MA) and thermally-treated (TT) conditions and Alloy 690 in the thermally-treated condition. Two models contained Alloy 800 tubes in the mill-annealed condition and one had Alloy 800 in the mill-annealed/cold-worked/glass-bead-peened condition. Two different sizes of tubesheet crevicesmore » were used in all model boilers. In the organics-faulted boiler, tubes of Alloy 600MA, Alloy 690TT and Alloy 800MA experienced no significant intergranular attack (IGA); however, the Alloy 600TT had intergranular attack (IGA) three to four grains deep. The carbonate-caustic faulted boiler experienced throughwall stress corrosion cracking (SCC) in all tubes of Alloy 600 MA and Alloy 800 MA. Eddy current indications were present in Alloy 690TT, Alloy 600TT and Alloy 800 in the mill-annealed/cold worked/glass-bead-peened condition. Metallographic examination of tubes from the third model boiler, faulted with sodium sulfate and caustic, revealed IGA in the mill-annealed Alloy 600 tubes. The IGA was more extensive in an Alloy 600 tube annealed at 1700/sup 0/F than an Alloy 600 tube annealed at 1875/sup 0/F.« less

Correlations induced by depressing synapses in critically self-organized networks with quenched dynamics

NASA Astrophysics Data System (ADS)

Campos, João Guilherme Ferreira; Costa, Ariadne de Andrade; Copelli, Mauro; Kinouchi, Osame

2017-04-01

In a recent work, mean-field analysis and computer simulations were employed to analyze critical self-organization in networks of excitable cellular automata where randomly chosen synapses in the network were depressed after each spike (the so-called annealed dynamics). Calculations agree with simulations of the annealed version, showing that the nominal branching ratio σ converges to unity in the thermodynamic limit, as expected of a self-organized critical system. However, the question remains whether the same results apply to the biological case where only the synapses of firing neurons are depressed (the so-called quenched dynamics). We show that simulations of the quenched model yield significant deviations from σ =1 due to spatial correlations. However, the model is shown to be critical, as the largest eigenvalue of the synaptic matrix approaches unity in the thermodynamic limit, that is, λc=1 . We also study the finite size effects near the critical state as a function of the parameters of the synaptic dynamics.

Mechanical properties of Inconel 718 and Nickel 201 alloys after thermal histories simulating brazing and high temperature service

NASA Technical Reports Server (NTRS)

James, W. F.

1985-01-01

An experimental investigation was made to evaluate two nickel base alloys (Nickel-201 and Inconel-718) in three heat treated conditions. These conditions were: (1) annealed; (2) after thermal exposure simulating a braze cycle; and (3) after a thermal exposure simulating a braze cycle plus one operational lifetime of high temperature service. For the Nickel-201, two different braze cycle temperatures were evaluated. A braze cycle utilizing a lower braze temperature resulted in less grain growth for Nickel-201 than the standard braze cycle used for joining Nickel-201 to Inconel-718. It was determined, however, that Nickel-201, was marginal for temperatures investigated due to large grain growth. After the thermal exposures described above, the mechanical properties of Nickel-201 were degraded, whereas similar exposure on Inconel-718 actually strengthened the material compared with the annealed condition. The investigation included tensile tests at both room temperature and elevated temperatures, stress-rupture tests, and metallographic examination.

Characterization of PEEK, PET and PI implanted with Mn ions and sub-sequently annealed

NASA Astrophysics Data System (ADS)

Mackova, A.; Malinsky, P.; Miksova, R.; Pupikova, H.; Khaibullin, R. I.; Slepicka, P.; Gombitová, A.; Kovacik, L.; Svorcik, V.; Matousek, J.

2014-04-01

Polyimide (PI), polyetheretherketone (PEEK) and polyethylene terephthalate (PET) foils were implanted with 80 keV Mn+ ions at room temperature at fluencies of 1.0 × 1015-1.0 × 1016 cm-2. Mn depth profiles determined by RBS were compared to SRIM 2012 and TRIDYN simulations. The processes taking place in implanted polymers under the annealing procedure were followed. The measured projected ranges RP differ slightly from the SRIM and TRIDYN simulation and the depth profiles are significantly broader (up to 2.4 times) than those simulated by SRIM, while TRIDYN simulations were in a reasonable agreement up to the fluence 0.5 × 1016 in PEEK. Oxygen and hydrogen escape from the implanted layer was examined using RBS and ERDA techniques. PET, PEEK and PI polymers exhibit oxygen depletion up to about 40% of its content in virgin polymers. The compositional changes induced by implantation to particular ion fluence are similar for all polymers examined. After annealing no significant changes of Mn depth distribution was observed even the further oxygen and hydrogen desorption from modified layers appeared. The surface morphology of implanted polymers was characterized using AFM. The most significant change in the surface roughness was observed on PEEK. Implanted Mn atoms tend to dissipate in the polymer matrix, but the Mn nanoparticles are too small to be observed on TEM micrographs. The electrical, optical and structural properties of the implanted and sub-sequently annealed polymers were investigated by sheet resistance measurement and UV-Vis spectroscopy. With increasing ion fluence, the sheet resistance decreases and UV-Vis absorbance increases simultaneously with the decline of optical band gap Eg. The most pronounced change in the resistance was found on PEEK. XPS spectroscopy shows that Mn appears as a mixture of Mn oxides. Mn metal component is not present. All results were discussed in comparison with implantation experiment using the various ion species (Ni, Co) and energies used in our former experiments. Interesting differences were found in Mn concentration distribution, Mn nano-particle creation and structural changes comparing to Ni, Co ions implantation into the same polymers.

Cislan-2 extension final document by University of Twente (Netherlands)

NASA Astrophysics Data System (ADS)

Niemegeers, Ignas; Baumann, Frank; Beuwer, Wim; Jordense, Marcel; Pras, Aiko; Schutte, Leon; Tracey, Ian

1992-01-01

Results of worked performed under the so called Cislan extension contract are presented. The adaptation of the Cislan 2 prototype design to an environment of interconnected Local Area Networks (LAN's) instead of a single 802.5 token ring LAN is considered. In order to extend the network architecture, the Interconnection Function (IF) protocol layer was subdivided into two protocol layers: a new IF layer, and below the Medium Enhancement (ME) protocol layer. Some small enhancements to the distributed bandwidth allocation protocol were developed, which in fact are also applicable to the 'normal' Cislan 2 system. The new services and protocols are described together with some scenarios and requirements for the new internetting Cislan 2 system. How to overcome the degradation of the quality of speech due to packet loss on the LAN subsystem was studied. Experiments were planned in order to measure this speech quality degradation. Simulations were performed of two Cislan subsystems, the bandwidth allocation protocol and the clock synchronization mechanism. Results on both simulations, performed on SUN workstations using QNAP as a simulation tool, are given. Results of the simulations of the clock synchronization mechanism, and results of the simulation of the distributed bandwidth allocation protocol are given.

The Local Minima Problem in Hierarchical Classes Analysis: An Evaluation of a Simulated Annealing Algorithm and Various Multistart Procedures

ERIC Educational Resources Information Center

Ceulemans, Eva; Van Mechelen, Iven; Leenen, Iwin

2007-01-01

Hierarchical classes models are quasi-order retaining Boolean decomposition models for N-way N-mode binary data. To fit these models to data, rationally started alternating least squares (or, equivalently, alternating least absolute deviations) algorithms have been proposed. Extensive simulation studies showed that these algorithms succeed quite…

Delay Tolerant Networking - Bundle Protocol Simulation

NASA Technical Reports Server (NTRS)

SeGui, John; Jenning, Esther

2006-01-01

In this paper, we report on the addition of MACHETE models needed to support DTN, namely: the Bundle Protocol (BP) model. To illustrate the useof MACHETE with the additional DTN model, we provide an example simulation to benchmark its performance. We demonstrate the use of the DTN protocol and discuss statistics gathered concerning the total time needed to simulate numerous bundle transmissions.

Piper-betle-shaped nano-S-catalyzed synthesis of 1-amidoalkyl-2-naphthols under solvent-free reaction condition: a greener "nanoparticle-catalyzed organic synthesis enhancement" approach.

PubMed

Das, Vijay K; Borah, Madhurjya; Thakur, Ashim J

2013-04-05

Nano-S prepared by an annealing process showed excellent catalytic activity for the synthesis of 1-amidoalkyl-2-naphthols under solvent-free reaction condition at 50 °C. The catalyst could be reused up to the fifth cycle without loss in its action. The green-ness of the present protocol was also measured using green metrics drawing its superiority.

Highly crystalline films of PCPDTBT with branched side chains by solvent vapor crystallization: influence on opto-electronic properties.

PubMed

Fischer, Florian S U; Trefz, Daniel; Back, Justus; Kayunkid, Navaphun; Tornow, Benjamin; Albrecht, Steve; Yager, Kevin G; Singh, Gurpreet; Karim, Alamgir; Neher, Dieter; Brinkmann, Martin; Ludwigs, Sabine

2015-02-18

PCPDTBT, a marginally crystallizable polymer, is crystallized into a new crystal structure using solvent-vapor annealing. Highly ordered areas with three different polymer-chain orientations are identified using TEM/ED, GIWAXS, and polarized Raman spectroscopy. The optical and structural properties differ significantly from films prepared by standard device preparation protocols. Bilayer solar cells, however, show similar performance. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Automatic CT simulation optimization for radiation therapy: A general strategy.

PubMed

Li, Hua; Yu, Lifeng; Anastasio, Mark A; Chen, Hsin-Chen; Tan, Jun; Gay, Hiram; Michalski, Jeff M; Low, Daniel A; Mutic, Sasa

2014-03-01

In radiation therapy, x-ray computed tomography (CT) simulation protocol specifications should be driven by the treatment planning requirements in lieu of duplicating diagnostic CT screening protocols. The purpose of this study was to develop a general strategy that allows for automatically, prospectively, and objectively determining the optimal patient-specific CT simulation protocols based on radiation-therapy goals, namely, maintenance of contouring quality and integrity while minimizing patient CT simulation dose. The authors proposed a general prediction strategy that provides automatic optimal CT simulation protocol selection as a function of patient size and treatment planning task. The optimal protocol is the one that delivers the minimum dose required to provide a CT simulation scan that yields accurate contours. Accurate treatment plans depend on accurate contours in order to conform the dose to actual tumor and normal organ positions. An image quality index, defined to characterize how simulation scan quality affects contour delineation, was developed and used to benchmark the contouring accuracy and treatment plan quality within the predication strategy. A clinical workflow was developed to select the optimal CT simulation protocols incorporating patient size, target delineation, and radiation dose efficiency. An experimental study using an anthropomorphic pelvis phantom with added-bolus layers was used to demonstrate how the proposed prediction strategy could be implemented and how the optimal CT simulation protocols could be selected for prostate cancer patients based on patient size and treatment planning task. Clinical IMRT prostate treatment plans for seven CT scans with varied image quality indices were separately optimized and compared to verify the trace of target and organ dosimetry coverage. Based on the phantom study, the optimal image quality index for accurate manual prostate contouring was 4.4. The optimal tube potentials for patient sizes of 38, 43, 48, 53, and 58 cm were 120, 140, 140, 140, and 140 kVp, respectively, and the corresponding minimum CTDIvol for achieving the optimal image quality index 4.4 were 9.8, 32.2, 100.9, 241.4, and 274.1 mGy, respectively. For patients with lateral sizes of 43-58 cm, 120-kVp scan protocols yielded up to 165% greater radiation dose relative to 140-kVp protocols, and 140-kVp protocols always yielded a greater image quality index compared to the same dose-level 120-kVp protocols. The trace of target and organ dosimetry coverage and the γ passing rates of seven IMRT dose distribution pairs indicated the feasibility of the proposed image quality index for the predication strategy. A general strategy to predict the optimal CT simulation protocols in a flexible and quantitative way was developed that takes into account patient size, treatment planning task, and radiation dose. The experimental study indicated that the optimal CT simulation protocol and the corresponding radiation dose varied significantly for different patient sizes, contouring accuracy, and radiation treatment planning tasks.

A hybrid genetic-simulated annealing algorithm for the location-inventory-routing problem considering returns under e-supply chain environment.

PubMed

Li, Yanhui; Guo, Hao; Wang, Lin; Fu, Jing

2013-01-01

Facility location, inventory control, and vehicle routes scheduling are critical and highly related problems in the design of logistics system for e-business. Meanwhile, the return ratio in Internet sales was significantly higher than in the traditional business. Many of returned merchandise have no quality defects, which can reenter sales channels just after a simple repackaging process. Focusing on the existing problem in e-commerce logistics system, we formulate a location-inventory-routing problem model with no quality defects returns. To solve this NP-hard problem, an effective hybrid genetic simulated annealing algorithm (HGSAA) is proposed. Results of numerical examples show that HGSAA outperforms GA on computing time, optimal solution, and computing stability. The proposed model is very useful to help managers make the right decisions under e-supply chain environment.

Memoryless cooperative graph search based on the simulated annealing algorithm

NASA Astrophysics Data System (ADS)

Hou, Jian; Yan, Gang-Feng; Fan, Zhen

2011-04-01

We have studied the problem of reaching a globally optimal segment for a graph-like environment with a single or a group of autonomous mobile agents. Firstly, two efficient simulated-annealing-like algorithms are given for a single agent to solve the problem in a partially known environment and an unknown environment, respectively. It shows that under both proposed control strategies, the agent will eventually converge to a globally optimal segment with probability 1. Secondly, we use multi-agent searching to simultaneously reduce the computation complexity and accelerate convergence based on the algorithms we have given for a single agent. By exploiting graph partition, a gossip-consensus method based scheme is presented to update the key parameter—radius of the graph, ensuring that the agents spend much less time finding a globally optimal segment.

Optimization of seasonal ARIMA models using differential evolution - simulated annealing (DESA) algorithm in forecasting dengue cases in Baguio City

NASA Astrophysics Data System (ADS)

Addawe, Rizavel C.; Addawe, Joel M.; Magadia, Joselito C.

2016-10-01

Accurate forecasting of dengue cases would significantly improve epidemic prevention and control capabilities. This paper attempts to provide useful models in forecasting dengue epidemic specific to the young and adult population of Baguio City. To capture the seasonal variations in dengue incidence, this paper develops a robust modeling approach to identify and estimate seasonal autoregressive integrated moving average (SARIMA) models in the presence of additive outliers. Since the least squares estimators are not robust in the presence of outliers, we suggest a robust estimation based on winsorized and reweighted least squares estimators. A hybrid algorithm, Differential Evolution - Simulated Annealing (DESA), is used to identify and estimate the parameters of the optimal SARIMA model. The method is applied to the monthly reported dengue cases in Baguio City, Philippines.

A simulated annealing approach for redesigning a warehouse network problem

NASA Astrophysics Data System (ADS)

Khairuddin, Rozieana; Marlizawati Zainuddin, Zaitul; Jiun, Gan Jia

2017-09-01

Now a day, several companies consider downsizing their distribution networks in ways that involve consolidation or phase-out of some of their current warehousing facilities due to the increasing competition, mounting cost pressure and taking advantage on the economies of scale. Consequently, the changes on economic situation after a certain period of time require an adjustment on the network model in order to get the optimal cost under the current economic conditions. This paper aimed to develop a mixed-integer linear programming model for a two-echelon warehouse network redesign problem with capacitated plant and uncapacitated warehouses. The main contribution of this study is considering capacity constraint for existing warehouses. A Simulated Annealing algorithm is proposed to tackle with the proposed model. The numerical solution showed the model and method of solution proposed was practical.

Ranking of Prokaryotic Genomes Based on Maximization of Sortedness of Gene Lengths

PubMed Central

Bolshoy, A; Salih, B; Cohen, I; Tatarinova, T

2014-01-01

How variations of gene lengths (some genes become longer than their predecessors, while other genes become shorter and the sizes of these factions are randomly different from organism to organism) depend on organismal evolution and adaptation is still an open question. We propose to rank the genomes according to lengths of their genes, and then find association between the genome rank and variousproperties, such as growth temperature, nucleotide composition, and pathogenicity. This approach reveals evolutionary driving factors. The main purpose of this study is to test effectiveness and robustness of several ranking methods. The selected method of evaluation is measuring of overall sortedness of the data. We have demonstrated that all considered methods give consistent results and Bubble Sort and Simulated Annealing achieve the highest sortedness. Also, Bubble Sort is considerably faster than the Simulated Annealing method. PMID:26146586

Ranking of Prokaryotic Genomes Based on Maximization of Sortedness of Gene Lengths.

PubMed

Bolshoy, A; Salih, B; Cohen, I; Tatarinova, T

How variations of gene lengths (some genes become longer than their predecessors, while other genes become shorter and the sizes of these factions are randomly different from organism to organism) depend on organismal evolution and adaptation is still an open question. We propose to rank the genomes according to lengths of their genes, and then find association between the genome rank and variousproperties, such as growth temperature, nucleotide composition, and pathogenicity. This approach reveals evolutionary driving factors. The main purpose of this study is to test effectiveness and robustness of several ranking methods. The selected method of evaluation is measuring of overall sortedness of the data. We have demonstrated that all considered methods give consistent results and Bubble Sort and Simulated Annealing achieve the highest sortedness. Also, Bubble Sort is considerably faster than the Simulated Annealing method.

Simulated Annealing Based Hybrid Forecast for Improving Daily Municipal Solid Waste Generation Prediction

PubMed Central

Song, Jingwei; He, Jiaying; Zhu, Menghua; Tan, Debao; Zhang, Yu; Ye, Song; Shen, Dingtao; Zou, Pengfei

2014-01-01

A simulated annealing (SA) based variable weighted forecast model is proposed to combine and weigh local chaotic model, artificial neural network (ANN), and partial least square support vector machine (PLS-SVM) to build a more accurate forecast model. The hybrid model was built and multistep ahead prediction ability was tested based on daily MSW generation data from Seattle, Washington, the United States. The hybrid forecast model was proved to produce more accurate and reliable results and to degrade less in longer predictions than three individual models. The average one-week step ahead prediction has been raised from 11.21% (chaotic model), 12.93% (ANN), and 12.94% (PLS-SVM) to 9.38%. Five-week average has been raised from 13.02% (chaotic model), 15.69% (ANN), and 15.92% (PLS-SVM) to 11.27%. PMID:25301508

GOSA, a simulated annealing-based program for global optimization of nonlinear problems, also reveals transyears

PubMed Central

Czaplicki, Jerzy; Cornélissen, Germaine; Halberg, Franz

2009-01-01

Summary Transyears in biology have been documented thus far by the extended cosinor approach, including linear-nonlinear rhythmometry. We here confirm the existence of transyears by simulated annealing, a method originally developed for a much broader use, but described and introduced herein for validating its application to time series. The method is illustrated both on an artificial test case with known components and on biological data. We provide a table comparing results by the two methods and trust that the procedure will serve the budding sciences of chronobiology (the study of mechanisms underlying biological time structure), chronomics (the mapping of time structures in and around us), and chronobioethics, using the foregoing disciplines to add to concern for illnesses of individuals, and to budding focus on diseases of nations and civilizations. PMID:20414480

Scheduling Earth Observing Satellites with Evolutionary Algorithms

NASA Technical Reports Server (NTRS)

Globus, Al; Crawford, James; Lohn, Jason; Pryor, Anna

2003-01-01

We hypothesize that evolutionary algorithms can effectively schedule coordinated fleets of Earth observing satellites. The constraints are complex and the bottlenecks are not well understood, a condition where evolutionary algorithms are often effective. This is, in part, because evolutionary algorithms require only that one can represent solutions, modify solutions, and evaluate solution fitness. To test the hypothesis we have developed a representative set of problems, produced optimization software (in Java) to solve them, and run experiments comparing techniques. This paper presents initial results of a comparison of several evolutionary and other optimization techniques; namely the genetic algorithm, simulated annealing, squeaky wheel optimization, and stochastic hill climbing. We also compare separate satellite vs. integrated scheduling of a two satellite constellation. While the results are not definitive, tests to date suggest that simulated annealing is the best search technique and integrated scheduling is superior.

Study of crystallization mechanisms of Fe nanoparticle

NASA Astrophysics Data System (ADS)

Kien, P. H.; Trang, G. T. T.; Hung, P. K.

2017-06-01

In this paper, the nanoparticle (NP) Fe was investigated by means of molecular dynamics simulation. The crystallization mechanism was studied through the time evolution of crystal cluster and potential energies of different atom types. The simulation shows that the NP was crystallized into bcc crystal structure when it was annealed at 900 K for long times. At early stage of the annealing, small nuclei form in different places of NP and dissolve for short times. After long times some nuclei form and gather nearby which create the stable clusters in the core of NP. After that the crystal clusters grow in the direction to cover the core and then to spread into the surface of NP. Analyzing the energies of different type atoms, we found that the crystal growth is originated from specific atomic arrangement in the boundary region of crystal clusters.

Shape optimization of electrostatically driven microcantilevers using simulated annealing to enhance static travel range

NASA Astrophysics Data System (ADS)

Trivedi, R. R.; Joglekar, M. M.; Shimpi, R. P.; Pawaskar, D. N.

2013-12-01

The objective of this paper is to present a systematic development of the generic shape optimization of elec- trostatically actuated microcantilever beams for extending their static travel range. Electrostatic actuators are widely used in micro electro mechanical system (MEMS) devices because of low power density and ease of fab- rication. However, their useful travel range is often restricted by a phenomenon known as pull-in instability. The Rayleigh- Ritz energy method is used for computation of pull-in parameters which includes electrostatic potential and fringing field effect. Appropriate width function and linear thickness functions are employed along the length of the non-prismatic beam to achieve enhanced travel range. Parameters used for varying the thick- ness and width functions are optimized using simulated annealing with pattern search method towards the end to refine the results. Appropriate penalties are imposed on the violation of volume, width, thickness and area constraints. Nine test cases are considered for demonstration of the said optimization method. Our results indicate that around 26% increase in the travel range of a non-prismatic beam can be achieved after optimiza- tion compared to that in a prismatic beam having the same volume. Our results also show an improvement in the pull-in displacement of around 5% compared to that of a variable width constant thickness actuator. We show that simulated annealing is an effective and flexible method to carry out design optimization of structural elements under electrostatic loading.

Clinical Simulation: A Protocol for Evaluation of Mobile Technology.

PubMed

Mather, Carey; Jensen, Sanne; Cummings, Elizabeth

2017-01-01

For mobile technology to be accepted at point of care in healthcare environments there is a need to demonstrate benefits whilst ameliorating the risks and challenges. To provide a standardised approach to evaluation of mobile technology a simulation protocol was developed to provide guidance for its use in healthcare environments. Simulated conditions provide the opportunity to assess intended and unintended consequences and identify potential workarounds when using technology. The protocol can also be used to demonstrate the importance of the development of digital professionalism by end-users prior to students entering the clinical practice setting. The mobile technology protocol was adapted from a health information systems protocol developed and used at the ITX Lab, Denmark for use in other simulation laboratories. Use case scenarios were developed to enable evaluation of mobile technology for mobile learning of nurses, nurse supervisors, students and patients. The scenarios can be used in a range of simulated environments including hospital bedside, outpatient clinic or community settings. A case study exemplar of a nurse and patient is included to demonstrate how the mobile technology protocol can be applied.

Photobacterium damselae ssp. piscicida: detection by direct amplification of 16S rRNA gene sequences and genotypic variation as determined by amplified fragment length polymorphism (AFLP).

PubMed

Kvitt, H; Ucko, M; Colorni, A; Batargias, C; Zlotkin, A; Knibb, W

2002-04-05

A PCR protocol for the rapid diagnosis of fish 'pasteurellosis' based on 16S rRNA gene sequences was developed. The procedure combines low annealing temperature that detects low titers of Photobacterium damselae but also related species, and high annealing temperature for the specific identification of P. damselae directly from infected fish. The PCR protocol was validated on 19 piscine isolates of P. damselae ssp. piscicida from different geographic regions (Japan, Italy, Spain, Greece and Israel), on spontaneously infected sea bream Sparus aurata and sea bass Dicentrarchus labrax, and on closely related American Type Culture Collection (ATCC) reference strains. PCR using high annealing temperature (64 degrees C) discriminated between P. damselae and closely related reference strains, including P. histaminum. Sixteen isolates of P. damselae ssp. piscicida, 2 P. damselae ssp. piscicida reference strains and 1 P. damselae ssp. damselae reference strain were subjected to Amplified Fragment Length Polymorphism (AFLP) analysis, and a similarity matrix was produced. Accordingly, the Japanese isolates of P. damselae ssp. piscicida were distinguished from the Mediterranean/European isolates at a cut-off value of 83% similarity. A further subclustering at a cut-off value of 97% allowed discrimination between the Israeli P. damselae ssp. piscicida isolates and the other Mediterranean/European isolates. The combination of PCR direct amplification and AFLP provides a 2-step procedure, where P. damselae is rapidly identified at genus level on the basis of its 16S rRNA gene sequence and then grouped into distinct clusters on the basis of AFLP polymorphisms. The first step of direct amplification is highly sensitive and has immediate practical consequences, offering fish farmers a rapid diagnosis, while the AFLP is more specific and detects intraspecific variation which, in our study, also reflected geographic correspondence. Because of its superior discriminative properties, AFLP can be an important tool for epidemiological and taxonomic studies of this highly homogeneous genus.

Evaluation of the Mechanism of the Gold Cluster Growth during Heating of the Composite Gold-Polytetrafluoroethylene Thin Film.

PubMed

Grytsenko, Konstantin; Lozovski, Valeri; Strilchuk, Galyna; Schrader, Sigurd

2012-11-07

Nanocomposite films consisting of gold inclusions in the polytetrafluoroethylene (PTFE) matrix were obtained by thermal vacuum deposition. Annealing of the obtained films with different temperatures was used to measure varying of film morphologies. The dependence of optical properties of the films on their morphology was studied. It was established that absorption and profile of the nanocomposite film obtained by thermal vacuum deposition can be changed with annealing owing to the fact that different annealing temperatures lead to different average particle sizes. A method to calculate the optical properties of nanocomposite thin films with inclusions of different sizes was proposed. Thus, comparison of experimental optical spectra with the spectra obtained during the simulation enables estimating average sizes of inclusions. The calculations give the possibility of understanding morphological changes in the structures.

High-temperature annealing of proton irradiated beryllium – A dilatometry-based study

DOE PAGES

Simos, Nikolaos; Elbakhshwan, Mohamed; Zhong, Zhong; ...

2016-04-07

S—200 F grade beryllium has been irradiated with 160 MeV protons up to 1.2 10 20 cm –2 peak fluence and irradiation temperatures in the range of 100–200 °C. To address the effect of proton irradiation on dimensional stability, an important parameter in its consideration in fusion reactor applications, and to simulate high temperature irradiation conditions, multi-stage annealing using high precision dilatometry to temperatures up to 740 °C were conducted in air. X-ray diffraction studies were also performed to compliment the macroscopic thermal study and offer a microscopic view of the irradiation effects on the crystal lattice. The primary objectivemore » was to qualify the competing dimensional change processes occurring at elevated temperatures namely manufacturing defect annealing, lattice parameter recovery, transmutation 4He and 3H diffusion and swelling and oxidation kinetics. Further, quantification of the effect of irradiation dose and annealing temperature and duration on dimensional changes is sought. Here, the study revealed the presence of manufacturing porosity in the beryllium grade, the oxidation acceleration effect of irradiation including the discontinuous character of oxidation advancement, the effect of annealing duration on the recovery of lattice parameters recovery and the triggering temperature for transmutation gas diffusion leading to swelling.« less

Impact of He and H relative depth distributions on the result of sequential He+ and H+ ion implantation and annealing in silicon

NASA Astrophysics Data System (ADS)

Cherkashin, N.; Daghbouj, N.; Seine, G.; Claverie, A.

2018-04-01

Sequential He++H+ ion implantation, being more effective than the sole implantation of H+ or He+, is used by many to transfer thin layers of silicon onto different substrates. However, due to the poor understanding of the basic mechanisms involved in such a process, the implantation parameters to be used for the efficient delamination of a superficial layer are still subject to debate. In this work, by using various experimental techniques, we have studied the influence of the He and H relative depth-distributions imposed by the ion energies onto the result of the sequential implantation and annealing of the same fluence of He and H ions. Analyzing the characteristics of the blister populations observed after annealing and deducing the composition of the gas they contain from FEM simulations, we show that the trapping efficiency of He atoms in platelets and blisters during annealing depends on the behavior of the vacancies generated by the two implants within the H-rich region before and after annealing. Maximum efficiency of the sequential ion implantation is obtained when the H-rich region is able to trap all implanted He ions, while the vacancies it generated are not available to favor the formation of V-rich complexes after implantation then He-filled nano-bubbles after annealing. A technological option is to implant He+ ions first at such an energy that the damage it generates is located on the deeper side of the H profile.

Molecular dynamics study on splitting of hydrogen-implanted silicon in Smart-Cut® technology

NASA Astrophysics Data System (ADS)

Bing, Wang; Bin, Gu; Rongying, Pan; Sijia, Zhang; Jianhua, Shen

2015-03-01

Defect evolution in a single crystal silicon which is implanted with hydrogen atoms and then annealed is investigated in the present paper by means of molecular dynamics simulation. By introducing defect density based on statistical average, this work aims to quantitatively examine defect nucleation and growth at nanoscale during annealing in Smart-Cut® technology. Research focus is put on the effects of the implantation energy, hydrogen implantation dose and annealing temperature on defect density in the statistical region. It is found that most defects nucleate and grow at the annealing stage, and that defect density increases with the increase of the annealing temperature and the decrease of the hydrogen implantation dose. In addition, the enhancement and the impediment effects of stress field on defect density in the annealing process are discussed. Project supported by the National Natural Science Foundation of China (No. 11372261), the Excellent Young Scientists Supporting Project of Science and Technology Department of Sichuan Province (No. 2013JQ0030), the Supporting Project of Department of Education of Sichuan Province (No. 2014zd3132), the Opening Project of Key Laboratory of Testing Technology for Manufacturing Process, Southwest University of Science and Technology-Ministry of Education (No. 12zxzk02), the Fund of Doctoral Research of Southwest University of Science and Technology (No. 12zx7106), and the Postgraduate Innovation Fund Project of Southwest University of Science and Technology (No. 14ycxjj0121).

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

DOE PAGES

Lee, Jumin; Cheng, Xi; Swails, Jason M.; ...

2015-11-12

Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find themore » optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.« less

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.

PubMed

Lee, Jumin; Cheng, Xi; Swails, Jason M; Yeom, Min Sun; Eastman, Peter K; Lemkul, Justin A; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; Jo, Sunhwan; Pande, Vijay S; Case, David A; Brooks, Charles L; MacKerell, Alexander D; Klauda, Jeffery B; Im, Wonpil

2016-01-12

Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.

Maximum-Entropy Inference with a Programmable Annealer

PubMed Central

Chancellor, Nicholas; Szoke, Szilard; Vinci, Walter; Aeppli, Gabriel; Warburton, Paul A.

2016-01-01

Optimisation problems typically involve finding the ground state (i.e. the minimum energy configuration) of a cost function with respect to many variables. If the variables are corrupted by noise then this maximises the likelihood that the solution is correct. The maximum entropy solution on the other hand takes the form of a Boltzmann distribution over the ground and excited states of the cost function to correct for noise. Here we use a programmable annealer for the information decoding problem which we simulate as a random Ising model in a field. We show experimentally that finite temperature maximum entropy decoding can give slightly better bit-error-rates than the maximum likelihood approach, confirming that useful information can be extracted from the excited states of the annealer. Furthermore we introduce a bit-by-bit analytical method which is agnostic to the specific application and use it to show that the annealer samples from a highly Boltzmann-like distribution. Machines of this kind are therefore candidates for use in a variety of machine learning applications which exploit maximum entropy inference, including language processing and image recognition. PMID:26936311

Heart murmur detection based on wavelet transformation and a synergy between artificial neural network and modified neighbor annealing methods.

PubMed

Eslamizadeh, Gholamhossein; Barati, Ramin

2017-05-01

Early recognition of heart disease plays a vital role in saving lives. Heart murmurs are one of the common heart problems. In this study, Artificial Neural Network (ANN) is trained with Modified Neighbor Annealing (MNA) to classify heart cycles into normal and murmur classes. Heart cycles are separated from heart sounds using wavelet transformer. The network inputs are features extracted from individual heart cycles, and two classification outputs. Classification accuracy of the proposed model is compared with five multilayer perceptron trained with Levenberg-Marquardt, Extreme-learning-machine, back-propagation, simulated-annealing, and neighbor-annealing algorithms. It is also compared with a Self-Organizing Map (SOM) ANN. The proposed model is trained and tested using real heart sounds available in the Pascal database to show the applicability of the proposed scheme. Also, a device to record real heart sounds has been developed and used for comparison purposes too. Based on the results of this study, MNA can be used to produce considerable results as a heart cycle classifier. Copyright © 2017 Elsevier B.V. All rights reserved.

SU-F-BRD-13: Quantum Annealing Applied to IMRT Beamlet Intensity Optimization

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

Nazareth, D; Spaans, J

Purpose: We report on the first application of quantum annealing (QA) to the process of beamlet intensity optimization for IMRT. QA is a new technology, which employs novel hardware and software techniques to address various discrete optimization problems in many fields. Methods: We apply the D-Wave Inc. proprietary hardware, which natively exploits quantum mechanical effects for improved optimization. The new QA algorithm, running on this hardware, is most similar to simulated annealing, but relies on natural processes to directly minimize the free energy of a system. A simple quantum system is slowly evolved into a classical system, representing the objectivemore » function. To apply QA to IMRT-type optimization, two prostate cases were considered. A reduced number of beamlets were employed, due to the current QA hardware limitation of ∼500 binary variables. The beamlet dose matrices were computed using CERR, and an objective function was defined based on typical clinical constraints, including dose-volume objectives. The objective function was discretized, and the QA method was compared to two standard optimization Methods: simulated annealing and Tabu search, run on a conventional computing cluster. Results: Based on several runs, the average final objective function value achieved by the QA was 16.9 for the first patient, compared with 10.0 for Tabu and 6.7 for the SA. For the second patient, the values were 70.7 for the QA, 120.0 for Tabu, and 22.9 for the SA. The QA algorithm required 27–38% of the time required by the other two methods. Conclusion: In terms of objective function value, the QA performance was similar to Tabu but less effective than the SA. However, its speed was 3–4 times faster than the other two methods. This initial experiment suggests that QA-based heuristics may offer significant speedup over conventional clinical optimization methods, as quantum annealing hardware scales to larger sizes.« less

Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2014-01-01

Coarse-grained (CG) modeling is a well-acknowledged simulation approach for getting insight into long-time scale protein folding events at reasonable computational cost. Depending on the design of a CG model, the simulation protocols vary from highly case-specific-requiring user-defined assumptions about the folding scenario-to more sophisticated blind prediction methods for which only a protein sequence is required. Here we describe the framework protocol for the simulations of long-term dynamics of globular proteins, with the use of the CABS CG protein model and sequence data. The simulations can start from a random or a selected (e.g., native) structure. The described protocol has been validated using experimental data for protein folding model systems-the prediction results agreed well with the experimental results.

Investigating the evolution of local structure around Er and Yb in ZnO:Er and ZnO:Er, Yb on annealing using X-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Anjana, R.; Jayaraj, M. K.; Yadav, A. K.; Jha, S. N.; Bhattacharyya, D.

2018-04-01

The local structure around Er and Yb centre in ZnO favouring upconversion luminescence was studied using EXAFS (Extended X-ray absorption fine structure spectroscopy). Due to the ionic radii difference between Zn and Er, Yb ions, the dopants cannot replace Zn in the ZnO lattice properly. Er2O3 and Yb2O3 impurity phases are formed at the grain boundaries of ZnO. It is found that the local structure around the Er centre in ZnO is modified on annealing in air. The symmetry around both erbium and ytterbium reduces with increase in annealing temperature. Symmetry reduction will favour the intra-4f transition and the energy transitions causing upconversion luminescence. By fitting the EXAFS data with theoretically simulated data, it is found that the Er centre forms a local structure similar to C4ν symmetry which is a distorted octahedron. On annealing the sample to 1200 °C, all the erbium centres are transformed to C4ν symmetry causing enhanced upconversion emission. Yb centre has also been modified on annealing. The decrease in co-ordination number with annealing temperature will decrease the symmetry and increase the near infrared absorption cross section. The decrease in symmetry around both the erbium and ytterbium centre and formation of C4ν symmetry around Er centre is the reason behind the activation of upconversion luminescence with high temperature annealing in both Er doped and Er, Yb co-doped ZnO samples. The study will be useful for the synthesis of high efficiency upconversion materials.

Thermal annealing response following irradiation of a CMOS imager for the JUICE JANUS instrument

NASA Astrophysics Data System (ADS)

Lofthouse-Smith, D.-D.; Soman, M. R.; Allanwood, E. A. H.; Stefanov, K. D.; Holland, A. D.; Leese, M.; Turne, P.

2018-03-01

ESA's JUICE (JUpiter ICy moon Explorer) spacecraft is an L-class mission destined for the Jovian system in 2030. Its primary goals are to investigate the conditions for planetary formation and the emergence of life, and how does the solar system work. The JANUS camera, an instrument on JUICE, uses a 4T back illuminated CMOS image sensor, the CIS115 designed by Teledyne e2v. JANUS imager test campaigns are studying the CIS115 following exposure to gammas, protons, electrons and heavy ions, simulating the harsh radiation environment present in the Jovian system. The degradation of 4T CMOS device performance following proton fluences is being studied, as well as the effectiveness of thermal annealing to reverse radiation damage. One key parameter for the JANUS mission is the Dark current of the CIS115, which has been shown to degrade in previous radiation campaigns. A thermal anneal of the CIS115 has been used to accelerate any annealing following the irradiation as well as to study the evolution of any performance characteristics. CIS115s have been irradiated to double the expected End of Life (EOL) levels for displacement damage radiation (2×1010 protons, 10 MeV equivalent). Following this, devices have undergone a thermal anneal cycle at 100oC for 168 hours to reveal the extent to which CIS115 recovers pre-irradiation performance. Dark current activation energy analysis following proton fluence gives information on trap species present in the device and how effective anneal is at removing these trap species. Thermal anneal shows no quantifiable change in the activation energy of the dark current following irradiation.

Scalable creation of gold nanostructures on high performance engineering polymeric substrate

NASA Astrophysics Data System (ADS)

Jia, Kun; Wang, Pan; Wei, Shiliang; Huang, Yumin; Liu, Xiaobo

2017-12-01

The article reveals a facile protocol for scalable production of gold nanostructures on a high performance engineering thermoplastic substrate made of polyarylene ether nitrile (PEN) for the first time. Firstly, gold thin films with different thicknesses of 2 nm, 4 nm and 6 nm were evaporated on a spin-coated PEN substrate on glass slide in vacuum. Next, the as-evaporated samples were thermally annealed around the glass transition temperature of the PEN substrate, on which gold nanostructures with island-like morphology were created. Moreover, it was found that the initial gold evaporation thickness and annealing atmosphere played an important role in determining the morphology and plasmonic properties of the formulated Au NPs. Interestingly, we discovered that isotropic Au NPs can be easily fabricated on the freestanding PEN substrate, which was fabricated by a cost-effective polymer solution casting method. More specifically, monodispersed Au nanospheres with an average size of ∼60 nm were obtained after annealing a 4 nm gold film covered PEN casting substrate at 220 °C for 2 h in oxygen. Therefore, the scalable production of Au NPs with controlled morphology on PEN substrate would open the way for development of robust flexible nanosensors and optical devices using high performance engineering polyarylene ethers.

Development of Simulation Methods in the Gibbs Ensemble to Predict Polymer-Solvent Phase Equilibria

NASA Astrophysics Data System (ADS)

Gartner, Thomas; Epps, Thomas; Jayaraman, Arthi

Solvent vapor annealing (SVA) of polymer thin films is a promising method for post-deposition polymer film morphology control. The large number of important parameters relevant to SVA (polymer, solvent, and substrate chemistries, incoming film condition, annealing and solvent evaporation conditions) makes systematic experimental study of SVA a time-consuming endeavor, motivating the application of simulation and theory to the SVA system to provide both mechanistic insight and scans of this wide parameter space. However, to rigorously treat the phase equilibrium between polymer film and solvent vapor while still probing the dynamics of SVA, new simulation methods must be developed. In this presentation, we compare two methods to study polymer-solvent phase equilibrium-Gibbs Ensemble Molecular Dynamics (GEMD) and Hybrid Monte Carlo/Molecular Dynamics (Hybrid MC/MD). Liquid-vapor equilibrium results are presented for the Lennard Jones fluid and for coarse-grained polymer-solvent systems relevant to SVA. We found that the Hybrid MC/MD method is more stable and consistent than GEMD, but GEMD has significant advantages in computational efficiency. We propose that Hybrid MC/MD simulations be used for unfamiliar systems in certain choice conditions, followed by much faster GEMD simulations to map out the remainder of the phase window.

Comparison Between Different Processing Schedules for the Development of Ultrafine-Grained Dual-Phase Steel

NASA Astrophysics Data System (ADS)

Karmakar, Anish; Sivaprasad, S.; Nath, S. K.; Misra, R. D. K.; Chakrabarti, Debalay

2014-05-01

A comparative study was carried out on the development of ultrafine-grained dual-phase (DP) (ferrite-martensite) structures in a low-carbon microalloyed steel processed using two thermomechanical processing routes, (i) intercritical deformation and (ii) warm-deformation and intercritical annealing. The samples were deformed using Gleeble3500® simulator, maintaining a constant total strain ( ɛ = 1) and strain rate ( = 1/s). Evolution of microstructure and micro-texture was investigated by SEM, TEM, and EBSD. Ultrafine-grained DP structures could be formed by careful selection of deformation temperature, T def (for intercritical deformation) or annealing temperature, T anneal (for warm-deformation and annealing). Overall, the ferrite grain sizes ranged from 1.5 to 4.0 μm, and the sizes and fractions of the uniformly distributed fine-martensitic islands ranged from 1.5 to 3.0 μm and 15 to 45 pct, respectively. Dynamic strain-induced austenite-to-ferrite transformation followed by continuous (dynamic) recrystallization of the ferrite dictated the grain refinement during intercritical deformation, while, continuous (static) recrystallization by pronounced recovery dictated the grain refinement during the warm-deformation and the annealing. Regarding intercritical deformation, the samples cooled to T def indicated finer grain size compared with the samples heated to T def, which are explained in terms of the effects of strain partitioning on the ferrite and the heating during deformation. Alpha-fiber components dominated the texture in all the samples, and the fraction of high-angle boundaries (with >15 deg misorientation) increased with the increasing T def or T anneal, depending on the processing schedule. Fine carbide particles, microalloyed precipitates and austenitic islands played important roles in defining the mechanism of grain refinement that involved retarding conventional ferrite recrystallization and ferrite grain growth. With regard to the intercritical deformation, warm-deformation followed by annealing is a simpler process to control in the rolling mill; however, the need for high-power rolling mill and controlled annealing facility imposes industrial challenges.

Seeking Global Minima

NASA Astrophysics Data System (ADS)

Tajuddin, Wan Ahmad

1994-02-01

Ease in finding the configuration at the global energy minimum in a symmetric neural network is important for combinatorial optimization problems. We carry out a comprehensive survey of available strategies for seeking global minima by comparing their performances in the binary representation problem. We recall our previous comparison of steepest descent with analog dynamics, genetic hill-climbing, simulated diffusion, simulated annealing, threshold accepting and simulated tunneling. To this, we add comparisons to other strategies including taboo search and one with field-ordered updating.

Estimates of point defect production in α-quartz using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Cowen, Benjamin J.; El-Genk, Mohamed S.

2017-07-01

Molecular dynamics (MD) simulations are performed to investigate the production of point defects in α-quartz by oxygen and silicon primary knock-on atoms (PKAs) of 0.25-2 keV. The Wigner-Seitz (WS) defect analysis is used to identify the produced vacancies, interstitials, and antisites, and the coordination defect analysis is used to identify the under and over-coordinated oxygen and silicon atoms. The defects at the end of the ballistic phase and the residual defects, after annealing, increase with increased PKA energy, and are statistically the same for the oxygen and silicon PKAs. The WS defect analysis results show that the numbers of the oxygen vacancies and interstitials (VO, Oi) at the end of the ballistic phase is the highest, followed closely by those of the silicon vacancies and interstitials (VSi, Sii). The number of the residual oxygen and silicon vacancies and interstitials are statistically the same. In addition, the under-coordinated OI and SiIII, which are the primary defects during the ballistic phase, have high annealing efficiencies (>89%). The over-coordinated defects of OIII and SiV, which are not nearly as abundant in the ballistic phase, have much lower annealing efficiencies (<63%) that decrease with increased PKA energy.

Mitigating IASCC of Reactor Core Internals by Post-Irradiation Annealing

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

Was, Gary

This final report summarizes research performed during the period between September 2012 and December 2016, with the objective of establishing the effectiveness of post-irradiation annealing (PIA) as an advanced mitigation strategy for irradiation-assisted stress corrosion cracking (IASCC). This was completed by using irradiated 304SS control blade material to conduct crack initiation and crack growth rate (CGR) experiments in simulated BWR environment. The mechanism by which PIA affects IASCC susceptibility will also be verified. The success of this project will provide a foundation for the use of PIA as a mitigation strategy for core internal components in commercial reactors.

Relaxation plastique d'un film mince par émission de dislocations filantes vis

NASA Astrophysics Data System (ADS)

Bonnet, Roland; Youssef, Sami; Neily, Salem; Gutakowskii, A. K.

2008-03-01

The system formed by a thin film coherent with a crystalline substrate can relax its internal energy by annealing. Threading dislocations emitted after ten minutes annealing at 350 °C of the Si 0.68Ge 0.32/Si(001) heterostructure are observed in transmission electron microscopy, and then identified by comparison to simulated images of angular dislocations placed in a semi infinite medium. They are of screw character, which explains the rapid coverage of the interface by 60° dislocations oriented <110>. To cite this article: R. Bonnet et al., C. R. Physique 9 (2008).

Activities of the Solid State Physics Research Institute

NASA Technical Reports Server (NTRS)

1985-01-01

Topics addressed include: muon spin rotation; annealing problems in gallium arsenides; Hall effect in semiconductors; computerized simulation of radiation damage; single-nucleon removal from Mg-24; and He-3 reaction at 200 and 400 MeV.

Hybrid simulated annealing and its application to optimization of hidden Markov models for visual speech recognition.

PubMed

Lee, Jong-Seok; Park, Cheol Hoon

2010-08-01

We propose a novel stochastic optimization algorithm, hybrid simulated annealing (SA), to train hidden Markov models (HMMs) for visual speech recognition. In our algorithm, SA is combined with a local optimization operator that substitutes a better solution for the current one to improve the convergence speed and the quality of solutions. We mathematically prove that the sequence of the objective values converges in probability to the global optimum in the algorithm. The algorithm is applied to train HMMs that are used as visual speech recognizers. While the popular training method of HMMs, the expectation-maximization algorithm, achieves only local optima in the parameter space, the proposed method can perform global optimization of the parameters of HMMs and thereby obtain solutions yielding improved recognition performance. The superiority of the proposed algorithm to the conventional ones is demonstrated via isolated word recognition experiments.

A Comparison of Techniques for Scheduling Fleets of Earth-Observing Satellites

NASA Technical Reports Server (NTRS)

Globus, Al; Crawford, James; Lohn, Jason; Pryor, Anna

2003-01-01

Earth observing satellite (EOS) scheduling is a complex real-world domain representative of a broad class of over-subscription scheduling problems. Over-subscription problems are those where requests for a facility exceed its capacity. These problems arise in a wide variety of NASA and terrestrial domains and are .XI important class of scheduling problems because such facilities often represent large capital investments. We have run experiments comparing multiple variants of the genetic algorithm, hill climbing, simulated annealing, squeaky wheel optimization and iterated sampling on two variants of a realistically-sized model of the EOS scheduling problem. These are implemented as permutation-based methods; methods that search in the space of priority orderings of observation requests and evaluate each permutation by using it to drive a greedy scheduler. Simulated annealing performs best and random mutation operators outperform our squeaky (more intelligent) operator. Furthermore, taking smaller steps towards the end of the search improves performance.

Cooling rate dependence of structural order in Ni 62 Nb 38 metallic glass

DOE PAGES

Wen, Tongqi; Sun, Yang; Ye, Beilin; ...

2018-01-31

In this article, molecular dynamics (MD) simulations are performed to study the structure of Ni 62Nb 38 bulk metallic glass at the atomistic level. Structural analysis based on the cluster alignment method is carried out and a new Ni-centered distorted-icosahedra (DISICO) motif is excavated. We show that the short-range order and medium-range order in the glass are enhanced with lower cooling rate. Almost 50% of the clusters around the Ni atoms in the well-annealed Ni 62Nb 38 glass sample from our MD simulations can be classified as DISICO. It is revealed that the structural distortion with respect to the perfectmore » icosahedra is driven by chemical ordering in the distorted region of the DISICO motif. The relationship between the structure, energy, and dynamics in this glass-forming alloy during the cooling and annealing processes is also established.« less

A Hybrid Genetic-Simulated Annealing Algorithm for the Location-Inventory-Routing Problem Considering Returns under E-Supply Chain Environment

PubMed Central

Guo, Hao; Fu, Jing

2013-01-01

Facility location, inventory control, and vehicle routes scheduling are critical and highly related problems in the design of logistics system for e-business. Meanwhile, the return ratio in Internet sales was significantly higher than in the traditional business. Many of returned merchandise have no quality defects, which can reenter sales channels just after a simple repackaging process. Focusing on the existing problem in e-commerce logistics system, we formulate a location-inventory-routing problem model with no quality defects returns. To solve this NP-hard problem, an effective hybrid genetic simulated annealing algorithm (HGSAA) is proposed. Results of numerical examples show that HGSAA outperforms GA on computing time, optimal solution, and computing stability. The proposed model is very useful to help managers make the right decisions under e-supply chain environment. PMID:24489489

A clustering method of Chinese medicine prescriptions based on modified firefly algorithm.

PubMed

Yuan, Feng; Liu, Hong; Chen, Shou-Qiang; Xu, Liang

2016-12-01

This paper is aimed to study the clustering method for Chinese medicine (CM) medical cases. The traditional K-means clustering algorithm had shortcomings such as dependence of results on the selection of initial value, trapping in local optimum when processing prescriptions form CM medical cases. Therefore, a new clustering method based on the collaboration of firefly algorithm and simulated annealing algorithm was proposed. This algorithm dynamically determined the iteration of firefly algorithm and simulates sampling of annealing algorithm by fitness changes, and increased the diversity of swarm through expansion of the scope of the sudden jump, thereby effectively avoiding premature problem. The results from confirmatory experiments for CM medical cases suggested that, comparing with traditional K-means clustering algorithms, this method was greatly improved in the individual diversity and the obtained clustering results, the computing results from this method had a certain reference value for cluster analysis on CM prescriptions.

Cooling rate dependence of structural order in Ni 62 Nb 38 metallic glass

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

Wen, Tongqi; Sun, Yang; Ye, Beilin

In this article, molecular dynamics (MD) simulations are performed to study the structure of Ni 62Nb 38 bulk metallic glass at the atomistic level. Structural analysis based on the cluster alignment method is carried out and a new Ni-centered distorted-icosahedra (DISICO) motif is excavated. We show that the short-range order and medium-range order in the glass are enhanced with lower cooling rate. Almost 50% of the clusters around the Ni atoms in the well-annealed Ni 62Nb 38 glass sample from our MD simulations can be classified as DISICO. It is revealed that the structural distortion with respect to the perfectmore » icosahedra is driven by chemical ordering in the distorted region of the DISICO motif. The relationship between the structure, energy, and dynamics in this glass-forming alloy during the cooling and annealing processes is also established.« less

Extended Information Ratio for Portfolio Optimization Using Simulated Annealing with Constrained Neighborhood

NASA Astrophysics Data System (ADS)

Orito, Yukiko; Yamamoto, Hisashi; Tsujimura, Yasuhiro; Kambayashi, Yasushi

The portfolio optimizations are to determine the proportion-weighted combination in the portfolio in order to achieve investment targets. This optimization is one of the multi-dimensional combinatorial optimizations and it is difficult for the portfolio constructed in the past period to keep its performance in the future period. In order to keep the good performances of portfolios, we propose the extended information ratio as an objective function, using the information ratio, beta, prime beta, or correlation coefficient in this paper. We apply the simulated annealing (SA) to optimize the portfolio employing the proposed ratio. For the SA, we make the neighbor by the operation that changes the structure of the weights in the portfolio. In the numerical experiments, we show that our portfolios keep the good performances when the market trend of the future period becomes different from that of the past period.

Cooling rate dependence of structural order in Ni62Nb38 metallic glass

NASA Astrophysics Data System (ADS)

Wen, Tongqi; Sun, Yang; Ye, Beilin; Tang, Ling; Yang, Zejin; Ho, Kai-Ming; Wang, Cai-Zhuang; Wang, Nan

2018-01-01

Molecular dynamics (MD) simulations are performed to study the structure of Ni62Nb38 bulk metallic glass at the atomistic level. Structural analysis based on the cluster alignment method is carried out and a new Ni-centered distorted-icosahedra (DISICO) motif is excavated. We show that the short-range order and medium-range order in the glass are enhanced with lower cooling rate. Almost 50% of the clusters around the Ni atoms in the well-annealed Ni62Nb38 glass sample from our MD simulations can be classified as DISICO. It is revealed that the structural distortion with respect to the perfect icosahedra is driven by chemical ordering in the distorted region of the DISICO motif. The relationship between the structure, energy, and dynamics in this glass-forming alloy during the cooling and annealing processes is also established.

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

Smedskjaer, Morten M., E-mail: mos@bio.aau.dk; Bauchy, Mathieu; Mauro, John C.

The properties of glass are determined not only by temperature, pressure, and composition, but also by their complete thermal and pressure histories. Here, we show that glasses of identical composition produced through thermal annealing and through quenching from elevated pressure can result in samples with identical density and mean interatomic distances, yet different bond angle distributions, medium-range structures, and, thus, macroscopic properties. We demonstrate that hardness is higher when the density increase is obtained through thermal annealing rather than through pressure-quenching. Molecular dynamics simulations reveal that this arises because pressure-quenching has a larger effect on medium-range order, while annealing hasmore » a larger effect on short-range structures (sharper bond angle distribution), which ultimately determine hardness according to bond constraint theory. Our work could open a new avenue towards industrially useful glasses that are identical in terms of composition and density, but with differences in thermodynamic, mechanical, and rheological properties due to unique structural characteristics.« less

Thermally activated decomposition of (Ga,Mn)As thin layer at medium temperature post growth annealing

NASA Astrophysics Data System (ADS)

Melikhov, Y.; Konstantynov, P.; Domagala, J.; Sadowski, J.; Chernyshova, M.; Wojciechowski, T.; Syryanyy, Y.; Demchenko, I. N.

2016-05-01

The redistribution of Mn atoms in Ga1-xMnxAs layer during medium-temperature annealing, 250-450 oC, by Mn K-edge X-ray absorption fine structure (XAFS) recorded at ALBA facility, was studied. For this purpose Ga1-xMnxAs thin layer with x=0.01 was grown on AlAs buffer layer deposited on GaAs(100) substrate by molecular beam epitaxy (MBE) followed by annealing. The examined layer was detached from the substrate using a “lift-off” procedure in order to eliminate elastic scattering in XAFS spectra. Fourier transform analysis of experimentally obtained EXAFS spectra allowed to propose a model which describes a redistribution/diffusion of Mn atoms in the host matrix. Theoretical XANES spectra, simulated using multiple scattering formalism (FEFF code) with the support of density functional theory (WIEN2k code), qualitatively describe the features observed in the experimental fine structure.

New Insights into Shape Memory Alloy Bimorph Actuators Formed by Electron Beam Evaporation

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

Sun, Hao; Nykypanchuk, Dmytro

In order to create shape memory alloy (SMA) bimorph microactuators with high-precision features, a novel fabrication process combined with electron beam (E-beam) evaporation, lift-off resist and isotropic XeF2 dry etching method was developed. To examine the effect of E-beam deposition and annealing process on nitinol (NiTi) characteristics, the NiTi thin film samples with different deposition rate and overflow conditions during annealing process were investigated. With the characterizations using scanning electron microscope and x-ray diffraction, the results indicated that low E-beam deposition rate and argon employed annealing process could benefit the formation of NiTi crystalline structure. In addition, SMA bimorph microactuatorsmore » with high-precision features as small as 5 microns were successfully fabricated. Furthermore, the thermomechanical performance was experimentally verified and compared with finite element analysis simulation results.« less

Effect of annealing temperature on the thermal stress and dislocation density of mc-Si ingot grown by DS process for solar cell application

NASA Astrophysics Data System (ADS)

Sanmugavel, S.; Srinivasan, M.; Aravinth, K.; Ramasamy, P.

2018-04-01

90% of the solar industries are using crystalline silicon. Cost wise the multi-crystalline silicon solar cells are better compared to mono crystalline silicon. But because of the presence of grain boundaries, dislocations and impurities, the efficiency of the multi-crystalline silicon solar cells is lower than that of mono crystalline silicon solar cells. By reducing the defect and dislocation we can achieve high conversion efficiency. The velocity of dislocation motion increases with stress. By annealing the grown ingot at proper temperature we can decrease the stress and dislocation. Our simulation results show that the value of stress and dislocation density is decreased by annealing the grown ingot at 1400K and the input parameters can be implemented in real system to grow a better mc-Si ingot for energy harvesting applications.

A graph-based watershed merging using fuzzy C-means and simulated annealing for image segmentation

NASA Astrophysics Data System (ADS)

Vadiveloo, Mogana; Abdullah, Rosni; Rajeswari, Mandava

2015-12-01

In this paper, we have addressed the issue of over-segmented regions produced in watershed by merging the regions using global feature. The global feature information is obtained from clustering the image in its feature space using Fuzzy C-Means (FCM) clustering. The over-segmented regions produced by performing watershed on the gradient of the image are then mapped to this global information in the feature space. Further to this, the global feature information is optimized using Simulated Annealing (SA). The optimal global feature information is used to derive the similarity criterion to merge the over-segmented watershed regions which are represented by the region adjacency graph (RAG). The proposed method has been tested on digital brain phantom simulated dataset to segment white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF) soft tissues regions. The experiments showed that the proposed method performs statistically better, with average of 95.242% regions are merged, than the immersion watershed and average accuracy improvement of 8.850% in comparison with RAG-based immersion watershed merging using global and local features.

A positional misalignment correction method for Fourier ptychographic microscopy based on simulated annealing

NASA Astrophysics Data System (ADS)

Sun, Jiasong; Zhang, Yuzhen; Chen, Qian; Zuo, Chao

2017-02-01

Fourier ptychographic microscopy (FPM) is a newly developed super-resolution technique, which employs angularly varying illuminations and a phase retrieval algorithm to surpass the diffraction limit of a low numerical aperture (NA) objective lens. In current FPM imaging platforms, accurate knowledge of LED matrix's position is critical to achieve good recovery quality. Furthermore, considering such a wide field-of-view (FOV) in FPM, different regions in the FOV have different sensitivity of LED positional misalignment. In this work, we introduce an iterative method to correct position errors based on the simulated annealing (SA) algorithm. To improve the efficiency of this correcting process, large number of iterations for several images with low illumination NAs are firstly implemented to estimate the initial values of the global positional misalignment model through non-linear regression. Simulation and experimental results are presented to evaluate the performance of the proposed method and it is demonstrated that this method can both improve the quality of the recovered object image and relax the LED elements' position accuracy requirement while aligning the FPM imaging platforms.

Scalability enhancement of AODV using local link repairing

NASA Astrophysics Data System (ADS)

Jain, Jyoti; Gupta, Roopam; Bandhopadhyay, T. K.

2014-09-01

Dynamic change in the topology of an ad hoc network makes it difficult to design an efficient routing protocol. Scalability of an ad hoc network is also one of the important criteria of research in this field. Most of the research works in ad hoc network focus on routing and medium access protocols and produce simulation results for limited-size networks. Ad hoc on-demand distance vector (AODV) is one of the best reactive routing protocols. In this article, modified routing protocols based on local link repairing of AODV are proposed. Method of finding alternate routes for next-to-next node is proposed in case of link failure. These protocols are beacon-less, means periodic hello message is removed from the basic AODV to improve scalability. Few control packet formats have been changed to accommodate suggested modification. Proposed protocols are simulated to investigate scalability performance and compared with basic AODV protocol. This also proves that local link repairing of proposed protocol improves scalability of the network. From simulation results, it is clear that scalability performance of routing protocol is improved because of link repairing method. We have tested protocols for different terrain area with approximate constant node densities and different traffic load.

Comparison of particle swarm optimization and simulated annealing for locating additional boreholes considering combined variance minimization

NASA Astrophysics Data System (ADS)

Soltani-Mohammadi, Saeed; Safa, Mohammad; Mokhtari, Hadi

2016-10-01

One of the most important stages in complementary exploration is optimal designing the additional drilling pattern or defining the optimum number and location of additional boreholes. Quite a lot research has been carried out in this regard in which for most of the proposed algorithms, kriging variance minimization as a criterion for uncertainty assessment is defined as objective function and the problem could be solved through optimization methods. Although kriging variance implementation is known to have many advantages in objective function definition, it is not sensitive to local variability. As a result, the only factors evaluated for locating the additional boreholes are initial data configuration and variogram model parameters and the effects of local variability are omitted. In this paper, with the goal of considering the local variability in boundaries uncertainty assessment, the application of combined variance is investigated to define the objective function. Thus in order to verify the applicability of the proposed objective function, it is used to locate the additional boreholes in Esfordi phosphate mine through the implementation of metaheuristic optimization methods such as simulated annealing and particle swarm optimization. Comparison of results from the proposed objective function and conventional methods indicates that the new changes imposed on the objective function has caused the algorithm output to be sensitive to the variations of grade, domain's boundaries and the thickness of mineralization domain. The comparison between the results of different optimization algorithms proved that for the presented case the application of particle swarm optimization is more appropriate than simulated annealing.

Optimization of parameter values for complex pulse sequences by simulated annealing: application to 3D MP-RAGE imaging of the brain.

PubMed

Epstein, F H; Mugler, J P; Brookeman, J R

1994-02-01

A number of pulse sequence techniques, including magnetization-prepared gradient echo (MP-GRE), segmented GRE, and hybrid RARE, employ a relatively large number of variable pulse sequence parameters and acquire the image data during a transient signal evolution. These sequences have recently been proposed and/or used for clinical applications in the brain, spine, liver, and coronary arteries. Thus, the need for a method of deriving optimal pulse sequence parameter values for this class of sequences now exists. Due to the complexity of these sequences, conventional optimization approaches, such as applying differential calculus to signal difference equations, are inadequate. We have developed a general framework for adapting the simulated annealing algorithm to pulse sequence parameter value optimization, and applied this framework to the specific case of optimizing the white matter-gray matter signal difference for a T1-weighted variable flip angle 3D MP-RAGE sequence. Using our algorithm, the values of 35 sequence parameters, including the magnetization-preparation RF pulse flip angle and delay time, 32 flip angles in the variable flip angle gradient-echo acquisition sequence, and the magnetization recovery time, were derived. Optimized 3D MP-RAGE achieved up to a 130% increase in white matter-gray matter signal difference compared with optimized 3D RF-spoiled FLASH with the same total acquisition time. The simulated annealing approach was effective at deriving optimal parameter values for a specific 3D MP-RAGE imaging objective, and may be useful for other imaging objectives and sequences in this general class.

Effective optimization using sample persistence: A case study on quantum annealers and various Monte Carlo optimization methods

NASA Astrophysics Data System (ADS)

Karimi, Hamed; Rosenberg, Gili; Katzgraber, Helmut G.

2017-10-01

We present and apply a general-purpose, multistart algorithm for improving the performance of low-energy samplers used for solving optimization problems. The algorithm iteratively fixes the value of a large portion of the variables to values that have a high probability of being optimal. The resulting problems are smaller and less connected, and samplers tend to give better low-energy samples for these problems. The algorithm is trivially parallelizable since each start in the multistart algorithm is independent, and could be applied to any heuristic solver that can be run multiple times to give a sample. We present results for several classes of hard problems solved using simulated annealing, path-integral quantum Monte Carlo, parallel tempering with isoenergetic cluster moves, and a quantum annealer, and show that the success metrics and the scaling are improved substantially. When combined with this algorithm, the quantum annealer's scaling was substantially improved for native Chimera graph problems. In addition, with this algorithm the scaling of the time to solution of the quantum annealer is comparable to the Hamze-de Freitas-Selby algorithm on the weak-strong cluster problems introduced by Boixo et al. Parallel tempering with isoenergetic cluster moves was able to consistently solve three-dimensional spin glass problems with 8000 variables when combined with our method, whereas without our method it could not solve any.

Effects of oxygen partial pressure, deposition temperature, and annealing on the optical response of CdS:O thin films as studied by spectroscopic ellipsometry

NASA Astrophysics Data System (ADS)

Junda, Maxwell M.; Grice, Corey R.; Subedi, Indra; Yan, Yanfa; Podraza, Nikolas J.

2016-07-01

Ex-situ spectroscopic ellipsometry measurements are made on radio frequency magnetron sputtered oxygenated cadmium sulfide (CdS:O) thin films. Films are deposited onto glass substrates at room temperature and at 270 °C with varying oxygen to total gas flow ratios in the sputtering ambient. Ellipsometric spectra from 0.74 to 5.89 eV are collected before and after annealing at 607 °C to simulate the thermal processes during close-space sublimation of overlying cadmium telluride in that solar cell configuration. Complex dielectric function (ɛ = ɛ1 + iɛ2) spectra are extracted for films as a function of oxygen gas flow ratio, deposition temperature, and post-deposition annealing using a parametric model accounting for critical point transitions and an Urbach tail for sub-band gap absorption. The results suggest an inverse relationship between degree of crystallinity and oxygen gas flow ratio, whereas annealing is shown to increase crystallinity in all samples. Direct band gap energies are determined from the parametric modeling of ɛ and linear extrapolations of the square of the absorption coefficient. As-deposited samples feature a range of band gap energies whereas annealing is shown to result in gap energies ranging only from 2.40 to 2.45 eV, which is close to typical band gaps for pure cadmium sulfide.

GPU accelerated population annealing algorithm

NASA Astrophysics Data System (ADS)

Barash, Lev Yu.; Weigel, Martin; Borovský, Michal; Janke, Wolfhard; Shchur, Lev N.

2017-11-01

Population annealing is a promising recent approach for Monte Carlo simulations in statistical physics, in particular for the simulation of systems with complex free-energy landscapes. It is a hybrid method, combining importance sampling through Markov chains with elements of sequential Monte Carlo in the form of population control. While it appears to provide algorithmic capabilities for the simulation of such systems that are roughly comparable to those of more established approaches such as parallel tempering, it is intrinsically much more suitable for massively parallel computing. Here, we tap into this structural advantage and present a highly optimized implementation of the population annealing algorithm on GPUs that promises speed-ups of several orders of magnitude as compared to a serial implementation on CPUs. While the sample code is for simulations of the 2D ferromagnetic Ising model, it should be easily adapted for simulations of other spin models, including disordered systems. Our code includes implementations of some advanced algorithmic features that have only recently been suggested, namely the automatic adaptation of temperature steps and a multi-histogram analysis of the data at different temperatures. Program Files doi:http://dx.doi.org/10.17632/sgzt4b7b3m.1 Licensing provisions: Creative Commons Attribution license (CC BY 4.0) Programming language: C, CUDA External routines/libraries: NVIDIA CUDA Toolkit 6.5 or newer Nature of problem: The program calculates the internal energy, specific heat, several magnetization moments, entropy and free energy of the 2D Ising model on square lattices of edge length L with periodic boundary conditions as a function of inverse temperature β. Solution method: The code uses population annealing, a hybrid method combining Markov chain updates with population control. The code is implemented for NVIDIA GPUs using the CUDA language and employs advanced techniques such as multi-spin coding, adaptive temperature steps and multi-histogram reweighting. Additional comments: Code repository at https://github.com/LevBarash/PAising. The system size and size of the population of replicas are limited depending on the memory of the GPU device used. For the default parameter values used in the sample programs, L = 64, θ = 100, β0 = 0, βf = 1, Δβ = 0 . 005, R = 20 000, a typical run time on an NVIDIA Tesla K80 GPU is 151 seconds for the single spin coded (SSC) and 17 seconds for the multi-spin coded (MSC) program (see Section 2 for a description of these parameters).

Exploration of DGVM Parameter Solution Space Using Simulated Annealing: Implications for Forecast Uncertainties

NASA Astrophysics Data System (ADS)

Wells, J. R.; Kim, J. B.

2011-12-01

Parameters in dynamic global vegetation models (DGVMs) are thought to be weakly constrained and can be a significant source of errors and uncertainties. DGVMs use between 5 and 26 plant functional types (PFTs) to represent the average plant life form in each simulated plot, and each PFT typically has a dozen or more parameters that define the way it uses resource and responds to the simulated growing environment. Sensitivity analysis explores how varying parameters affects the output, but does not do a full exploration of the parameter solution space. The solution space for DGVM parameter values are thought to be complex and non-linear; and multiple sets of acceptable parameters may exist. In published studies, PFT parameters are estimated from published literature, and often a parameter value is estimated from a single published value. Further, the parameters are "tuned" using somewhat arbitrary, "trial-and-error" methods. BIOMAP is a new DGVM created by fusing MAPSS biogeography model with Biome-BGC. It represents the vegetation of North America using 26 PFTs. We are using simulated annealing, a global search method, to systematically and objectively explore the solution space for the BIOMAP PFTs and system parameters important for plant water use. We defined the boundaries of the solution space by obtaining maximum and minimum values from published literature, and where those were not available, using +/-20% of current values. We used stratified random sampling to select a set of grid cells representing the vegetation of the conterminous USA. Simulated annealing algorithm is applied to the parameters for spin-up and a transient run during the historical period 1961-1990. A set of parameter values is considered acceptable if the associated simulation run produces a modern potential vegetation distribution map that is as accurate as one produced by trial-and-error calibration. We expect to confirm that the solution space is non-linear and complex, and that multiple acceptable parameter sets exist. Further we expect to demonstrate that the multiple parameter sets produce significantly divergent future forecasts in NEP, C storage, and ET and runoff; and thereby identify a highly important source of DGVM uncertainty

Estimation of residual stresses in railroad commuter car wheels following manufacture

DOT National Transportation Integrated Search

2003-06-01

A finite element simulation is presented for the prediction of : residual stresses resulting from the heat treatment of railroad : commuter car wheels during manufacture. The quenching and : annealing segments of the wheel manufacturing process are s...

Estimation of residual stresses in railroad commuter car wheels following manufacture

DOT National Transportation Integrated Search

1998-11-01

A finite element simulation is presented for the prediction of residual stresses resulting from the heat treatment of railroad commuter car wheels during manufacture. The quenching and annealing segments of the wheel manufacturing process are simulat...

Tuning charge carrier transport and optical birefringence in liquid-crystalline thin films: A new design space for organic light-emitting diodes.

PubMed

Keum, Chang-Min; Liu, Shiyi; Al-Shadeedi, Akram; Kaphle, Vikash; Callens, Michiel Koen; Han, Lu; Neyts, Kristiaan; Zhao, Hongping; Gather, Malte C; Bunge, Scott D; Twieg, Robert J; Jakli, Antal; Lüssem, Björn

2018-01-15

Liquid-crystalline organic semiconductors exhibit unique properties that make them highly interesting for organic optoelectronic applications. Their optical and electrical anisotropies and the possibility to control the alignment of the liquid-crystalline semiconductor allow not only to optimize charge carrier transport, but to tune the optical property of organic thin-film devices as well. In this study, the molecular orientation in a liquid-crystalline semiconductor film is tuned by a novel blading process as well as by different annealing protocols. The altered alignment is verified by cross-polarized optical microscopy and spectroscopic ellipsometry. It is shown that a change in alignment of the liquid-crystalline semiconductor improves charge transport in single charge carrier devices profoundly. Comparing the current-voltage characteristics of single charge carrier devices with simulations shows an excellent agreement and from this an in-depth understanding of single charge carrier transport in two-terminal devices is obtained. Finally, p-i-n type organic light-emitting diodes (OLEDs) compatible with vacuum processing techniques used in state-of-the-art OLEDs are demonstrated employing liquid-crystalline host matrix in the emission layer.

Novel recombinant insulin analogue with flexible C-terminus in B chain. NMR structure of biosynthetic engineered A22G-B31K-B32R human insulin monomer in water/acetonitrile solution.

PubMed

Borowicz, Piotr; Bocian, Wojciech; Sitkowski, Jerzy; Bednarek, Elżbieta; Mikiewicz-Syguła, Diana; Błażej-Sosnowska, Sylwia; Bogiel, Monika; Rusek, Dorota; Kurzynoga, Dariusz; Kozerski, Lech

2011-11-01

A tertiary structure of recombinant A22(G)-B31(K)-B32(R)-human insulin monomer (insulin GKR) has been characterized by (1)H, (13)C NMR at natural isotopic abundance using NOESY, TOCSY, (1)H/(13)C-GHSQC, and (1)H/(13)C-GHSQC-TOCSY spectra. Translational diffusion studies indicate the monomer structure in water/acetonitrile (65/35vol.%). CSI analysis confirms existence of secondary structure motifs present in human insulin standard (HIS). Both techniques allow to establish that in this solvent recombinant insulin GKR exists as a monomer. Starting from structures calculated by the program CYANA, two different refinement protocols used molecular dynamics simulated annealing with the program AMBER; in vacuum (AMBER_VC), and including a generalized Born solvent model (AMBER_GB). From these calculations an ensemble of 20 structures of lowest energy was chosen which represents the tertiary structure of studied insulin. Here we present novel insulin with added A22(G) amino acid which interacts with β-turn environment resulting in high flexibility of B chain C-terminus. Copyright © 2011 Elsevier B.V. All rights reserved.

The use of a photoionization detector to detect harmful volatile chemicals by emergency personnel

PubMed Central

Patel, Neil D; Fales, William D; Farrell, Robert N

2009-01-01

Objective The objective of this investigation was to determine if a photoionization detector (PID) could be used to detect the presence of a simulated harmful chemical on simulated casualties of a chemical release. Methods A screening protocol, based on existing radiation screening protocols, was developed for the purposes of the investigation. Three simulated casualties were contaminated with a simulated chemical agent and two groups of emergency responders were involved in the trials. The success–failure ratio of the participants was used to judge the performance of the PID in this application. Results A high success rate was observed when the screening protocol was properly adhered to (97.67%). Conversely, the success rate suffered when participants deviated from the protocol (86.31%). With one exception, all failures were noted to have been the result of a failure to correctly observe the established screening protocol. Conclusions The results of this investigation indicate that the PID may be an effective screening tool for emergency responders. However, additional study is necessary to both confirm the effectiveness of the PID and refine the screening protocol if necessary. PMID:27147829

Constructing Cross-Linked Polymer Networks Using Monte Carlo Simulated Annealing Technique for Atomistic Molecular Simulations

DTIC Science & Technology

2014-10-01

the angles and dihedrals that are truly unique will be indicated by the user by editing NewAngleTypesDump and NewDihedralTypesDump. The program ...Atomistic Molecular Simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Robert M Elder, Timothy W Sirk, and...Antechamber program in Assisted Model Building with Energy Refinement (AMBER) Tools to assign partial charges (using the Austin Model 1 [AM1]-bond charge

Effect of Water Vapor, Temperature, and Rapid Annealing on Formamidinium Lead Triiodide Perovskite Crystallization

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

Aguiar, Jeffery A.; Wozny, Sarah; Alkurd, Nooraldeen R.

Perovskite-based solar cells are one of the emerging candidates for radically lower cost photovoltaics. Herein, we report on the synthesis and crystallization of organic-inorganic formamidinium lead triiodide perovskite films under controlled atmospheric and environmental conditions. Using in situ (scanning) transmission electron microscopy, we make observations of the crystallization process of these materials in nitrogen and oxygen gas with and without the presence of water vapor. Complementary planar samples were also fabricated in the presence of water vapor and characterized by in situ X-ray diffraction. Direct observations of the material structure and final morphology indicate that the exposure to water vapormore » results in a porous film that is metastable, regardless of the presence of argon, nitrogen, or oxygen. However, the optimal crystallization temperature of 175 degrees C is unperturbed across conditions. Rapid modulation about the annealing temperature of 175 degrees C in +/-25 degrees C steps (150-200 degrees C) promotes crystallization and significantly improves the film morphology by overcoming the presence of impregnated water trapped in the material. Following this processing protocol, we demonstrate substantial growth to micron-size grains via observation inside of an environmentally controlled transmission electron microscope. Adapting this insight from our in situ microscopy, we are able to provide an informed materials protocol to control the structure and morphology of these organic-inorganic semiconductors, which is readily applicable to benchtop device growth strategies.« less

Effect of Water Vapor, Temperature, and Rapid Annealing on Formamidinium Lead Triiodide Perovskite Crystallization

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

Aguiar, Jeffery A.; Wozny, Sarah; Alkurd, Nooraldeen R.

Perovskite-based solar cells are one of the emerging candidates for radically lower cost photovoltaics. Herein, we report on the synthesis and crystallization of organic-inorganic formamidinium lead triiodide perovskite films under controlled atmospheric and environmental conditions. Using in situ (scanning) transmission electron microscopy, we make observations of the crystallization process of these materials in nitrogen and oxygen gas with and without the presence of water vapor. Complementary planar samples were also fabricated in the presence of water vapor and characterized by in situ X-ray diffraction. Direct observations of the material structure and final morphology indicate that the exposure to water vapormore » results in a porous film that is metastable, regardless of the presence of argon, nitrogen, or oxygen. However, the optimal crystallization temperature of 175 °C is unperturbed across conditions. Rapid modulation about the annealing temperature of 175 °C in ±25 °C steps (150-200 °C) promotes crystallization and significantly improves the film morphology by overcoming the presence of impregnated water trapped in the material. Following this processing protocol, we demonstrate substantial growth to micron-size grains via observation inside of an environmentally controlled transmission electron microscope. Adapting this insight from our in situ microscopy, we are able to provide an informed materials protocol to control the structure and morphology of these organic-inorganic semiconductors, which is readily applicable to benchtop device growth strategies.« less

Robotic Enrichment Processing of Roche 454 Titanium Emlusion PCR at the DOE Joint Genome Institute

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

Hamilton, Matthew; Wilson, Steven; Bauer, Diane

2010-05-28

Enrichment of emulsion PCR product is the most laborious and pipette-intensive step in the 454 Titanium process, posing the biggest obstacle for production-oriented scale up. The Joint Genome Institute has developed a pair of custom-made robots based on the Microlab Star liquid handling deck manufactured by Hamilton to mediate the complexity and ergonomic demands of the 454 enrichment process. The robot includes a custom built centrifuge, magnetic deck positions, as well as heating and cooling elements. At present processing eight emulsion cup samples in a single 2.5 hour run, these robots are capable of processing up to 24 emulsion cupmore » samples. Sample emulsions are broken using the standard 454 breaking process and transferred from a pair of 50ml conical tubes to a single 2ml tube and loaded on the robot. The robot performs the enrichment protocol and produces beads in 2ml tubes ready for counting. The robot follows the Roche 454 enrichment protocol with slight exceptions to the manner in which it resuspends beads via pipette mixing rather than vortexing and a set number of null bead removal washes. The robotic process is broken down in similar discrete steps: First Melt and Neutralization, Enrichment Primer Annealing, Enrichment Bead Incubation, Null Bead Removal, Second Melt and Neutralization and Sequencing Primer Annealing. Data indicating our improvements in enrichment efficiency and total number of bases per run will also be shown.« less

Finding Maximum Cliques on the D-Wave Quantum Annealer

DOE PAGES

Chapuis, Guillaume; Djidjev, Hristo; Hahn, Georg; ...

2018-05-03

This work assesses the performance of the D-Wave 2X (DW) quantum annealer for finding a maximum clique in a graph, one of the most fundamental and important NP-hard problems. Because the size of the largest graphs DW can directly solve is quite small (usually around 45 vertices), we also consider decomposition algorithms intended for larger graphs and analyze their performance. For smaller graphs that fit DW, we provide formulations of the maximum clique problem as a quadratic unconstrained binary optimization (QUBO) problem, which is one of the two input types (together with the Ising model) acceptable by the machine, andmore » compare several quantum implementations to current classical algorithms such as simulated annealing, Gurobi, and third-party clique finding heuristics. We further estimate the contributions of the quantum phase of the quantum annealer and the classical post-processing phase typically used to enhance each solution returned by DW. We demonstrate that on random graphs that fit DW, no quantum speedup can be observed compared with the classical algorithms. On the other hand, for instances specifically designed to fit well the DW qubit interconnection network, we observe substantial speed-ups in computing time over classical approaches.« less

Electron microscopy observations of radiation damage in irradiated and annealed tungsten

NASA Astrophysics Data System (ADS)

Grzonka, J.; Ciupiński, Ł.; Smalc-Koziorowska, J.; Ogorodnikova, O. V.; Mayer, M.; Kurzydłowski, K. J.

2014-12-01

In the present work tungsten samples were irradiated with W6+ ions with a kinetic energy of 20 MeV in order to simulate radiation damage by fast neutrons. Two samples with cumulative damage of 2.3 and 6.36 displacements per atom were produced. The scanning transmission electron microscopy investigations were carried out in order to determine structure changes resulting from the irradiation. The evolution of the damage with post implantation annealing in the temperature range 673-1100 K was also assessed. Damage profiles were studied at cross-sections. Scanning transmission electron microscopy studies of the lamellae after annealing revealed aggregation of defects and rearrangement as well as partial healing of dislocations at higher temperatures. The results confirm the higher density of radiation-induced dislocations in the near surface area of the sample (1.8 * 1014 m-2) in comparison with a deeper damage area (1.5 * 1014 m-2). Significant decrease of dislocation density was observed after annealing with a concurrent growth of dislocation loops. Transmission electron microscopy analyses show that the dislocation loops are perfect dislocations with the Burgers vectors of b = ½[ 1 1 1].

Finding Maximum Cliques on the D-Wave Quantum Annealer

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

Chapuis, Guillaume; Djidjev, Hristo; Hahn, Georg

This work assesses the performance of the D-Wave 2X (DW) quantum annealer for finding a maximum clique in a graph, one of the most fundamental and important NP-hard problems. Because the size of the largest graphs DW can directly solve is quite small (usually around 45 vertices), we also consider decomposition algorithms intended for larger graphs and analyze their performance. For smaller graphs that fit DW, we provide formulations of the maximum clique problem as a quadratic unconstrained binary optimization (QUBO) problem, which is one of the two input types (together with the Ising model) acceptable by the machine, andmore » compare several quantum implementations to current classical algorithms such as simulated annealing, Gurobi, and third-party clique finding heuristics. We further estimate the contributions of the quantum phase of the quantum annealer and the classical post-processing phase typically used to enhance each solution returned by DW. We demonstrate that on random graphs that fit DW, no quantum speedup can be observed compared with the classical algorithms. On the other hand, for instances specifically designed to fit well the DW qubit interconnection network, we observe substantial speed-ups in computing time over classical approaches.« less

Chapter 15: Commercial New Construction Evaluation Protocol. The Uniform Methods Project: Methods for Determining Energy Efficiency Savings for Specific Measures

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

Kurnik, Charles W.; Keates, Steven

This protocol is intended to describe the recommended method when evaluating the whole-building performance of new construction projects in the commercial sector. The protocol focuses on energy conservation measures (ECMs) or packages of measures where evaluators can analyze impacts using building simulation. These ECMs typically require the use of calibrated building simulations under Option D of the International Performance Measurement and Verification Protocol (IPMVP).

The Simulation of Read-time Scalable Coherent Interface

NASA Technical Reports Server (NTRS)

Li, Qiang; Grant, Terry; Grover, Radhika S.

1997-01-01

Scalable Coherent Interface (SCI, IEEE/ANSI Std 1596-1992) (SCI1, SCI2) is a high performance interconnect for shared memory multiprocessor systems. In this project we investigate an SCI Real Time Protocols (RTSCI1) using Directed Flow Control Symbols. We studied the issues of efficient generation of control symbols, and created a simulation model of the protocol on a ring-based SCI system. This report presents the results of the study. The project has been implemented using SES/Workbench. The details that follow encompass aspects of both SCI and Flow Control Protocols, as well as the effect of realistic client/server processing delay. The report is organized as follows. Section 2 provides a description of the simulation model. Section 3 describes the protocol implementation details. The next three sections of the report elaborate on the workload, results and conclusions. Appended to the report is a description of the tool, SES/Workbench, used in our simulation, and internal details of our implementation of the protocol.

Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations

DOE PAGES

Radak, Brian K.; Roux, Benoît

2016-10-07

Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance.more » An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Lastly, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.« less

CATO: a CAD tool for intelligent design of optical networks and interconnects

NASA Astrophysics Data System (ADS)

Chlamtac, Imrich; Ciesielski, Maciej; Fumagalli, Andrea F.; Ruszczyk, Chester; Wedzinga, Gosse

1997-10-01

Increasing communication speed requirements have created a great interest in very high speed optical and all-optical networks and interconnects. The design of these optical systems is a highly complex task, requiring the simultaneous optimization of various parts of the system, ranging from optical components' characteristics to access protocol techniques. Currently there are no computer aided design (CAD) tools on the market to support the interrelated design of all parts of optical communication systems, thus the designer has to rely on costly and time consuming testbed evaluations. The objective of the CATO (CAD tool for optical networks and interconnects) project is to develop a prototype of an intelligent CAD tool for the specification, design, simulation and optimization of optical communication networks. CATO allows the user to build an abstract, possible incomplete, model of the system, and determine its expected performance. Based on design constraints provided by the user, CATO will automatically complete an optimum design, using mathematical programming techniques, intelligent search methods and artificial intelligence (AI). Initial design and testing of a CATO prototype (CATO-1) has been completed recently. The objective was to prove the feasibility of combining AI techniques, simulation techniques, an optical device library and a graphical user interface into a flexible CAD tool for obtaining optimal communication network designs in terms of system cost and performance. CATO-1 is an experimental tool for designing packet-switching wavelength division multiplexing all-optical communication systems using a LAN/MAN ring topology as the underlying network. The two specific AI algorithms incorporated are simulated annealing and a genetic algorithm. CATO-1 finds the optimal number of transceivers for each network node, using an objective function that includes the cost of the devices and the overall system performance.

Discrete-State Simulated Annealing For Traveling-Wave Tube Slow-Wave Circuit Optimization

NASA Technical Reports Server (NTRS)

Wilson, Jeffrey D.; Bulson, Brian A.; Kory, Carol L.; Williams, W. Dan (Technical Monitor)

2001-01-01

Algorithms based on the global optimization technique of simulated annealing (SA) have proven useful in designing traveling-wave tube (TWT) slow-wave circuits for high RF power efficiency. The characteristic of SA that enables it to determine a globally optimized solution is its ability to accept non-improving moves in a controlled manner. In the initial stages of the optimization, the algorithm moves freely through configuration space, accepting most of the proposed designs. This freedom of movement allows non-intuitive designs to be explored rather than restricting the optimization to local improvement upon the initial configuration. As the optimization proceeds, the rate of acceptance of non-improving moves is gradually reduced until the algorithm converges to the optimized solution. The rate at which the freedom of movement is decreased is known as the annealing or cooling schedule of the SA algorithm. The main disadvantage of SA is that there is not a rigorous theoretical foundation for determining the parameters of the cooling schedule. The choice of these parameters is highly problem dependent and the designer needs to experiment in order to determine values that will provide a good optimization in a reasonable amount of computational time. This experimentation can absorb a large amount of time especially when the algorithm is being applied to a new type of design. In order to eliminate this disadvantage, a variation of SA known as discrete-state simulated annealing (DSSA), was recently developed. DSSA provides the theoretical foundation for a generic cooling schedule which is problem independent, Results of similar quality to SA can be obtained, but without the extra computational time required to tune the cooling parameters. Two algorithm variations based on DSSA were developed and programmed into a Microsoft Excel spreadsheet graphical user interface (GUI) to the two-dimensional nonlinear multisignal helix traveling-wave amplifier analysis program TWA3. The algorithms were used to optimize the computed RF efficiency of a TWT by determining the phase velocity profile of the slow-wave circuit. The mathematical theory and computational details of the DSSA algorithms will be presented and results will be compared to those obtained with a SA algorithm.

Stress corrosion crack initiation of alloy 600 in PWR primary water

DOE PAGES

Zhai, Ziqing; Toloczko, Mychailo B.; Olszta, Matthew J.; ...

2017-04-27

Stress corrosion crack (SCC) initiation of three mill-annealed alloy 600 heats in simulated pressurized water reactor primary water has been investigated using constant load tests equipped with in-situ direct current potential drop (DCPD) measurement capabilities. SCC initiation times were greatly reduced by a small amount of cold work. Shallow intergranular attack and/or cracks were found on most high-energy grain boundaries intersecting the surface with only a small fraction evolving into larger cracks and intergranular SCC growth. Crack depth profiles were measured and related to DCPD-detected initiation response. Lastly, we discuss processes controlling the SCC initiation in mill-annealed alloy 600.

Stress corrosion crack initiation of alloy 600 in PWR primary water

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

Zhai, Ziqing; Toloczko, Mychailo B.; Olszta, Matthew J.

Stress corrosion crack (SCC) initiation of three mill-annealed alloy 600 heats in simulated pressurized water reactor primary water has been investigated using constant load tests equipped with in-situ direct current potential drop (DCPD) measurement capabilities. SCC initiation times were greatly reduced by a small amount of cold work. Shallow intergranular attack and/or cracks were found on most high-energy grain boundaries intersecting the surface with only a small fraction evolving into larger cracks and intergranular SCC growth. Crack depth profiles were measured and related to DCPD-detected initiation response. Lastly, we discuss processes controlling the SCC initiation in mill-annealed alloy 600.

UAV Mission Planning under Uncertainty

DTIC Science & Technology

2006-06-01

algorithm , adapted from [13] . 57 4-5 Robust Optimization considers only a subset of the feasible region . 61 5-1 Overview of simulation with parameter...incorporates the robust optimization method suggested by Bertsimas and Sim [12], and is solved with a standard Branch- and-Cut algorithm . The chapter... algorithms , and the heuristic methods of Local Search methods and Simulated Annealing. With each method, we attempt to give a review of research that has

Generalizable, Electroless, Template-Assisted Synthesis and Electrocatalytic Mechanistic Understanding of Perovskite LaNiO3 Nanorods as Viable, Supportless Oxygen Evolution Reaction Catalysts in Alkaline Media.

PubMed

McBean, Coray L; Liu, Haiqing; Scofield, Megan E; Li, Luyao; Wang, Lei; Bernstein, Ashley; Wong, Stanislaus S

2017-07-26

The oxygen evolution reaction (OER) is a key reaction for water electrolysis cells and air-powered battery applications. However, conventional metal oxide catalysts, used for high-performing OER, tend to incorporate comparatively expensive and less abundant precious metals such as Ru and Ir, and, moreover, suffer from poor stability. To attempt to mitigate for all of these issues, we have prepared one-dimensional (1D) OER-active perovskite nanorods using a unique, simple, generalizable, and robust method. Significantly, our work demonstrates the feasibility of a novel electroless, seedless, surfactant-free, wet solution-based protocol for fabricating "high aspect ratio" LaNiO 3 and LaMnO 3 nanostructures. As the main focus of our demonstration of principle, we prepared as-synthesized LaNiO 3 rods and correlated the various temperatures at which these materials were annealed with their resulting OER performance. We observed generally better OER performance for samples prepared with lower annealing temperatures. Specifically, when annealed at 600 °C, in the absence of a conventional conductive carbon support, our as-synthesized LaNiO 3 rods not only evinced (i) a reasonable level of activity toward OER but also displayed (ii) an improved stability, as demonstrated by chronoamperometric measurements, especially when compared with a control sample of commercially available (and more expensive) RuO 2 .

Extended PCR conditions to reduce drop-out frequencies in low template STR typing including unequal mixtures.

PubMed

Weiler, Natalie E C; Matai, Anuska S; Sijen, Titia

2012-01-01

Forensic laboratories employ various approaches to obtain short tandem repeat (STR) profiles from minimal traces (<100 pg DNA input). Most approaches aim to sensitize DNA profiling by increasing the amplification level by a higher cycle number or enlarging the amount of PCR products analyzed during capillary electrophoresis. These methods have limitations when unequal mixtures are genotyped, since the major component will be over-amplified or over-loaded. This study explores an alternative strategy for improved detection of the minor components in low template (LT) DNA typing that may be better suited for the detection of the minor component in mixtures. The strategy increases the PCR amplification efficiency by extending the primer annealing time several folds. When the AmpFℓSTR(®) Identifiler(®) amplification parameters are changed to an annealing time of 20 min during all 28 cycles, the drop-out frequency is reduced for both pristine DNA and single or multiple donor mock case work samples. In addition, increased peak heights and slightly more drop-ins are observed while the heterozygous peak balance remains similar as with the conventional Identifiler protocol. By this extended protocol, full DNA profiles were obtained from only 12 sperm heads (which corresponds to 36 pg of DNA) that were collected by laser micro dissection. Notwithstanding the improved detection, allele drop-outs do persist, albeit in lower frequencies. Thus a LT interpretation strategy such as deducing consensus profiles from multiple independent amplifications is appropriate. The use of extended PCR conditions represents a general approach to improve detection of unequal mixtures as shown using four commercially available kits (AmpFℓSTR(®) Identifiler, SEfiler Plus, NGM and Yfiler). The extended PCR protocol seems to amplify more of the molecules in LT samples during PCR, which results in a lower drop-out frequency. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Evaluation and development the routing protocol of a fully functional simulation environment for VANETs

NASA Astrophysics Data System (ADS)

Ali, Azhar Tareq; Warip, Mohd Nazri Mohd; Yaakob, Naimah; Abduljabbar, Waleed Khalid; Atta, Abdu Mohammed Ali

2017-11-01

Vehicular Ad-hoc Networks (VANETs) is an area of wireless technologies that is attracting a great deal of interest. There are still several areas of VANETS, such as security and routing protocols, medium access control, that lack large amounts of research. There is also a lack of freely available simulators that can quickly and accurately simulate VANETs. The main goal of this paper is to develop a freely available VANETS simulator and to evaluate popular mobile ad-hoc network routing protocols in several VANETS scenarios. The VANETS simulator consisted of a network simulator, traffic (mobility simulator) and used a client-server application to keep the two simulators in sync. The VANETS simulator also models buildings to create a more realistic wireless network environment. Ad-Hoc Distance Vector routing (AODV), Dynamic Source Routing (DSR) and Dynamic MANET On-demand (DYMO) were initially simulated in a city, country, and highway environment to provide an overall evaluation.

In situ TEM observation of alpha-particle induced annealing of radiation damage in Durango apatite.

PubMed

Li, Weixing; Shen, Yahui; Zhou, Yueqing; Nan, Shuai; Chen, Chien-Hung; Ewing, Rodney C

2017-10-26

A major issue in thermochronology and U-Th-Pb dating is the effect of radiation damage, created by α-recoils from α-decay events, on the diffusion of radiogenic elements (e.g., He and Pb) in host mineral. Up until now, thermal events have been considered as the only source of energy for the recovery of radiation-damage. However, irradiation, such as from the α-particle of the α-decay event, can itself induce damage recovery. Quantification of radiation-induced recovery caused by α-particles during α-decay events has not been possible, as the recovery process at the atomic-scale has been difficult to observe. Here we present details of the dynamics of the amorphous-to-crystalline transition process during α-particle irradiations using in situ transmission electron microscopy (TEM) and consecutive ion-irradiations: 1 MeV Kr 2+ (simulating α-recoil damage), followed by 400 keV He + (simulating α-particle annealing). Upon the He + irradiation, partial recrystallization of the original, fully-amorphous Durango apatite was clearly evident and quantified based on the gradual appearance of new crystalline domains in TEM images and new diffraction maxima in selected area electron diffraction patterns. Thus, α-particle induced annealing occurs and must be considered in models of α-decay event damage and its effect on the diffusion of radiogenic elements in geochronology and thermochronology.

Thermal stability of Cu-Cr-Zr alloy processed by equal-channel angular pressing

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

Abib, Khadidja

Thermal stability of a Cu-Cr-Zr alloy processed by equal-channel angular pressing up to16 passes was investigated using isochronal annealing ranging from 250 to 850 °C for 1 h. The microstructure, crystallographic texture and micro hardness of samples were characterized through electron back scatter diffraction and Vickers micro hardness measurements. The recrystallized grain size was stable between 250 °C and 500 °C then increased quickly. The achieved mean grain size, after 1, 4 and 16 ECAP passes, was around 5.5 μm. A discontinuous mode of recrystallization was found to occur and a Particle Simulated Nucleation mechanism was evidenced. The evolution ofmore » the high angle grain boundary fraction increased notably after annealing above 550 °C. The crystallographic texture after isochronal annealing was similar to that of ECAP simple shear, no change of the texture during annealing was observed but only slight intensity variations. Micro hardness of all Cu–Cr–Zr samples showed a hardening with two peaks at 400 and 500 °C associated with precipitation of Cu cluster and Cu{sub 5}Zr phase respectively, followed by a subsequent softening upon increasing the annealing temperature due to recrystallization. - Highlight: •The Cu-1Cr-0.1Zr alloy shows a very good thermal stability up to 550 °C after ECAP. •A discontinuous recrystallization was found to occur and PSN mechanism was evidenced. •The annealing texture was found weak and some new components appear. •Hardening is attributed to the Cr clustering followed by the Cu{sub 51}Zr{sub 14} precipitation. •Softening is a result of recrystallization and grain growth progressing.« less

In situ synthesis of metal nanoparticles in polymer matrix and their optical limiting applications.

PubMed

Porel, S; Venkatram, N; Rao, D Narayana; Radhakrishnan, T P

2007-06-01

We present an overview of the simple and environmentally benign protocol we have developed recently, for the in situ generation of metal nanoparticles inside polymer films by mild thermal annealing, leading to free-standing as well as supported thin films of nanoparticle-embedded polymer. The fabrication chemistry is discussed and spectroscopic/microscopic characterizations of silver and gold nanoparticles in poly(vinyl alcohol) film are presented. Optical limiting characteristics of the silver-polymer system are investigated in detail and preliminary results for the gold-polymer system are reported.

Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

PubMed

Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A

2017-01-01

Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

Joint Optimization of Vertical Component Gravity and Seismic P-wave First Arrivals by Simulated Annealing

NASA Astrophysics Data System (ADS)

Louie, J. N.; Basler-Reeder, K.; Kent, G. M.; Pullammanappallil, S. K.

2015-12-01

Simultaneous joint seismic-gravity optimization improves P-wave velocity models in areas with sharp lateral velocity contrasts. Optimization is achieved using simulated annealing, a metaheuristic global optimization algorithm that does not require an accurate initial model. Balancing the seismic-gravity objective function is accomplished by a novel approach based on analysis of Pareto charts. Gravity modeling uses a newly developed convolution algorithm, while seismic modeling utilizes the highly efficient Vidale eikonal equation traveltime generation technique. Synthetic tests show that joint optimization improves velocity model accuracy and provides velocity control below the deepest headwave raypath. Detailed first arrival picking followed by trial velocity modeling remediates inconsistent data. We use a set of highly refined first arrival picks to compare results of a convergent joint seismic-gravity optimization to the Plotrefa™ and SeisOpt® Pro™ velocity modeling packages. Plotrefa™ uses a nonlinear least squares approach that is initial model dependent and produces shallow velocity artifacts. SeisOpt® Pro™ utilizes the simulated annealing algorithm and is limited to depths above the deepest raypath. Joint optimization increases the depth of constrained velocities, improving reflector coherency at depth. Kirchoff prestack depth migrations reveal that joint optimization ameliorates shallow velocity artifacts caused by limitations in refraction ray coverage. Seismic and gravity data from the San Emidio Geothermal field of the northwest Basin and Range province demonstrate that joint optimization changes interpretation outcomes. The prior shallow-valley interpretation gives way to a deep valley model, while shallow antiformal reflectors that could have been interpreted as antiformal folds are flattened. Furthermore, joint optimization provides a clearer image of the rangefront fault. This technique can readily be applied to existing datasets and could replace the existing strategy of forward modeling to match gravity data.

Short-term prediction of solar energy in Saudi Arabia using automated-design fuzzy logic systems

PubMed Central

2017-01-01

Solar energy is considered as one of the main sources for renewable energy in the near future. However, solar energy and other renewable energy sources have a drawback related to the difficulty in predicting their availability in the near future. This problem affects optimal exploitation of solar energy, especially in connection with other resources. Therefore, reliable solar energy prediction models are essential to solar energy management and economics. This paper presents work aimed at designing reliable models to predict the global horizontal irradiance (GHI) for the next day in 8 stations in Saudi Arabia. The designed models are based on computational intelligence methods of automated-design fuzzy logic systems. The fuzzy logic systems are designed and optimized with two models using fuzzy c-means clustering (FCM) and simulated annealing (SA) algorithms. The first model uses FCM based on the subtractive clustering algorithm to automatically design the predictor fuzzy rules from data. The second model is using FCM followed by simulated annealing algorithm to enhance the prediction accuracy of the fuzzy logic system. The objective of the predictor is to accurately predict next-day global horizontal irradiance (GHI) using previous-day meteorological and solar radiation observations. The proposed models use observations of 10 variables of measured meteorological and solar radiation data to build the model. The experimentation and results of the prediction are detailed where the root mean square error of the prediction was approximately 88% for the second model tuned by simulated annealing compared to 79.75% accuracy using the first model. This results demonstrate a good modeling accuracy of the second model despite that the training and testing of the proposed models were carried out using spatially and temporally independent data. PMID:28806754

Optimization for high-dose-rate brachytherapy of cervical cancer with adaptive simulated annealing and gradient descent.

PubMed

Yao, Rui; Templeton, Alistair K; Liao, Yixiang; Turian, Julius V; Kiel, Krystyna D; Chu, James C H

2014-01-01

To validate an in-house optimization program that uses adaptive simulated annealing (ASA) and gradient descent (GD) algorithms and investigate features of physical dose and generalized equivalent uniform dose (gEUD)-based objective functions in high-dose-rate (HDR) brachytherapy for cervical cancer. Eight Syed/Neblett template-based cervical cancer HDR interstitial brachytherapy cases were used for this study. Brachytherapy treatment plans were first generated using inverse planning simulated annealing (IPSA). Using the same dwell positions designated in IPSA, plans were then optimized with both physical dose and gEUD-based objective functions, using both ASA and GD algorithms. Comparisons were made between plans both qualitatively and based on dose-volume parameters, evaluating each optimization method and objective function. A hybrid objective function was also designed and implemented in the in-house program. The ASA plans are higher on bladder V75% and D2cc (p=0.034) and lower on rectum V75% and D2cc (p=0.034) than the IPSA plans. The ASA and GD plans are not significantly different. The gEUD-based plans have higher homogeneity index (p=0.034), lower overdose index (p=0.005), and lower rectum gEUD and normal tissue complication probability (p=0.005) than the physical dose-based plans. The hybrid function can produce a plan with dosimetric parameters between the physical dose-based and gEUD-based plans. The optimized plans with the same objective value and dose-volume histogram could have different dose distributions. Our optimization program based on ASA and GD algorithms is flexible on objective functions, optimization parameters, and can generate optimized plans comparable with IPSA. Copyright © 2014 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Short-term prediction of solar energy in Saudi Arabia using automated-design fuzzy logic systems.

PubMed

Almaraashi, Majid

2017-01-01

Solar energy is considered as one of the main sources for renewable energy in the near future. However, solar energy and other renewable energy sources have a drawback related to the difficulty in predicting their availability in the near future. This problem affects optimal exploitation of solar energy, especially in connection with other resources. Therefore, reliable solar energy prediction models are essential to solar energy management and economics. This paper presents work aimed at designing reliable models to predict the global horizontal irradiance (GHI) for the next day in 8 stations in Saudi Arabia. The designed models are based on computational intelligence methods of automated-design fuzzy logic systems. The fuzzy logic systems are designed and optimized with two models using fuzzy c-means clustering (FCM) and simulated annealing (SA) algorithms. The first model uses FCM based on the subtractive clustering algorithm to automatically design the predictor fuzzy rules from data. The second model is using FCM followed by simulated annealing algorithm to enhance the prediction accuracy of the fuzzy logic system. The objective of the predictor is to accurately predict next-day global horizontal irradiance (GHI) using previous-day meteorological and solar radiation observations. The proposed models use observations of 10 variables of measured meteorological and solar radiation data to build the model. The experimentation and results of the prediction are detailed where the root mean square error of the prediction was approximately 88% for the second model tuned by simulated annealing compared to 79.75% accuracy using the first model. This results demonstrate a good modeling accuracy of the second model despite that the training and testing of the proposed models were carried out using spatially and temporally independent data.

A design protocol for tailoring ice-templated scaffold structure

PubMed Central

Pawelec, K. M.; Husmann, A.; Best, S. M.; Cameron, R. E.

2014-01-01

In this paper, we show, for the first time, the key link between scaffold architecture and latent heat evolution during the production of porous biomedical collagen structures using freeze-drying. Collagen scaffolds are used widely in the biomedical industry for the repair and reconstruction of skeletal tissues and organs. Freeze-drying of collagen slurries is a standard industrial process, and, until now, the literature has sought to characterize the influence of set processing parameters including the freezing protocol and weight percentage of collagen. However, we are able to demonstrate, by monitoring the local thermal events within the slurry during solidification, that nucleation, growth and annealing processes can be controlled, and therefore we are able to control the resulting scaffold architecture. Based on our correlation of thermal profile measurements with scaffold architecture, we hypothesize that there is a link between the fundamental freezing of ice and the structure of scaffolds, which suggests that this concept is applicable not only for collagen but also for ceramics and pharmaceuticals. We present a design protocol of strategies for tailoring the ice-templated scaffold structure. PMID:24402916

Characterization of Novel Thin-Films and Structures for Integrated Circuit and Photovoltaic Applications

NASA Astrophysics Data System (ADS)

Zhao, Zhao

Thin films have been widely used in various applications. This research focuses on the characterization of novel thin films in the integrated circuits and photovoltaic techniques. The ion implanted layer in silicon can be treated as ion implanted thin film, which plays an essential role in the integrated circuits fabrication. Novel rapid annealing methods, i.e. microwave annealing and laser annealing, are conducted to activate ion dopants and repair the damages, and then are compared with the conventional rapid thermal annealing (RTA). In terms of As+ and P+ implanted Si, the electrical and structural characterization confirms that the microwave and laser annealing can achieve more efficient dopant activation and recrystallization than conventional RTA. The efficient dopant activation in microwave annealing is attributed to ion hopping under microwave field, while the liquid phase growth in laser annealing provides its efficient dopant activation. The characterization of dopants diffusion shows no visible diffusion after microwave annealing, some extent of end range of diffusion after RTA, and significant dopant diffusion after laser annealing. For photovoltaic applications, an indium-free novel three-layer thin-film structure (transparent composited electrode (TCE)) is demonstrated as a promising transparent conductive electrode for solar cells. The characterization of TCE mainly focuses on its optical and electrical properties. Transfer matrix method for optical transmittance calculation is validated and proved to be a desirable method for predicting transmittance of TCE containing continuous metal layer, and can estimate the trend of transmittance as the layer thickness changes. TiO2/Ag/TiO2 (TAgT) electrode for organic solar cells (OSCs) is then designed using numerical simulation and shows much higher Haacke figure of merit than indium tin oxide (ITO). In addition, TAgT based OSC shows better performance than ITO based OSC when compatible hole transfer layer is employed. The electrical and structural characterization of hole transfer layers (HTLs) in OSCs reveals MoO3 is the compatible HTL for TAgT anode. In the end, the reactive ink printed Ag film for solar cell contact application is studied by characterizing its electromigration lifetime. A percolative model is proposed and validated for predicting the resistivity and lifetime of printed Ag thin films containing porous structure.

The Effect of Heat Treatment on the Crystallography and Mineral Magnetism of Pyrrhotite

NASA Astrophysics Data System (ADS)

Hobart, K.; Feinberg, J. M.; Jones, D. S.

2017-12-01

Pyrrhotite (Fe1-xS, 0 ≤ x ≤ 0.125) is the second most common sulfide mineral after pyrite in the Earth's crust, and its properties are of interest to a wide variety of scientific disciplines, including electrical engineering, physical chemistry, planetary geology and meteoritics, and economic geology. The physical properties of pyrrhotite are highly dependent on slight variations in composition and the ordering of iron vacancies, resulting in a number of possible phases between the endmember compositions of FeS and Fe7S8­­. A common complication in studies on pyrrhotite is that different phases are frequently intergrown, making it difficult to isolate a natural single phase. This has led many researchers to rely on synthesis techniques, which produce a specific structure by using precise iron/sulfur ratios, heating protocols, and controlled cooling. One of the most common synthesis treatments used to create 4C pyrrhotite is an extended heating and annealing process, which is believed to allow the reordering of vacancies to a more thermodynamically stable, ordered state with elevated saturation magnetization. The process was first studied in detail by Schwarz and Vaughan (1972) who produced synthetic pyrrhotite at varying Fe/S ratios with annealing at either 700, 300, or 144°C. The most common method for producing 4C pyrrhotite is heating at 500°C for 24 hours under a vacuum followed by annealing at 250°C for 50 hours. While this technique has been broadly applied in diverse disciplines, there is debate about whether it produces ferrimagnetic, monoclinic 4C pyrrhotite or a different metastable disordered phase. We examined this process using a combination of rock magnetic, X-ray diffraction, and electron imaging techniques to study the effect of heating and annealing on a natural sample of pyrrhotite. Due to the lack of a Besnus transition in the annealed material, our data suggest that the increased magnetization we found following annealing, rather than being an increase in 4C ferrimagnetic pyrrhotite, was the preservation of a ferrimagnetic metastable phase which represents an intermediate to the original intergrown phases. Further work will examine the differences between heat treatments on synthetic and natural pyrrhotites.

Hydrological Modelling and Sensitivity Analysis Using Topmodel and Simulated Annealing Techniques.application To The Haute-mentue Catchment(switzerland).

NASA Astrophysics Data System (ADS)

Balin Talamba, D.; Higy, C.; Joerin, C.; Musy, A.

The paper presents an application concerning the hydrological modelling for the Haute-Mentue catchment, located in western Switzerland. A simplified version of Topmodel, developed in a Labview programming environment, was applied in the aim of modelling the hydrological processes on this catchment. Previous researches car- ried out in this region outlined the importance of the environmental tracers in studying the hydrological behaviour and an important knowledge has been accumulated dur- ing this period concerning the mechanisms responsible for runoff generation. In con- formity with the theoretical constraints, Topmodel was applied for an Haute-Mentue sub-catchment where tracing experiments showed constantly low contributions of the soil water during the flood events. The model was applied for two humid periods in 1998. First, the model calibration was done in order to provide the best estimations for the total runoff. Instead, the simulated components (groundwater and rapid flow) showed far deviations from the reality indicated by the tracing experiments. Thus, a new calibration was performed including additional information given by the environ- mental tracing. The calibration of the model was done by using simulated annealing (SA) techniques, which are easy to implement and statistically allow for converging to a global minimum. The only problem is that the method is time and computer consum- ing. To improve this, a version of SA was used which is known as very fast-simulated annealing (VFSA). The principles are the same as for the SA technique. The random search is guided by certain probability distribution and the acceptance criterion is the same as for SA but the VFSA allows for better taking into account the ranges of vari- ation of each parameter. Practice with Topmodel showed that the energy function has different sensitivities along different dimensions of the parameter space. The VFSA algorithm allows differentiated search in relation with the sensitivity of the param- eters. The environmental tracing was used in the aim of constraining the parameter space in order to better simulate the hydrological behaviour of the catchment. VFSA outlined issues for characterising the significance of Topmodel input parameters as well as their uncertainty for the hydrological modelling.

A fragment-based approach to the SAMPL3 Challenge

NASA Astrophysics Data System (ADS)

Kulp, John L.; Blumenthal, Seth N.; Wang, Qiang; Bryan, Richard L.; Guarnieri, Frank

2012-05-01

The success of molecular fragment-based design depends critically on the ability to make predictions of binding poses and of affinity ranking for compounds assembled by linking fragments. The SAMPL3 Challenge provides a unique opportunity to evaluate the performance of a state-of-the-art fragment-based design methodology with respect to these requirements. In this article, we present results derived from linking fragments to predict affinity and pose in the SAMPL3 Challenge. The goal is to demonstrate how incorporating different aspects of modeling protein-ligand interactions impact the accuracy of the predictions, including protein dielectric models, charged versus neutral ligands, ΔΔGs solvation energies, and induced conformational stress. The core method is based on annealing of chemical potential in a Grand Canonical Monte Carlo (GC/MC) simulation. By imposing an initially very high chemical potential and then automatically running a sequence of simulations at successively decreasing chemical potentials, the GC/MC simulation efficiently discovers statistical distributions of bound fragment locations and orientations not found reliably without the annealing. This method accounts for configurational entropy, the role of bound water molecules, and results in a prediction of all the locations on the protein that have any affinity for the fragment. Disregarding any of these factors in affinity-rank prediction leads to significantly worse correlation with experimentally-determined free energies of binding. We relate three important conclusions from this challenge as applied to GC/MC: (1) modeling neutral ligands—regardless of the charged state in the active site—produced better affinity ranking than using charged ligands, although, in both cases, the poses were almost exactly overlaid; (2) simulating explicit water molecules in the GC/MC gave better affinity and pose predictions; and (3) applying a ΔΔGs solvation correction further improved the ranking of the neutral ligands. Using the GC/MC method under a variety of parameters in the blinded SAMPL3 Challenge provided important insights to the relevant parameters and boundaries in predicting binding affinities using simulated annealing of chemical potential calculations.

Effect of Annealing Temperature on Microstructure and Mechanical Properties of Hot-Dip Galvanizing DP600 Steel

NASA Astrophysics Data System (ADS)

Hai-yan, Sun; Zhi-li, Liu; Yang, Xu; Jian-qiang, Shi; Lian-xuan, Wang

Hot-dip galvanizing dual phase steel DP600 steel grade with low Si was produced by steel plant and experiments by simulating galvanizing thermal history. The microstructure was observed and analyzed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The effect of different annealing temperatures on the microstructure and mechanical properties of dual-phase steel was also discussed. The experimental results show that the dual-phase steel possesses excellent strength and elongation that match EN10346 600MPa standards. The microstructure is ferrite and martensite. TEM micrograph shows that white ferrite with black martensite islands inlay with a diameter of around 1um and the content of 14 18%. The volume will expand and phase changing take the form of shear transformation when ferrite converted to martensite. So there are high density dislocations in ferrite crystalline grain near martensite. The martensite content growing will be obvious along with annealing temperature going up. But the tendency will be weak when temperature high.

Manufacture of radio frequency micromachined switches with annealing.

PubMed

Lin, Cheng-Yang; Dai, Ching-Liang

2014-01-17

The fabrication and characterization of a radio frequency (RF) micromachined switch with annealing were presented. The structure of the RF switch consists of a membrane, coplanar waveguide (CPW) lines, and eight springs. The RF switch is manufactured using the complementary metal oxide semiconductor (CMOS) process. The switch requires a post-process to release the membrane and springs. The post-process uses a wet etching to remove the sacrificial silicon dioxide layer, and to obtain the suspended structures of the switch. In order to improve the residual stress of the switch, an annealing process is applied to the switch, and the membrane obtains an excellent flatness. The finite element method (FEM) software CoventorWare is utilized to simulate the stress and displacement of the RF switch. Experimental results show that the RF switch has an insertion loss of 0.9 dB at 35 GHz and an isolation of 21 dB at 39 GHz. The actuation voltage of the switch is 14 V.

Manufacture of Radio Frequency Micromachined Switches with Annealing

PubMed Central

Lin, Cheng-Yang; Dai, Ching-Liang

2014-01-01

The fabrication and characterization of a radio frequency (RF) micromachined switch with annealing were presented. The structure of the RF switch consists of a membrane, coplanar waveguide (CPW) lines, and eight springs. The RF switch is manufactured using the complementary metal oxide semiconductor (CMOS) process. The switch requires a post-process to release the membrane and springs. The post-process uses a wet etching to remove the sacrificial silicon dioxide layer, and to obtain the suspended structures of the switch. In order to improve the residual stress of the switch, an annealing process is applied to the switch, and the membrane obtains an excellent flatness. The finite element method (FEM) software CoventorWare is utilized to simulate the stress and displacement of the RF switch. Experimental results show that the RF switch has an insertion loss of 0.9 dB at 35 GHz and an isolation of 21 dB at 39 GHz. The actuation voltage of the switch is 14 V. PMID:24445415

Regulation of multispanning membrane protein topology via post-translational annealing.

PubMed

Van Lehn, Reid C; Zhang, Bin; Miller, Thomas F

2015-09-26

The canonical mechanism for multispanning membrane protein topogenesis suggests that protein topology is established during cotranslational membrane integration. However, this mechanism is inconsistent with the behavior of EmrE, a dual-topology protein for which the mutation of positively charged loop residues, even close to the C-terminus, leads to dramatic shifts in its topology. We use coarse-grained simulations to investigate the Sec-facilitated membrane integration of EmrE and its mutants on realistic biological timescales. This work reveals a mechanism for regulating membrane-protein topogenesis, in which initially misintegrated configurations of the proteins undergo post-translational annealing to reach fully integrated multispanning topologies. The energetic barriers associated with this post-translational annealing process enforce kinetic pathways that dictate the topology of the fully integrated proteins. The proposed mechanism agrees well with the experimentally observed features of EmrE topogenesis and provides a range of experimentally testable predictions regarding the effect of translocon mutations on membrane protein topogenesis.

Nanosecond laser ablated copper superhydrophobic surface with tunable ultrahigh adhesion and its renewability with low temperature annealing

NASA Astrophysics Data System (ADS)

He, An; Liu, Wenwen; Xue, Wei; Yang, Huan; Cao, Yu

2018-03-01

Recently, metallic superhydrophobic surfaces with ultrahigh adhesion have got plentiful attention on account of their significance in scientific researches and industrial applications like droplet transport, drug delivery and novel microfluidic devices. However, the long lead time and transience hindered its in-depth development and industrial application. In this work, nanosecond laser ablation was carried out to construct grid of micro-grooves on copper surface, whereafter, by applying fast ethanol assisted low-temperature annealing, we obtained surface with superhydrophobicity and ultrahigh adhesion within hours. And the ultrahigh adhesion force was found tunable by varying the groove spacing. Using ultrasonic cleaning as the simulation of natural wear and tear in service, the renewability of superhydrophobicity was also investigated, and the result shows that the contact angle can rehabilitate promptly by the processing of ethanol assisted low-temperature annealing, which gives a promising fast and cheap circuitous strategy to realize the long wish durable metallic superhydrophobic surfaces in practical applications.

Optical and electronic properties of sub-surface conducting layers in diamond created by MeV B-implantation at elevated temperatures

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

Willems van Beveren, L. H., E-mail: laurensw@unimelb.edu.au; Bowers, H.; Ganesan, K.

2016-06-14

Boron implantation with in-situ dynamic annealing is used to produce highly conductive sub-surface layers in type IIa (100) diamond plates for the search of a superconducting phase transition. Here, we demonstrate that high-fluence MeV ion-implantation, at elevated temperatures avoids graphitization and can be used to achieve doping densities of 6 at. %. In order to quantify the diamond crystal damage associated with implantation Raman spectroscopy was performed, demonstrating high temperature annealing recovers the lattice. Additionally, low-temperature electronic transport measurements show evidence of charge carrier densities close to the metal-insulator-transition. After electronic characterization, secondary ion mass spectrometry was performed to mapmore » out the ion profile of the implanted plates. The analysis shows close agreement with the simulated ion-profile assuming scaling factors that take into account an average change in diamond density due to device fabrication. Finally, the data show that boron diffusion is negligible during the high temperature annealing process.« less

Elevated temperature strengthening of a melt spun austenitic steel by TiB2

NASA Technical Reports Server (NTRS)

Michal, G. M.; Glasgow, T. K.; Moore, T. J.

1986-01-01

Mechanical properties of an iron-based alloy containing (by wt pct) 33Ni, 2Al, 6Ti, and 2B (resulting in an alloy containing 10 vol pct TiB2) were evaluated by hardness and tensile testing. The alloy was cast as a ribbon using a dual 'free-jet' variation of Jech et al. (1984) method of chill-block melt-spinning against a copper wheel; to simulate thermal cycles the alloy ribbon would experience during compaction into shapes, various segments of the ribbon were annealed under a vacuum at temperatures ranging from 500 to 1150 C. The results show that maximum strengths at 650 and 760 C were developed in ribbons annealed at 1100 C; in these ribbons an optimal combination of grain coarsening with minimum TiB2 particle growth was observed. However, the elevated-temperature strength of the TiB2-strengthened alloy under optimal annealing conditions was poorer than that of conventional iron-based superalloys strengthened by gamma-prime precipitates.

Using an improved association rules mining optimization algorithm in web-based mobile-learning system

NASA Astrophysics Data System (ADS)

Huang, Yin; Chen, Jianhua; Xiong, Shaojun

2009-07-01

Mobile-Learning (M-learning) makes many learners get the advantages of both traditional learning and E-learning. Currently, Web-based Mobile-Learning Systems have created many new ways and defined new relationships between educators and learners. Association rule mining is one of the most important fields in data mining and knowledge discovery in databases. Rules explosion is a serious problem which causes great concerns, as conventional mining algorithms often produce too many rules for decision makers to digest. Since Web-based Mobile-Learning System collects vast amounts of student profile data, data mining and knowledge discovery techniques can be applied to find interesting relationships between attributes of learners, assessments, the solution strategies adopted by learners and so on. Therefore ,this paper focus on a new data-mining algorithm, combined with the advantages of genetic algorithm and simulated annealing algorithm , called ARGSA(Association rules based on an improved Genetic Simulated Annealing Algorithm), to mine the association rules. This paper first takes advantage of the Parallel Genetic Algorithm and Simulated Algorithm designed specifically for discovering association rules. Moreover, the analysis and experiment are also made to show the proposed method is superior to the Apriori algorithm in this Mobile-Learning system.

Galvanizability of Advanced High-Strength Steels 1180TRIP and 1180CP

NASA Astrophysics Data System (ADS)

Kim, M. S.; Kwak, J. H.; Kim, J. S.; Liu, Y. H.; Gao, N.; Tang, N.-Y.

2009-08-01

In general, Si-bearing advanced high-strength steels (AHSS) possess excellent mechanical properties but poor galvanizability. The galvanizability of a transformation-induced plasticity (TRIP) steel 1180TRIP containing 2.2 pct Mn and 1.7 pct Si and a complex phase steel 1180CP containing 2.7 pct Mn and 0.2 pct Si was extensively studied using a galvanizing simulator. The steel coupons were annealed at fixed dew points in the simulator. The surface features of the as-annealed steel coupons, together with galvanized and galvannealed coatings, were carefully examined using a variety of advanced analysis techniques. It was found that various oxides formed on the surface of these steels, depending on the steel composition and on the dew point control. Coating quality was good at 0 °C dew point but deteriorated as the dew point decreased to -35 °C and -65 °C. Based on the findings, guidance was provided for improving galvanizability by adjusting the Mn:Si ratio in steel compositions according to the dew point.

Technique Developed for Optimizing Traveling-Wave Tubes

NASA Technical Reports Server (NTRS)

Wilson, Jeffrey D.

1999-01-01

A traveling-wave tube (TWT) is an electron beam device that is used to amplify electromagnetic communication waves at radio and microwave frequencies. TWT s are critical components in deep-space probes, geosynchronous communication satellites, and high-power radar systems. Power efficiency is of paramount importance for TWT s employed in deep-space probes and communications satellites. Consequently, increasing the power efficiency of TWT s has been the primary goal of the TWT group at the NASA Lewis Research Center over the last 25 years. An in-house effort produced a technique (ref. 1) to design TWT's for optimized power efficiency. This technique is based on simulated annealing, which has an advantage over conventional optimization techniques in that it enables the best possible solution to be obtained (ref. 2). A simulated annealing algorithm was created and integrated into the NASA TWT computer model (ref. 3). The new technique almost doubled the computed conversion power efficiency of a TWT from 7.1 to 13.5 percent (ref. 1).

Conformational energy landscape of the acyl pocket loop in acetylcholinesterase: a Monte Carlo-generalized Born model study.

PubMed

Carlacci, Louis; Millard, Charles B; Olson, Mark A

2004-10-01

The X-ray crystal structure of the reaction product of acetylcholinesterase (AChE) with the inhibitor diisopropylphosphorofluoridate (DFP) showed significant structural displacement in a loop segment of residues 287-290. To understand this conformational selection, a Monte Carlo (MC) simulation study was performed of the energy landscape for the loop segment. A computational strategy was applied by using a combined simulated annealing and room temperature Metropolis sampling approach with solvent polarization modeled by a generalized Born (GB) approximation. Results from thermal annealing reveal a landscape topology of broader basin opening and greater distribution of energies for the displaced loop conformation, while the ensemble average of conformations at 298 K favored a shift in populations toward the native by a free-energy difference in good agreement with the estimated experimental value. Residue motions along a reaction profile of loop conformational reorganization are proposed where Arg-289 is critical in determining electrostatic effects of solvent interaction versus Coulombic charging.

Grain growth in U–7Mo alloy: A combined first-principles and phase field study

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

Mei, Zhi-Gang; Liang, Linyun; Kim, Yeon Soo

2016-05-01

Grain size is an important factor in controlling the swelling behavior in irradiated U-Mo dispersion fuels. Increasing the grain size in UeMo fuel particles by heat treatment is believed to delay the fuel swelling at high fission density. In this work, a multiscale simulation approach combining first-principles calculation and phase field modeling is used to investigate the grain growth behavior in U-7Mo alloy. The density functional theory based first-principles calculations were used to predict the material properties of U-7Mo alloy. The obtained grain boundary energies were then adopted as an input parameter for mesoscale phase field simulations. The effects ofmore » annealing temperature, annealing time and initial grain structures of fuel particles on the grain growth in U-7Mo alloy were examined. The predicted grain growth rate compares well with the empirical correlation derived from experiments. (C) 2016 Elsevier B.V. All rights reserved.« less

Alternative Zoning Scenarios for Regional Sustainable Land Use Controls in China: A Knowledge-Based Multiobjective Optimisation Model

PubMed Central

Xia, Yin; Liu, Dianfeng; Liu, Yaolin; He, Jianhua; Hong, Xiaofeng

2014-01-01

Alternative land use zoning scenarios provide guidance for sustainable land use controls. This study focused on an ecologically vulnerable catchment on the Loess Plateau in China, proposed a novel land use zoning model, and generated alternative zoning solutions to satisfy the various requirements of land use stakeholders and managers. This model combined multiple zoning objectives, i.e., maximum zoning suitability, maximum planning compatibility and maximum spatial compactness, with land use constraints by using goal programming technique, and employed a modified simulated annealing algorithm to search for the optimal zoning solutions. The land use zoning knowledge was incorporated into the initialisation operator and neighbourhood selection strategy of the simulated annealing algorithm to improve its efficiency. The case study indicates that the model is both effective and robust. Five optimal zoning scenarios of the study area were helpful for satisfying the requirements of land use controls in loess hilly regions, e.g., land use intensification, agricultural protection and environmental conservation. PMID:25170679

Research on ion implantation in MEMS device fabrication by theory, simulation and experiments

NASA Astrophysics Data System (ADS)

Bai, Minyu; Zhao, Yulong; Jiao, Binbin; Zhu, Lingjian; Zhang, Guodong; Wang, Lei

2018-06-01

Ion implantation is widely utilized in microelectromechanical systems (MEMS), applied for embedded lead, resistors, conductivity modifications and so forth. In order to achieve an expected device, the principle of ion implantation must be carefully examined. The elementary theory of ion implantation including implantation mechanism, projectile range and implantation-caused damage in the target were studied, which can be regarded as the guidance of ion implantation in MEMS device design and fabrication. Critical factors including implantations dose, energy and annealing conditions are examined by simulations and experiments. The implantation dose mainly determines the dopant concentration in the target substrate. The implantation energy is the key factor of the depth of the dopant elements. The annealing time mainly affects the repair degree of lattice damage and thus the activated elements’ ratio. These factors all together contribute to ions’ behavior in the substrates and characters of the devices. The results can be referred to in the MEMS design, especially piezoresistive devices.

Predictive process simulation of cryogenic implants for leading edge transistor design

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

Gossmann, Hans-Joachim; Zographos, Nikolas; Park, Hugh

2012-11-06

Two cryogenic implant TCAD-modules have been developed: (i) A continuum-based compact model targeted towards a TCAD production environment calibrated against an extensive data-set for all common dopants. Ion-specific calibration parameters related to damage generation and dynamic annealing were used and resulted in excellent fits to the calibration data-set. (ii) A Kinetic Monte Carlo (kMC) model including the full time dependence of ion-exposure that a particular spot on the wafer experiences, as well as the resulting temperature vs. time profile of this spot. It was calibrated by adjusting damage generation and dynamic annealing parameters. The kMC simulations clearly demonstrate the importancemore » of the time-structure of the beam for the amorphization process: Assuming an average dose-rate does not capture all of the physics and may lead to incorrect conclusions. The model enables optimization of the amorphization process through tool parameters such as scan speed or beam height.« less

A Comparison of Techniques for Scheduling Earth-Observing Satellites

NASA Technical Reports Server (NTRS)

Globus, Al; Crawford, James; Lohn, Jason; Pryor, Anna

2004-01-01

Scheduling observations by coordinated fleets of Earth Observing Satellites (EOS) involves large search spaces, complex constraints and poorly understood bottlenecks, conditions where evolutionary and related algorithms are often effective. However, there are many such algorithms and the best one to use is not clear. Here we compare multiple variants of the genetic algorithm: stochastic hill climbing, simulated annealing, squeaky wheel optimization and iterated sampling on ten realistically-sized EOS scheduling problems. Schedules are represented by a permutation (non-temperal ordering) of the observation requests. A simple deterministic scheduler assigns times and resources to each observation request in the order indicated by the permutation, discarding those that violate the constraints created by previously scheduled observations. Simulated annealing performs best. Random mutation outperform a more 'intelligent' mutator. Furthermore, the best mutator, by a small margin, was a novel approach we call temperature dependent random sampling that makes large changes in the early stages of evolution and smaller changes towards the end of search.

A genetic algorithm-based approach to flexible flow-line scheduling with variable lot sizes.

PubMed

Lee, I; Sikora, R; Shaw, M J

1997-01-01

Genetic algorithms (GAs) have been used widely for such combinatorial optimization problems as the traveling salesman problem (TSP), the quadratic assignment problem (QAP), and job shop scheduling. In all of these problems there is usually a well defined representation which GA's use to solve the problem. We present a novel approach for solving two related problems-lot sizing and sequencing-concurrently using GAs. The essence of our approach lies in the concept of using a unified representation for the information about both the lot sizes and the sequence and enabling GAs to evolve the chromosome by replacing primitive genes with good building blocks. In addition, a simulated annealing procedure is incorporated to further improve the performance. We evaluate the performance of applying the above approach to flexible flow line scheduling with variable lot sizes for an actual manufacturing facility, comparing it to such alternative approaches as pair wise exchange improvement, tabu search, and simulated annealing procedures. The results show the efficacy of this approach for flexible flow line scheduling.

Mathematical model and metaheuristics for simultaneous balancing and sequencing of a robotic mixed-model assembly line

NASA Astrophysics Data System (ADS)

Li, Zixiang; Janardhanan, Mukund Nilakantan; Tang, Qiuhua; Nielsen, Peter

2018-05-01

This article presents the first method to simultaneously balance and sequence robotic mixed-model assembly lines (RMALB/S), which involves three sub-problems: task assignment, model sequencing and robot allocation. A new mixed-integer programming model is developed to minimize makespan and, using CPLEX solver, small-size problems are solved for optimality. Two metaheuristics, the restarted simulated annealing algorithm and co-evolutionary algorithm, are developed and improved to address this NP-hard problem. The restarted simulated annealing method replaces the current temperature with a new temperature to restart the search process. The co-evolutionary method uses a restart mechanism to generate a new population by modifying several vectors simultaneously. The proposed algorithms are tested on a set of benchmark problems and compared with five other high-performing metaheuristics. The proposed algorithms outperform their original editions and the benchmarked methods. The proposed algorithms are able to solve the balancing and sequencing problem of a robotic mixed-model assembly line effectively and efficiently.

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

Aziz, Mohd Khairul Bazli Mohd, E-mail: mkbazli@yahoo.com; Yusof, Fadhilah, E-mail: fadhilahy@utm.my; Daud, Zalina Mohd, E-mail: zalina@ic.utm.my

Recently, many rainfall network design techniques have been developed, discussed and compared by many researchers. Present day hydrological studies require higher levels of accuracy from collected data. In numerous basins, the rain gauge stations are located without clear scientific understanding. In this study, an attempt is made to redesign rain gauge network for Johor, Malaysia in order to meet the required level of accuracy preset by rainfall data users. The existing network of 84 rain gauges in Johor is optimized and redesigned into a new locations by using rainfall, humidity, solar radiation, temperature and wind speed data collected during themore » monsoon season (November - February) of 1975 until 2008. This study used the combination of geostatistics method (variance-reduction method) and simulated annealing as the algorithm of optimization during the redesigned proses. The result shows that the new rain gauge location provides minimum value of estimated variance. This shows that the combination of geostatistics method (variance-reduction method) and simulated annealing is successful in the development of the new optimum rain gauge system.« less

Optimizing Adversary Training and the Structure of the Navy Adversary Fleet

DTIC Science & Technology

2013-09-01

ORGANIZATION REPORT NUMBER 9. SPONSORING /MONITORING AGENCY NAME(S) AND ADDRESS(ES) OPNAV N98 2000 Navy Pentagon , Room 5C469 Washington DC, 20350...an overhaul of existing computers and encryption in the range operations centers (CDR R. Van Diepen, OPNAV Simulator Requirements Officer, personal...1.0. Using a simulated annealing heuristic algorithm in conjunction with the utility assignments, CNA found, in order of priority, that the following

Structural consequences of metallothionein dimerization: solution structure of the isolated Cd4-alpha-domain and comparison with the holoprotein dimer.

PubMed

Ejnik, John W; Muñoz, Amalia; DeRose, Eugene; Shaw, C Frank; Petering, David H

2003-07-22

The NMR determination of the structure of Cd(7)-metallothionein was done previously using a relatively large protein concentration that favors dimer formation. The reactivity of the protein is also affected under this condition. To examine the influence of protein concentration on metallothionein conformation, the isolated Cd(4)-alpha-domain was prepared from rabbit metallothionein-2 (MT 2), and its three-dimensional structure was determined by heteronuclear, (1)H-(111)Cd, and homonuclear, (1)H-(1)H NMR, correlation experiments. The three-dimensional structure was refined using distance and angle constraints derived from these two-dimensional NMR data sets and a distance geometry/simulated annealing protocol. The backbone superposition of the alpha-domain from rabbit holoprotein Cd(7)-MT 2 and the isolated rabbit Cd(4)-alpha was measured at a RMSD of 2.0 A. Nevertheless, the conformations of the two Cd-thiolate clusters were distinctly different at two of the cadmium centers. In addition, solvent access to the sulfhydryl ligands of the isolated Cd(4)-alpha cluster was 130% larger due to this small change in cluster geometry. To probe whether these differences were an artifact of the structure calculation, the Cd(4)-alpha-domain structure in rabbit Cd(7)-MT 2 was redetermined, using the previously defined set of NOEs and the present calculation protocol. All calculations employed the same ionic radius for Cd(2+) and same cadmium-thiolate bond distance. The newly calculated structure matched the original with an RMSD of 1.24 A. It is hypothesized that differences in the two alpha-domain structures result from a perturbation of the holoprotein structure because of head-to-tail dimerization under the conditions of the NMR experiments.

LANES - LOCAL AREA NETWORK EXTENSIBLE SIMULATOR

NASA Technical Reports Server (NTRS)

Gibson, J.

1994-01-01

The Local Area Network Extensible Simulator (LANES) provides a method for simulating the performance of high speed local area network (LAN) technology. LANES was developed as a design and analysis tool for networking on board the Space Station. The load, network, link and physical layers of a layered network architecture are all modeled. LANES models to different lower-layer protocols, the Fiber Distributed Data Interface (FDDI) and the Star*Bus. The load and network layers are included in the model as a means of introducing upper-layer processing delays associated with message transmission; they do not model any particular protocols. FDDI is an American National Standard and an International Organization for Standardization (ISO) draft standard for a 100 megabit-per-second fiber-optic token ring. Specifications for the LANES model of FDDI are taken from the Draft Proposed American National Standard FDDI Token Ring Media Access Control (MAC), document number X3T9.5/83-16 Rev. 10, February 28, 1986. This is a mature document describing the FDDI media-access-control protocol. Star*Bus, also known as the Fiber Optic Demonstration System, is a protocol for a 100 megabit-per-second fiber-optic star-topology LAN. This protocol, along with a hardware prototype, was developed by Sperry Corporation under contract to NASA Goddard Space Flight Center as a candidate LAN protocol for the Space Station. LANES can be used to analyze performance of a networking system based on either FDDI or Star*Bus under a variety of loading conditions. Delays due to upper-layer processing can easily be nullified, allowing analysis of FDDI or Star*Bus as stand-alone protocols. LANES is a parameter-driven simulation; it provides considerable flexibility in specifying both protocol an run-time parameters. Code has been optimized for fast execution and detailed tracing facilities have been included. LANES was written in FORTRAN 77 for implementation on a DEC VAX under VMS 4.6. It consists of two programs, a simulation program and a user-interface program. The simulation program requires the SLAM II simulation library from Pritsker and Associates, W. Lafayette IN; the user interface is implemented using the Ingres database manager from Relational Technology, Inc. Information about running the simulation program without the user-interface program is contained in the documentation. The memory requirement is 129,024 bytes. LANES was developed in 1988.

Decoherence in adiabatic quantum computation

NASA Astrophysics Data System (ADS)

Albash, Tameem; Lidar, Daniel A.

2015-06-01

Recent experiments with increasingly larger numbers of qubits have sparked renewed interest in adiabatic quantum computation, and in particular quantum annealing. A central question that is repeatedly asked is whether quantum features of the evolution can survive over the long time scales used for quantum annealing relative to standard measures of the decoherence time. We reconsider the role of decoherence in adiabatic quantum computation and quantum annealing using the adiabatic quantum master-equation formalism. We restrict ourselves to the weak-coupling and singular-coupling limits, which correspond to decoherence in the energy eigenbasis and in the computational basis, respectively. We demonstrate that decoherence in the instantaneous energy eigenbasis does not necessarily detrimentally affect adiabatic quantum computation, and in particular that a short single-qubit T2 time need not imply adverse consequences for the success of the quantum adiabatic algorithm. We further demonstrate that boundary cancellation methods, designed to improve the fidelity of adiabatic quantum computing in the closed-system setting, remain beneficial in the open-system setting. To address the high computational cost of master-equation simulations, we also demonstrate that a quantum Monte Carlo algorithm that explicitly accounts for a thermal bosonic bath can be used to interpolate between classical and quantum annealing. Our study highlights and clarifies the significantly different role played by decoherence in the adiabatic and circuit models of quantum computing.

Measurement and Simulation of Thermal Conductivity of Hafnium-Aluminum Thermal Neutron Absorber Material

DOE PAGES

Guillen, Donna Post; Harris, William H.

2016-05-11

A metal matrix composite (MMC) material comprised of hafnium aluminide (Al3Hf) intermetallic particles in an aluminum matrix has been identified as a promising material for fast-flux irradiation testing applications. This material can filter thermal neutrons while simultaneously providing high rates of conductive cooling for experiment capsules. Our purpose is to investigate effects of Hf-Al material composition and neutron irradiation on thermophysical properties, which were measured before and after irradiation. When performing differential scanning calorimetry (DSC) on the irradiated specimens, a large exotherm corresponding to material annealment was observed. Thus, a test procedure was developed to perform DSC and laser flashmore » analysis (LFA) to obtain the specific heat and thermal diffusivity of pre- and post-annealment specimens. This paper presents the thermal properties for three states of the MMC material: (1) unirradiated, (2) as-irradiated, and (3) irradiated and annealed. Microstructure-property relationships were obtained for the thermal conductivity. These relationships are useful for designing components from this material to operate in irradiation environments. Furthermore, the ability of this material to effectively conduct heat as a function of temperature, volume fraction Al 3Hf, radiation damage and annealing is assessed using the MOOSE suite of computational tools.« less

Large Scale Laser Crystallization of Solution-based Alumina-doped Zinc Oxide (AZO) Nanoinks for Highly Transparent Conductive Electrode

PubMed Central

Nian, Qiong; Callahan, Michael; Saei, Mojib; Look, David; Efstathiadis, Harry; Bailey, John; Cheng, Gary J.

2015-01-01

A new method combining aqueous solution printing with UV Laser crystallization (UVLC) and post annealing is developed to deposit highly transparent and conductive Aluminum doped Zinc Oxide (AZO) films. This technique is able to rapidly produce large area AZO films with better structural and optoelectronic properties than most high vacuum deposition, suggesting a potential large-scale manufacturing technique. The optoelectronic performance improvement attributes to UVLC and forming gas annealing (FMG) induced grain boundary density decrease and electron traps passivation at grain boundaries. The physical model and computational simulation developed in this work could be applied to thermal treatment of many other metal oxide films. PMID:26515670

spsann - optimization of sample patterns using spatial simulated annealing

NASA Astrophysics Data System (ADS)

Samuel-Rosa, Alessandro; Heuvelink, Gerard; Vasques, Gustavo; Anjos, Lúcia

2015-04-01

There are many algorithms and computer programs to optimize sample patterns, some private and others publicly available. A few have only been presented in scientific articles and text books. This dispersion and somewhat poor availability is holds back to their wider adoption and further development. We introduce spsann, a new R-package for the optimization of sample patterns using spatial simulated annealing. R is the most popular environment for data processing and analysis. Spatial simulated annealing is a well known method with widespread use to solve optimization problems in the soil and geo-sciences. This is mainly due to its robustness against local optima and easiness of implementation. spsann offers many optimizing criteria for sampling for variogram estimation (number of points or point-pairs per lag distance class - PPL), trend estimation (association/correlation and marginal distribution of the covariates - ACDC), and spatial interpolation (mean squared shortest distance - MSSD). spsann also includes the mean or maximum universal kriging variance (MUKV) as an optimizing criterion, which is used when the model of spatial variation is known. PPL, ACDC and MSSD were combined (PAN) for sampling when we are ignorant about the model of spatial variation. spsann solves this multi-objective optimization problem scaling the objective function values using their maximum absolute value or the mean value computed over 1000 random samples. Scaled values are aggregated using the weighted sum method. A graphical display allows to follow how the sample pattern is being perturbed during the optimization, as well as the evolution of its energy state. It is possible to start perturbing many points and exponentially reduce the number of perturbed points. The maximum perturbation distance reduces linearly with the number of iterations. The acceptance probability also reduces exponentially with the number of iterations. R is memory hungry and spatial simulated annealing is a computationally intensive method. As such, many strategies were used to reduce the computation time and memory usage: a) bottlenecks were implemented in C++, b) a finite set of candidate locations is used for perturbing the sample points, and c) data matrices are computed only once and then updated at each iteration instead of being recomputed. spsann is available at GitHub under a licence GLP Version 2.0 and will be further developed to: a) allow the use of a cost surface, b) implement other sensitive parts of the source code in C++, c) implement other optimizing criteria, d) allow to add or delete points to/from an existing point pattern.

Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

PubMed

Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F

2017-01-01

Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

Graphical user interface for wireless sensor networks simulator

NASA Astrophysics Data System (ADS)

Paczesny, Tomasz; Paczesny, Daniel; Weremczuk, Jerzy

2008-01-01

Wireless Sensor Networks (WSN) are currently very popular area of development. It can be suited in many applications form military through environment monitoring, healthcare, home automation and others. Those networks, when working in dynamic, ad-hoc model, need effective protocols which must differ from common computer networks algorithms. Research on those protocols would be difficult without simulation tool, because real applications often use many nodes and tests on such a big networks take much effort and costs. The paper presents Graphical User Interface (GUI) for simulator which is dedicated for WSN studies, especially in routing and data link protocols evaluation.

Response of LiF:Mg,Ti thermoluminescent dosimeters at photon energies relevant to the dosimetry of brachytherapy (<1 MeV).

PubMed

Tedgren, Asa Carlsson; Hedman, Angelica; Grindborg, Jan-Erik; Carlsson, Gudrun Alm

2011-10-01

High energy photon beams are used in calibrating dosimeters for use in brachytherapy since absorbed dose to water can be determined accurately and with traceability to primary standards in such beams, using calibrated ion chambers and standard dosimetry protocols. For use in brachytherapy, beam quality correction factors are needed, which include corrections for differences in mass energy absorption properties between water and detector as well as variations in detector response (intrinsic efficiency) with radiation quality, caused by variations in the density of ionization (linear energy transfer (LET) -distributions) along the secondary electron tracks. The aim of this work was to investigate experimentally the detector response of LiF:Mg,Ti thermoluminescent dosimeters (TLD) for photon energies below 1 MeV relative to (60)Co and to address discrepancies between the results found in recent publications of detector response. LiF:Mg,Ti dosimeters of formulation MTS-N Poland were irradiated to known values of air kerma free-in-air in x-ray beams at tube voltages 25-250 kV, in (137)Cs- and (60)Co-beams at the Swedish Secondary Standards Dosimetry Laboratory. Conversions from air kerma free-in-air into values of mean absorbed dose in the dosimeters in the actual irradiation geometries were made using EGSnrc Monte Carlo simulations. X-ray energy spectra were measured or calculated for the actual beams. Detector response relative to that for (60)Co was determined at each beam quality. An increase in relative response was seen for all beam qualities ranging from 8% at tube voltage 25 kV (effective energy 13 keV) to 3%-4% at 250 kV (122 keV effective energy) and (137)Cs with a minimum at 80 keV effective energy (tube voltage 180 kV). The variation with effective energy was similar to that reported by Davis et al. [Radiat. Prot. Dosim. 106, 33-43 (2003)] with our values being systematically lower by 2%-4%. Compared to the results by Nunn et al. [Med. Phys. 35, 1861-1869 (2008)], the relative detector response as a function of effective energy differed in both shape and magnitude. This could be explained by the higher maximum read-out temperature (350 °C) used by Nunn et al. [Med. Phys. 35, 1861-1869 (2008)], allowing light emitted from high-temperature peaks with a strong LET dependence to be registered. Use of TLD-100 by Davis et al. [Radiat. Prot. Dosim. 106, 33-43 (2003)] with a stronger super-linear dose response compared to MTS-N was identified as causing the lower relative detector response in this work. Both careful dosimetry and strict protocols for handling the TLDs are required to reach solid experimental data on relative detector response. This work confirms older findings that an over-response relative to (60)Co exists for photon energies below 200-300 keV. Comparison with the results from the literature indicates that using similar protocols for annealing and read-out, dosimeters of different makes (TLD-100, MTS-N) differ in relative detector response. Though universality of the results has not been proven and further investigation is needed, it is anticipated that with the use of strict protocols for annealing and read-out, it will be possible to determine correction factors that can be used to reduce uncertainties in dose measurements around brachytherapy sources at photon energies where primary standards for absorbed dose to water are not available.

Adaptive temperature-accelerated dynamics

NASA Astrophysics Data System (ADS)

Shim, Yunsic; Amar, Jacques G.

2011-02-01

We present three adaptive methods for optimizing the high temperature Thigh on-the-fly in temperature-accelerated dynamics (TAD) simulations. In all three methods, the high temperature is adjusted periodically in order to maximize the performance. While in the first two methods the adjustment depends on the number of observed events, the third method depends on the minimum activation barrier observed so far and requires an a priori knowledge of the optimal high temperature T^{opt}_{high}(E_a) as a function of the activation barrier Ea for each accepted event. In order to determine the functional form of T^{opt}_{high}(E_a), we have carried out extensive simulations of submonolayer annealing on the (100) surface for a variety of metals (Ag, Cu, Ni, Pd, and Au). While the results for all five metals are different, when they are scaled with the melting temperature Tm, we find that they all lie on a single scaling curve. Similar results have also been obtained for (111) surfaces although in this case the scaling function is slightly different. In order to test the performance of all three methods, we have also carried out adaptive TAD simulations of Ag/Ag(100) annealing and growth at T = 80 K and compared with fixed high-temperature TAD simulations for different values of Thigh. We find that the performance of all three adaptive methods is typically as good as or better than that obtained in fixed high-temperature TAD simulations carried out using the effective optimal fixed high temperature. In addition, we find that the final high temperatures obtained in our adaptive TAD simulations are very close to our results for T^{opt}_{high}(E_a). The applicability of the adaptive methods to a variety of TAD simulations is also briefly discussed.

Engineering on-chip nanoporous gold material libraries via precision photothermal treatment [Precision Photothermal Annealing of Nanoporous Gold Thin Films for the Microfabrication of a Single-ship Material Libraries

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

Chapman, Christopher A. R.; Wang, Ling; Biener, Juergen

Single-chip material libraries of thin films of nanostructured materials are a promising approach for high throughput studies of structure-property relationship in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material of specific interest in both these fields. One attractive property of np-Au is its self-similar coarsening behavior by thermally induced surface diffusion. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Laser micromachining offers an attractive solution to this problemmore » by providing a means to apply energy with high spatial and temporal resolution. In our present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and supporting substrate thermal conductivity on the local np-Au film temperatures during photothermal annealing and subsequently investigate the mechanisms by which the np-Au network is coarsening. Our simulations predict that continuous-wave mode laser irradiation on a silicon supporting substrate supports the widest range of morphologies that can be created through the photothermal annealing of thin film np-Au. Using this result we successfully fabricate a single-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in increased throughput material interaction studies.« less

Precision Photothermal Annealing of Nanoporous Gold Thin Films for the Microfabrication of a Single-chip Material Libraries

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

Harris, C. D.; Shen, N.; Rubenchik, A.

2015-06-30

Single-chip material libraries of thin films of nanostructured materials are a promising approach for high throughput studies of structure-property relationship in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material of specific interest in both these fields. One attractive property of np-Au is its self-similar coarsening behavior by thermally induced surface diffusion. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Laser micromachining offers an attractive solution to this problemmore » by providing a means to apply energy with high spatial and temporal resolution. In the present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and supporting substrate thermal conductivity on the local np-Au film temperatures during photothermal annealing and subsequently investigate the mechanisms by which the np-Au network is coarsening. Our simulations predict that continuous-wave mode laser irradiation on a silicon supporting substrate supports the widest range of morphologies that can be created through the photothermal annealing of thin film np-Au. Using this result we successfully fabricate a single-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in increased throughput material interaction studies.« less

Engineering on-chip nanoporous gold material libraries via precision photothermal treatment [Precision Photothermal Annealing of Nanoporous Gold Thin Films for the Microfabrication of a Single-ship Material Libraries

DOE PAGES

Chapman, Christopher A. R.; Wang, Ling; Biener, Juergen; ...

2016-01-01

Single-chip material libraries of thin films of nanostructured materials are a promising approach for high throughput studies of structure-property relationship in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material of specific interest in both these fields. One attractive property of np-Au is its self-similar coarsening behavior by thermally induced surface diffusion. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Laser micromachining offers an attractive solution to this problemmore » by providing a means to apply energy with high spatial and temporal resolution. In our present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and supporting substrate thermal conductivity on the local np-Au film temperatures during photothermal annealing and subsequently investigate the mechanisms by which the np-Au network is coarsening. Our simulations predict that continuous-wave mode laser irradiation on a silicon supporting substrate supports the widest range of morphologies that can be created through the photothermal annealing of thin film np-Au. Using this result we successfully fabricate a single-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in increased throughput material interaction studies.« less

Self-assembly of multi-stranded RNA motifs into lattices and tubular structures

DOE PAGES

Stewart, Jaimie Marie; Subramanian, Hari K. K.; Franco, Elisa

2017-02-16

Rational design of nucleic acidmolecules yields selfassembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. We demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 m in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowlymore » annealed, and a one-pot transcription and anneal procedure. We then identify the tile nick position as a structural requirement for lattice formation. These results demonstrate that stable RNA structures can be obtained with design tools imported from DNA nanotechnology. These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components.« less

Self-assembly of multi-stranded RNA motifs into lattices and tubular structures

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

Stewart, Jaimie Marie; Subramanian, Hari K. K.; Franco, Elisa

Rational design of nucleic acidmolecules yields selfassembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. We demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 m in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowlymore » annealed, and a one-pot transcription and anneal procedure. We then identify the tile nick position as a structural requirement for lattice formation. These results demonstrate that stable RNA structures can be obtained with design tools imported from DNA nanotechnology. These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components.« less

Two-dimensional phase separated structures of block copolymers on solids

NASA Astrophysics Data System (ADS)

Sen, Mani; Jiang, Naisheng; Endoh, Maya; Koga, Tadanori; Ribbe, Alexander

The fundamental, yet unsolved question in block copolymer (BCP) thin films is the self-organization process of BCPs at the solid-polymer melt interface. We here focus on the self-organization processes of cylinder-forming polystyrene-block-poly (4-vinylpyridine) diblock copolymer and lamellar-forming poly (styrene-block-butadiene-block-styrene) triblock copolymer on Si substrates as model systems. In order to reveal the buried interfacial structures, the following experimental protocols were utilized: the BCP monolayer films were annealed under vacuum at T>Tg of the blocks (to equilibrate the melts); vitrification of the annealed BCP films via rapid quench to room temperature; subsequent intensive solvent leaching (to remove unadsorbed chains) with chloroform, a non-selective good solvent for the blocks. The strongly bound BCP layers were then characterized by using atomic force microscopy, scanning electron microscopy, grazing incidence small angle X-ray scattering, and X-ray reflectivity. The results showed that both blocks lie flat on the substrate, forming the two-dimensional, randomly phase-separated structure irrespective of their microdomain structures and interfacial energetics. Acknowledgement of financial support from NSF Grant (CMMI -1332499).

Self-assembly of multi-stranded RNA motifs into lattices and tubular structures

PubMed Central

Stewart, Jaimie Marie; Subramanian, Hari K. K.

2017-01-01

Abstract Rational design of nucleic acid molecules yields self-assembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. Here we demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 μm in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowly annealed, and a one-pot transcription and anneal procedure. We identify the tile nick position as a structural requirement for lattice formation. Our results demonstrate that stable RNA structures can be obtained with design tools imported from DNA nanotechnology. These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components. PMID:28204562

Generalizable, Electroless, Template-Assisted Synthesis and Electrocatalytic Mechanistic Understanding of Perovskite LaNiO 3 Nanorods as Viable, Supportless Oxygen Evolution Reaction Catalysts in Alkaline Media

DOE PAGES

McBean, Coray L.; Liu, Haiqing; Scofield, Megan E.; ...

2017-07-17

We present that the oxygen evolution reaction (OER) is a key reaction for water electrolysis cells and air-powered battery applications. However, conventional metal oxide catalysts, used for high-performing OER, tend to incorporate comparatively expensive and less abundant precious metals such as Ru and Ir, and, moreover, suffer from poor stability. To attempt to mitigate for all of these issues, we have prepared one-dimensional (1D) OER-active perovskite nanorods using a unique, simple, generalizable, and robust method. Significantly, our work demonstrates the feasibility of a novel electroless, seedless, surfactant-free, wet solution-based protocol for fabricating “high aspect ratio” LaNiO 3 and LaMnO 3more » nanostructures. As the main focus of our demonstration of principle, we prepared as-synthesized LaNiO 3 rods and correlated the various temperatures at which these materials were annealed with their resulting OER performance. In addition, we observed generally better OER performance for samples prepared with lower annealing temperatures. Specifically, when annealed at 600 °C, in the absence of a conventional conductive carbon support, our as-synthesized LaNiO 3 rods not only evinced (i) a reasonable level of activity toward OER but also displayed (ii) an improved stability, as demonstrated by chronoamperometric measurements, especially when compared with a control sample of commercially available (and more expensive) RuO 2.« less

The crystallization and crystalline properties of LARC-TPI

NASA Technical Reports Server (NTRS)

Theil, Michael H.; Gangal, Pravin D.

1992-01-01

LARC-TPI, a thermoplastic polyimide, has been studied in order to develop an understanding of its crystalline phase transition. Our experiments suggest that samples synthesized in different laboratories apparently had different degrees of imidization and their thermal behaviors differed accordingly. When the most crystalline of these polyimides was studied in some detail, we found that it melted irreversibly in that once a sample was completely melted it would not recrystallize. A polymer that did not recrystallize displayed a glass transition, which increased in temperature upon subsequent cooling and reheating. Solubility experiments indicated that heating above the crystalline melting temperature led to network formation in the polymer, a conclusion that is consistent with other behavior just mentioned. Differential calorimetric studies revealed that annealing at slow heating rates or under isothermal conditions resulted in dual melting transitions. These studies, supported by X-ray diffraction results, strongly indicate that the annealing process involves a solid-liquid-solid transformation. From an existing phenomenological model for the kinetics of phase transitions, kinetic parameters for these crystallizations have been evaluated. The Avrami exponents n increased with the annealing temperature in the protocol used in this study. Their values were about 2 or lower, thus indicating that crystallization may have followed a mechanism that included heterogeneous nucleation of a low dimensional order in which all the embryonic crystallites formed at the beginning of the process. A positive temperature coefficient for these crystallizations indicated that diffusion may have had a rate controlling influence and affected the values of n.

Diffusion behavior of Cu/Ta heterogeneous interface under high temperature and high strain: An atomistic investigation

NASA Astrophysics Data System (ADS)

Li, Ganglong; Wu, Houya; Luo, Honglong; Chen, Zhuo; Tay, Andrew A. O.; Zhu, Wenhui

2017-09-01

Three-dimensional (3D) integration technology using Cu interconnections has emerged as a promising solution to improve the performance of silicon microelectronic devices. However, Cu diffuses into SiO2 and requires a barrier layer such as Ta to ensure acceptable reliability. In this paper, the effects of temperature and strain normal to the interface on the inter-diffusion of Cu and Ta at annealing conditions are investigated using a molecular dynamics (MD) technique with embedded atomic method (EAM) potentials. Under thermal annealing conditions without strain, it is found that a Cu-rich diffusion region approximately 2 nm thick is formed at 1000 K after 10 ns of annealing. Ta is capable of diffusing into the interior of Cu but Cu hardly diffuses into the inner lattice of Ta. At the Cu side near the interface an amorphous structure is formed due to the process of diffusion. The diffusion activation energy of Cu and Ta are found to be 0.9769 and 0.586 eV, respectively. However, when a strain is applied, a large number of crystal defects are generated in the sample. As the strain is increased, extrinsic stacking faults (ESFs) and lots of Shockley partial dislocations appear. The density of the dislocations and the diffusion channels increase, promoting the diffusion of Cu atoms into the inner lattice of Ta. The thickness of the diffusion layer increases to 4 times the value when only a temperature load of 700 K is applied. The MD simulations demonstrated that Ta is very effective as a barrier layer under thermal loading only, and its effectiveness is impaired by tensile strain at the Cu/Ta interface. The simulations also clarified the mechanism that caused the impairment. The methodology and approach described in this paper can be followed further to study the effectiveness of barrier layers under various annealing and strain conditions, and to determine the minimum thickness of barrier layers required for a particular application.

Extremely high data-rate, reliable network systems research

NASA Technical Reports Server (NTRS)

Foudriat, E. C.; Maly, Kurt J.; Mukkamala, R.; Murray, Nicholas D.; Overstreet, C. Michael

1990-01-01

Significant progress was made over the year in the four focus areas of this research group: gigabit protocols, extensions of metropolitan protocols, parallel protocols, and distributed simulations. Two activities, a network management tool and the Carrier Sensed Multiple Access Collision Detection (CSMA/CD) protocol, have developed to the point that a patent is being applied for in the next year; a tool set for distributed simulation using the language SIMSCRIPT also has commercial potential and is to be further refined. The year's results for each of these areas are summarized and next year's activities are described.

Improved Modeling of Side-Chain–Base Interactions and Plasticity in Protein–DNA Interface Design

PubMed Central

Thyme, Summer B.; Baker, David; Bradley, Philip

2012-01-01

Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed “motifs”) was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein–DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent. PMID:22426128

Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules.

PubMed

Cornilescu, Gabriel; Ramos Alvarenga, René F; Wyche, Thomas P; Bugni, Tim S; Gil, Roberto R; Cornilescu, Claudia C; Westler, William M; Markley, John L; Schwieters, Charles D

2017-08-18

Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data). A unique configuration (for rigid molecules) or a very small number of configurations (for less rigid molecules) of the structural models having the lowest chiral angle energies and reasonable magnitudes of the alignment tensor are provided as the best predictions of the unknown configuration. For highly flexible molecules, the progressive locking of their stereocenters into their statistically dominant R or S state dramatically reduces the number of possible relative configurations. The result is verified by checking that the same configuration is obtained by initiating the locking from different regions of the molecule. For all molecules tested having known configurations (with conformations ranging from mostly rigid to highly flexible), the method accurately determined the correct configuration.

Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.

PubMed

Thyme, Summer B; Baker, David; Bradley, Philip

2012-06-08

Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed "motifs") was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein-DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent. Published by Elsevier Ltd.

A detailed dosimetric comparison between manual and inverse plans in HDR intracavitary/interstitial cervical cancer brachytherapy.

PubMed

Trnková, Petra; Baltas, Dimos; Karabis, Andreas; Stock, Markus; Dimopoulos, Johannes; Georg, Dietmar; Pötter, Richard; Kirisits, Christian

2010-12-01

The purpose of this study was to compare two inverse planning algorithms for cervical cancer brachytherapy and a conventional manual treatment planning according to the MUW (Medical University of Vienna) protocol. For 20 patients, manually optimized, and, inversely optimized treatment plans with Hybrid Inverse treatment Planning and Optimization (HIPO) and with Inverse Planning Simulated Annealing (IPSA) were created. Dosimetric parameters, absolute volumes of normal tissue receiving reference doses, absolute loading times of tandem, ring and interstitial needles, Paddick and COIN conformity indices were evaluated. HIPO was able to achieve a similar dose distribution to manual planning with the restriction of high dose regions. It reduced the loading time of needles and the overall treatment time. The values of both conformity indices were the lowest. IPSA was able to achieve acceptable dosimetric results. However, it overloaded the needles. This resulted in high dose regions located in the normal tissue. The Paddick index for the volume of two times prescribed dose was outstandingly low. HIPO can produce clinically acceptable treatment plans with the elimination of high dose regions in normal tissue. Compared to IPSA, it is an inverse optimization method which takes into account current clinical experience gained from manual treatment planning.

A detailed dosimetric comparison between manual and inverse plans in HDR intracavitary/interstitial cervical cancer brachytherapy

PubMed Central

Baltas, Dimos; Karabis, Andreas; Stock, Markus; Dimopoulos, Johannes; Georg, Dietmar; Pötter, Richard; Kirisits, Christian

2011-01-01

Purpose The purpose of this study was to compare two inverse planning algorithms for cervical cancer brachytherapy and a conventional manual treatment planning according to the MUW (Medical University of Vienna) protocol. Material and methods For 20 patients, manually optimized, and, inversely optimized treatment plans with Hybrid Inverse treatment Planning and Optimization (HIPO) and with Inverse Planning Simulated Annealing (IPSA) were created. Dosimetric parameters, absolute volumes of normal tissue receiving reference doses, absolute loading times of tandem, ring and interstitial needles, Paddick and COIN conformity indices were evaluated. Results HIPO was able to achieve a similar dose distribution to manual planning with the restriction of high dose regions. It reduced the loading time of needles and the overall treatment time. The values of both conformity indices were the lowest. IPSA was able to achieve acceptable dosimetric results. However, it overloaded the needles. This resulted in high dose regions located in the normal tissue. The Paddick index for the volume of two times prescribed dose was outstandingly low. Conclusions HIPO can produce clinically acceptable treatment plans with the elimination of high dose regions in normal tissue. Compared to IPSA, it is an inverse optimization method which takes into account current clinical experience gained from manual treatment planning. PMID:27853479

Solar Flare Prediction Science-to-Operations: the ESA/SSA SWE A-EFFort Service

NASA Astrophysics Data System (ADS)

Georgoulis, Manolis K.; Tziotziou, Konstantinos; Themelis, Konstantinos; Magiati, Margarita; Angelopoulou, Georgia

2016-07-01

We attempt a synoptical overview of the scientific origins of the Athens Effective Solar Flare Forecasting (A-EFFort) utility and the actions taken toward transitioning it into a pre-operational service of ESA's Space Situational Awareness (SSA) Programme. The preferred method for solar flare prediction, as well as key efforts to make it function in a fully automated environment by coupling calculations with near-realtime data-downloading protocols (from the Solar Dynamics Observatory [SDO] mission), pattern recognition (solar active-region identification) and optimization (magnetic connectivity by simulated annealing) will be highlighted. In addition, the entire validation process of the service will be described, with its results presented. We will conclude by stressing the need for across-the-board efforts and synergistic work in order to bring science of potentially limited/restricted interest into realizing a much broader impact and serving the best public interests. The above presentation was partially supported by the ESA/SSA SWE A-EFFort project, ESA Contract No. 4000111994/14/D/MRP. Special thanks go to the ESA Project Officers R. Keil, A. Glover, and J.-P. Luntama (ESOC), M. Bobra and C. Balmer of the SDO/HMI team at Stanford University, and M. Zoulias at the RCAAM of the Academy of Athens for valuable technical help.

Punctuated equilibrium as an emergent process and its modified thermodynamic characterization.

PubMed

Wosniack, M E; da Luz, M G E; Schulman, L S

2017-01-07

We address evolutionary dynamics and consider under which conditions the ecosystem interaction network allows punctuated equilibrium (i.e., alternation between hectic and quasi-stable phases). We focus on the links connecting various species and on the strength and sign of those links. For this study we consider the Tangled Nature model, which allows considerable flexibility and plasticity in the analysis of interspecies interactions. We find that it is necessary to have a proper balance of connectivity and interaction intensities so as to establish the kind of mutual cooperation and competition found in nature. It suggests evolutionary punctuated equilibrium as an emergent process, thus displaying features of complex systems. To explicitly demonstrate this fact we consider an extended form of thermodynamics, defining (for the present context) relevant out-of-equilibrium "collective" functions. We then show how to characterize the punctuated equilibrium through entropy-like and free energy-like quantities. Finally, from a close analogy to thermodynamic systems, we propose a protocol similar to simulated annealing. It is based on controlling the species' rate of mutation during the hectic periods, in this way enhancing the exploration of the genome space (similar to the known behavior of bacteria in stressful environments). This allows the system to more rapidly converge to long-duration quasi-stable phases. Copyright © 2016 Elsevier Ltd. All rights reserved.

Overall Traveling-Wave-Tube Efficiency Improved By Optimized Multistage Depressed Collector Design

NASA Technical Reports Server (NTRS)

Vaden, Karl R.

2002-01-01

Depressed Collector Design The microwave traveling wave tube (TWT) is used widely for space communications and high-power airborne transmitting sources. One of the most important features in designing a TWT is overall efficiency. Yet, overall TWT efficiency is strongly dependent on the efficiency of the electron beam collector, particularly for high values of collector efficiency. For these reasons, the NASA Glenn Research Center developed an optimization algorithm based on simulated annealing to quickly design highly efficient multistage depressed collectors (MDC's). Simulated annealing is a strategy for solving highly nonlinear combinatorial optimization problems. Its major advantage over other methods is its ability to avoid becoming trapped in local minima. Simulated annealing is based on an analogy to statistical thermodynamics, specifically the physical process of annealing: heating a material to a temperature that permits many atomic rearrangements and then cooling it carefully and slowly, until it freezes into a strong, minimum-energy crystalline structure. This minimum energy crystal corresponds to the optimal solution of a mathematical optimization problem. The TWT used as a baseline for optimization was the 32-GHz, 10-W, helical TWT developed for the Cassini mission to Saturn. The method of collector analysis and design used was a 2-1/2-dimensional computational procedure that employs two types of codes, a large signal analysis code and an electron trajectory code. The large signal analysis code produces the spatial, energetic, and temporal distributions of the spent beam entering the MDC. An electron trajectory code uses the resultant data to perform the actual collector analysis. The MDC was optimized for maximum MDC efficiency and minimum final kinetic energy of all collected electrons (to reduce heat transfer). The preceding figure shows the geometric and electrical configuration of an optimized collector with an efficiency of 93.8 percent. The results show the improvement in collector efficiency from 89.7 to 93.8 percent, resulting in an increase of three overall efficiency points. In addition, the time to design a highly efficient MDC was reduced from a month to a few days. All work was done in-house at Glenn for the High Rate Data Delivery Program. Future plans include optimizing the MDC and TWT interaction circuit in tandem to further improve overall TWT efficiency.

Analysis of MD5 authentication in various routing protocols using simulation tools

NASA Astrophysics Data System (ADS)

Dinakaran, M.; Darshan, K. N.; Patel, Harsh

2017-11-01

Authentication being an important paradigm of security and Computer Networks require secure paths to make the flow of the data even more secure through some security protocols. So MD-5(Message Digest 5) helps in providing data integrity to the data being sent through it and authentication to the network devices. This paper gives a brief introduction to the MD-5, simulation of the networks by including MD-5 authentication using various routing protocols like OSPF, EIGRP and RIPv2. GNS3 is being used to simulate the scenarios. Analysis of the MD-5 authentication is done in the later sections of the paper.

Laboratory simulations of thermal annealing in proto-planetary discs - II. Crystallization of enstatite from amorphous thin films

NASA Astrophysics Data System (ADS)

Droeger, J.; Burchard, M.; Lattard, D.

2011-12-01

Amorphous silicates of olivine and pyroxene composition are thought to be common constituents of circumstellar, interstellar, and interplanetary dust. In proto-planetary discs amorphous dust crystallize essentially as a result of thermal annealing. The present project aims at deciphering the kinetics of crystallization pyroxene in proto-planetary dust on the basis of experiments on amorphous thin films. The thin films are deposited on Si-wafers (111) by pulsed laser deposition (PLD). The thin films are completely amorphous, chemically homogeneous (on the MgSiO3 composition) and with a continuous and flat surface. They are subsequently annealed for 1 to 216 h at 1073K and 1098K in a vertical quench furnace and drop-quenched on a copper block. To monitor the progress of crystallization, the samples are characterized by AFM and SEM imaging and IR spectroscopy. After short annealing durations (1 to 12 h) AFM and SE imaging reveal small shallow polygonal features (diameter 0.5-1 μm; height 2-3 nm) evenly distributed at the otherwise flat surface of the thin films. These shallow features are no longer visible after about 3 h at 1098 K, resp. >12 h at 1073 K. Meanwhile, two further types of features appear small protruding pyramids and slightly depressed spherolites. The orders of appearance of these features depend on temperature, but both persist and steadily grow with increasing annealing duration. Their sizes can reach about 12 μm. From TEM investigations on annealed thin films on the Mg2SiO4 composition we know that these features represent crystalline sites, which can be surrounded by a still amorphous matrix (Oehm et al. 2010). A quantitative evaluation of the size of the features will give insights on the progress of crystallization. IR spectra of the unprocessed thin films show only broad bands. In contrast, bands characteristic of crystalline enstatite are clearly recognizable in annealed samples, e.g. after 12 h at 1078 K. Small bands can also be assigned to crystalline forsterite. Compared to the findings of Murata et al. (2009), our preliminary results point to smaller crystallization rates of enstatite from amorphous precursors.

Quantifying the nonlocality of Greenberger-Horne-Zeilinger quantum correlations by a bounded communication simulation protocol.

PubMed

Branciard, Cyril; Gisin, Nicolas

2011-07-08

The simulation of quantum correlations with finite nonlocal resources, such as classical communication, gives a natural way to quantify their nonlocality. While multipartite nonlocal correlations appear to be useful resources, very little is known on how to simulate multipartite quantum correlations. We present a protocol that reproduces tripartite Greenberger-Horne-Zeilinger correlations with bounded communication: 3 bits in total turn out to be sufficient to simulate all equatorial Von Neumann measurements on the tripartite Greenberger-Horne-Zeilinger state.

An adaptive transmission protocol for managing dynamic shared states in collaborative surgical simulation.

PubMed

Qin, J; Choi, K S; Ho, Simon S M; Heng, P A

2008-01-01

A force prediction algorithm is proposed to facilitate virtual-reality (VR) based collaborative surgical simulation by reducing the effect of network latencies. State regeneration is used to correct the estimated prediction. This algorithm is incorporated into an adaptive transmission protocol in which auxiliary features such as view synchronization and coupling control are equipped to ensure the system consistency. We implemented this protocol using multi-threaded technique on a cluster-based network architecture.

Safe bunker designing for the 18 MV Varian 2100 Clinac: a comparison between Monte Carlo simulation based upon data and new protocol recommendations.

PubMed

Beigi, Manije; Afarande, Fatemeh; Ghiasi, Hosein

2016-01-01

The aim of this study was to compare two bunkers designed by only protocols recommendations and Monte Carlo (MC) based upon data derived for an 18 MV Varian 2100Clinac accelerator. High energy radiation therapy is associated with fast and thermal photoneutrons. Adequate shielding against the contaminant neutron has been recommended by IAEA and NCRP new protocols. The latest protocols released by the IAEA (safety report No. 47) and NCRP report No. 151 were used for the bunker designing calculations. MC method based upon data was also derived. Two bunkers using protocols and MC upon data were designed and discussed. From designed door's thickness, the door designed by the MC simulation and Wu-McGinley analytical method was closer in both BPE and lead thickness. In the case of the primary and secondary barriers, MC simulation resulted in 440.11 mm for the ordinary concrete, total concrete thickness of 1709 mm was required. Calculating the same parameters value with the recommended analytical methods resulted in 1762 mm for the required thickness using 445 mm as recommended by TVL for the concrete. Additionally, for the secondary barrier the thickness of 752.05 mm was obtained. Our results showed MC simulation and the followed protocols recommendations in dose calculation are in good agreement in the radiation contamination dose calculation. Difference between the two analytical and MC simulation methods revealed that the application of only one method for the bunker design may lead to underestimation or overestimation in dose and shielding calculations.

Simulation Modeling and Performance Evaluation of Space Networks

NASA Technical Reports Server (NTRS)

Jennings, Esther H.; Segui, John

2006-01-01

In space exploration missions, the coordinated use of spacecraft as communication relays increases the efficiency of the endeavors. To conduct trade-off studies of the performance and resource usage of different communication protocols and network designs, JPL designed a comprehensive extendable tool, the Multi-mission Advanced Communications Hybrid Environment for Test and Evaluation (MACHETE). The design and development of MACHETE began in 2000 and is constantly evolving. Currently, MACHETE contains Consultative Committee for Space Data Systems (CCSDS) protocol standards such as Proximity-1, Advanced Orbiting Systems (AOS), Packet Telemetry/Telecommand, Space Communications Protocol Specification (SCPS), and the CCSDS File Delivery Protocol (CFDP). MACHETE uses the Aerospace Corporation s Satellite Orbital Analysis Program (SOAP) to generate the orbital geometry information and contact opportunities. Matlab scripts provide the link characteristics. At the core of MACHETE is a discrete event simulator, QualNet. Delay Tolerant Networking (DTN) is an end-to-end architecture providing communication in and/or through highly stressed networking environments. Stressed networking environments include those with intermittent connectivity, large and/or variable delays, and high bit error rates. To provide its services, the DTN protocols reside at the application layer of the constituent internets, forming a store-and-forward overlay network. The key capabilities of the bundling protocols include custody-based reliability, ability to cope with intermittent connectivity, ability to take advantage of scheduled and opportunistic connectivity, and late binding of names to addresses. In this presentation, we report on the addition of MACHETE models needed to support DTN, namely: the Bundle Protocol (BP) model. To illustrate the use of MACHETE with the additional DTN model, we provide an example simulation to benchmark its performance. We demonstrate the use of the DTN protocol and discuss statistics gathered concerning the total time needed to simulate numerous bundle transmissions

Finite-key security analyses on passive decoy-state QKD protocols with different unstable sources.

PubMed

Song, Ting-Ting; Qin, Su-Juan; Wen, Qiao-Yan; Wang, Yu-Kun; Jia, Heng-Yue

2015-10-16

In quantum communication, passive decoy-state QKD protocols can eliminate many side channels, but the protocols without any finite-key analyses are not suitable for in practice. The finite-key securities of passive decoy-state (PDS) QKD protocols with two different unstable sources, type-II parametric down-convention (PDC) and phase randomized weak coherent pulses (WCPs), are analyzed in our paper. According to the PDS QKD protocols, we establish an optimizing programming respectively and obtain the lower bounds of finite-key rates. Under some reasonable values of quantum setup parameters, the lower bounds of finite-key rates are simulated. The simulation results show that at different transmission distances, the affections of different fluctuations on key rates are different. Moreover, the PDS QKD protocol with an unstable PDC source can resist more intensity fluctuations and more statistical fluctuation.

Atomistic Simulations of Grain Boundary Pinning in CuFe Alloys

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

Zepeda-Ruiz, L A; Gilmer, G H; Sadigh, B

2005-05-22

The authors apply a hybrid Monte Carlo-molecular dynamics code to the study of grain boundary motion upon annealing of pure Cu and Cu with low concentrations of Fe. The hybrid simulations account for segregation and precipitation of the low solubility Fe, together with curvature driven grain boundary motion. Grain boundaries in two different systems, a {Sigma}7+U-shaped half-loop grain and a nanocrystalline sample, were found to be pinned in the presence of Fe concentrations exceeding 3%.

On the Critical Behaviour, Crossover Point and Complexity of the Exact Cover Problem

NASA Technical Reports Server (NTRS)

Morris, Robin D.; Smelyanskiy, Vadim N.; Shumow, Daniel; Koga, Dennis (Technical Monitor)

2003-01-01

Research into quantum algorithms for NP-complete problems has rekindled interest in the detailed study a broad class of combinatorial problems. A recent paper applied the quantum adiabatic evolution algorithm to the Exact Cover problem for 3-sets (EC3), and provided an empirical evidence that the algorithm was polynomial. In this paper we provide a detailed study of the characteristics of the exact cover problem. We present the annealing approximation applied to EC3, which gives an over-estimate of the phase transition point. We also identify empirically the phase transition point. We also study the complexity of two classical algorithms on this problem: Davis-Putnam and Simulated Annealing. For these algorithms, EC3 is significantly easier than 3-SAT.

Angular filter refractometry analysis using simulated annealing.

PubMed

Angland, P; Haberberger, D; Ivancic, S T; Froula, D H

2017-10-01

Angular filter refractometry (AFR) is a novel technique used to characterize the density profiles of laser-produced, long-scale-length plasmas [Haberberger et al., Phys. Plasmas 21, 056304 (2014)]. A new method of analysis for AFR images was developed using an annealing algorithm to iteratively converge upon a solution. A synthetic AFR image is constructed by a user-defined density profile described by eight parameters, and the algorithm systematically alters the parameters until the comparison is optimized. The optimization and statistical uncertainty calculation is based on the minimization of the χ 2 test statistic. The algorithm was successfully applied to experimental data of plasma expanding from a flat, laser-irradiated target, resulting in an average uncertainty in the density profile of 5%-20% in the region of interest.

Code Samples Used for Complexity and Control

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir G.; Reid, Darryn J.

2015-11-01

The following sections are included: * MathematicaⓇ Code * Generic Chaotic Simulator * Vector Differential Operators * NLS Explorer * 2C++ Code * C++ Lambda Functions for Real Calculus * Accelerometer Data Processor * Simple Predictor-Corrector Integrator * Solving the BVP with the Shooting Method * Linear Hyperbolic PDE Solver * Linear Elliptic PDE Solver * Method of Lines for a Set of the NLS Equations * C# Code * Iterative Equation Solver * Simulated Annealing: A Function Minimum * Simple Nonlinear Dynamics * Nonlinear Pendulum Simulator * Lagrangian Dynamics Simulator * Complex-Valued Crowd Attractor Dynamics * Freeform Fortran Code * Lorenz Attractor Simulator * Complex Lorenz Attractor * Simple SGE Soliton * Complex Signal Presentation * Gaussian Wave Packet * Hermitian Matrices * Euclidean L2-Norm * Vector/Matrix Operations * Plain C-Code: Levenberg-Marquardt Optimizer * Free Basic Code: 2D Crowd Dynamics with 3000 Agents

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

Kasemer, Matthew; Quey, Romain; Dawson, Paul

Discussed is a computational study of the influence of the microstructure’s geometric morphology on the yield strength and ductility of Ti-6Al-4V. Uniaxial tension tests were conducted on physical specimens to determine the macroscopic yield strength and ductility of two microstructural variations (mill annealed and β annealed) to establish comparisons of macroscopic properties. A multi-experimental approach was utilized to gather two dimensional and three dimensional data, which were used to inform the construction of representative β annealed polycrystals. A highly parallelized crystal plasticity finite element framework was employed to model the deformation response of the generated polycrystals subjected to uniaxial tension.more » To gauge the macroscopic response’s sensitivity to the morphology of the geometry, the key geometrical features - namely the number of high temperature β phase grains, α phase colonies, and size of remnant secondary β phase lamellae - were altered systematically in a suite of simulations. Both single phase and dual phase aggregates were studied. Presented are the calculated yield strengths and ductilities, and the resulting trends as functions of geometric parameters are examined in light of the heterogeneity in deformation at the crystal scale.« less

Design and development of multilayer wideband antireflection coating and its annealing study

NASA Astrophysics Data System (ADS)

Jena, S.; Tokas, R. B.; Udupa, D. V.; Thakur, S.; Sahoo, N. K.

2018-04-01

Reflection loss occurs at the glass-air interface, limits performance of many optical devices such as eyeglass, camera lenses, and photovoltaic solar cells. Antireflection (AR) coating on the glass reduces the reflection loss and improves efficiency of such devices. In this paper, wideband AR coating in the visible region has been designed and developed using ZrO2-MgO/SiO2 multilayer. The thicknesses of individual thin layers are numerically optimized to get maximum transmission of the visible light. The optimized four thin layers have been deposited on BK7 glass substrate using electron beam evaporation technique. The measured transmission spectrum of the 4-layer AR coating is compared with that of simulated spectrum. The transmission of the single side AR coating increases by more than 3% as compared to that of bare glass substrate in the wavelength region of 470 nm - 810 nm. The wideband AR coating has been annealed at 200°C for 4 hours in ambient condition. The transmission of the AR coating decreases after the annealing, resulting degradation in its wideband AR characteristics.

Detection of deep-level defects and reduced carrier concentration in Mg-ion-implanted GaN before high-temperature annealing

NASA Astrophysics Data System (ADS)

Akazawa, Masamichi; Yokota, Naoshige; Uetake, Kei

2018-02-01

We report experimental results for the detection of deep-level defects in GaN after Mg ion implantation before high-temperature annealing. The n-type GaN samples were grown on GaN free-standing substrates by metalorganic vapor phase epitaxy. Mg ions were implanted at 50 keV with a small dosage of 1.5×1011 cm-2, which did not change the conduction type of the n-GaN. By depositing Al2O3 and a Ni/Au electrode onto the implanted n-GaN, metal-oxide-semiconductor (MOS) diodes were fabricated and tested. The measured capacitance-voltage (C-V) characteristics showed a particular behavior with a plateau region and a region with an anomalously steep slope. Fitting to the experimental C-V curves by simulation showed the existence of deep-level defects and a reduction of the carrier concentration near the GaN surface. By annealing at 800oC, the density of the deep-level defects was reduced and the carrier concentration partially recovered.

Reduction of Defects on Microstructure Aluminium Nitride Using High Temperature Annealing Heat Treatment

NASA Astrophysics Data System (ADS)

Tanasta, Z.; Muhamad, P.; Kuwano, N.; Norfazrina, H. M. Y.; Unuh, M. H.

2018-03-01

Aluminium Nitride (AlN) is a ceramic 111-nitride material that is used widely as components in functional devices. Besides good thermal conductivity, it also has a high band gap in emitting light which is 6 eV. AlN thin film is grown on the sapphire substrate (0001). However, lattice mismatch between both materials has caused defects to exist along the microstructure of AlN thin films. The defects have affected the properties of Aluminium Nitride. Annealing heat treatment has been proved by the previous researcher to be the best method to improve the microstructure of Aluminium Nitride thin films. Hence, this method is applied at four different temperatures for two hour. The changes of Aluminium Nitride microstructures before and after annealing is observed using Transmission Electron Microscope. It is observed that inversion domains start to occur at temperature of 1500 °C. Convergent Beam Electron Diffraction pattern simulation has confirmed the defects as inversion domain. Therefore, this paper is about to extract the matters occurred during the process of producing high quality Aluminium Nitride thin films and the ways to overcome this problem.

Phase separation in SiGe nanocrystals embedded in SiO{sub 2} matrix during high temperature annealing

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

Mogaddam, N. A. P.; Turan, R.; Alagoz, A. S.

2008-12-15

SiGe nanocrystals have been formed in SiO{sub 2} matrix by cosputtering Si, Ge, and SiO{sub 2} independently on Si substrate. Effects of the annealing time and temperature on structural and compositional properties are studied by transmission electron microscopy, x-ray diffraction (XRD), and Raman spectroscopy measurements. It is observed that Ge-rich Si{sub (1-x)}Ge{sub x} nanocrystals do not hold their compositional uniformity when annealed at high temperatures for enough long time. A segregation process leading to separation of Ge and Si atoms from each other takes place. This process has been evidenced by a double peak formation in the XRD and Ramanmore » spectra. We attributed this phase separation to the differences in atomic size, surface energy, and surface diffusion disparity between Si and Ge atoms leading to the formation of nonhomogenous structure consist of a Si-rich SiGe core covered by a Ge-rich SiGe shell. This experimental observation is consistent with the result of reported theoretical and simulation methods.« less

Multichannel Interdiffusion Driven FASnI3 Film Formation Using Aqueous Hybrid Salt/Polymer Solutions toward Flexible Lead-Free Perovskite Solar Cells.

PubMed

Xi, Jun; Wu, Zhaoxin; Jiao, Bo; Dong, Hua; Ran, Chenxin; Piao, Chengcheng; Lei, Ting; Song, Tze-Bin; Ke, Weijun; Yokoyama, Takamichi; Hou, Xun; Kanatzidis, Mercouri G

2017-06-01

Tin (Sn)-based perovskites are increasingly attractive because they offer lead-free alternatives in perovskite solar cells. However, depositing high-quality Sn-based perovskite films is still a challenge, particularly for low-temperature planar heterojunction (PHJ) devices. Here, a "multichannel interdiffusion" protocol is demonstrated by annealing stacked layers of aqueous solution deposited formamidinium iodide (FAI)/polymer layer followed with an evaporated SnI 2 layer to create uniform FASnI 3 films. In this protocol, tiny FAI crystals, significantly inhibited by the introduced polymer, can offer multiple interdiffusion pathways for complete reaction with SnI 2 . What is more, water, rather than traditional aprotic organic solvents, is used to dissolve the precursors. The best-performing FASnI 3 PHJ solar cell assembled by this protocol exhibits a power conversion efficiency (PCE) of 3.98%. In addition, a flexible FASnI 3 -based flexible solar cell assembled on a polyethylene naphthalate-indium tin oxide flexible substrate with a PCE of 3.12% is demonstrated. This novel interdiffusion process can help to further boost the performance of lead-free Sn-based perovskites. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the passive and semiconducting behavior of severely deformed pure titanium in Ringer's physiological solution at 37°C: A trial of the point defect model.

PubMed

Ansari, Ghazaleh; Fattah-Alhosseini, Arash

2017-06-01

The effects of sever plastic deformation through multi-pass accumulative roll bonding on the passive and semiconducting behavior of pure titanium is evaluated in Ringer's physiological solution at 37°C in the present paper. Produced results by polarization plots and electrochemical impedance spectroscopy measurements revealed a significant advance in the passive response of the nano-grained sample compared to that of the annealed pure titanium. Also, Mott-Schottky test results of the nano-grained pure titanium represented a lower donor density and reduced flat-band potential in the formed passive film in comparison with the annealed sample. Moreover, based on the Mott-Schottky analysis in conjunction with the point defect model, it was suggested that with increase in formation potential, the calculated donor density of both annealed and nano-grained samples decreases exponentially and the thickness of the passive film linearly increases. These observations were consistent with the point defect model predictions, considering that the point defects within the passive film are metal interstitials, oxygen vacancies, or both. From the viewpoint of passive and semiconducting behavior, nano-grained pure titanium appeared to be more suitable for implant applications in simulate human body environment compared to annealed pure titanium. Copyright © 2017 Elsevier B.V. All rights reserved.

Amorphous Carbon Nanospheres

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

None

Amorphous carbon nanosphere used as the anode material for Li-intercalation in Lithium-ion energy storage. This structure was obtained through a thermal annealing process at a temperature of 3000 degree Kelvin, simulated using the LAMMPS molecular dynamics code on the LCRC Fusion resource. Science: Kah Chun Lau and Larry Curtiss Visualization: Aaron Knoll, Mark Hereld and Michael E. Papka

Assignment Of Finite Elements To Parallel Processors

NASA Technical Reports Server (NTRS)

Salama, Moktar A.; Flower, Jon W.; Otto, Steve W.

1990-01-01

Elements assigned approximately optimally to subdomains. Mapping algorithm based on simulated-annealing concept used to minimize approximate time required to perform finite-element computation on hypercube computer or other network of parallel data processors. Mapping algorithm needed when shape of domain complicated or otherwise not obvious what allocation of elements to subdomains minimizes cost of computation.

Exemplar-Based Clustering via Simulated Annealing

ERIC Educational Resources Information Center

Brusco, Michael J.; Kohn, Hans-Friedrich

2009-01-01

Several authors have touted the p-median model as a plausible alternative to within-cluster sums of squares (i.e., K-means) partitioning. Purported advantages of the p-median model include the provision of "exemplars" as cluster centers, robustness with respect to outliers, and the accommodation of a diverse range of similarity data. We developed…

Influence of GaAs substrate properties on the congruent evaporation temperature

NASA Astrophysics Data System (ADS)

Spirina, A. A.; Nastovjak, A. G.; Shwartz, N. L.

2018-03-01

High-temperature annealing of GaAs(111)A and GaAs(111)B substrates under Langmuir evaporation conditions was studied using Monte Carlo simulation. The maximal value of the congruent evaporation temperature was estimated. The congruent evaporation temperature was demonstrated to be dependent on the surface orientation and concentration of surface defects.

Simulation-based Randomized Comparative Assessment of Out-of-Hospital Cardiac Arrest Resuscitation Bundle Completion by Emergency Medical Service Teams Using Standard Life Support or an Experimental Automation-assisted Approach.

PubMed

Choi, Bryan; Asselin, Nicholas; Pettit, Catherine C; Dannecker, Max; Machan, Jason T; Merck, Derek L; Merck, Lisa H; Suner, Selim; Williams, Kenneth A; Jay, Gregory D; Kobayashi, Leo

2016-12-01

Effective resuscitation of out-of-hospital cardiac arrest (OHCA) patients is challenging. Alternative resuscitative approaches using electromechanical adjuncts may improve provider performance. Investigators applied simulation to study the effect of an experimental automation-assisted, goal-directed OHCA management protocol on EMS providers' resuscitation performance relative to standard protocols and equipment. Two-provider (emergency medical technicians (EMT)-B and EMT-I/C/P) teams were randomized to control or experimental group. Each team engaged in 3 simulations: baseline simulation (standard roles); repeat simulation (standard roles); and abbreviated repeat simulation (reversed roles, i.e., basic life support provider performing ALS tasks). Control teams used standard OHCA protocols and equipment (with high-performance cardiopulmonary resuscitation training intervention); for second and third simulations, experimental teams performed chest compression, defibrillation, airway, pulmonary ventilation, vascular access, medication, and transport tasks with goal-directed protocol and resuscitation-automating devices. Videorecorders and simulator logs collected resuscitation data. Ten control and 10 experimental teams comprised 20 EMT-B's; 1 EMT-I, 8 EMT-C's, and 11 EMT-P's; study groups were not fully matched. Both groups suboptimally performed chest compressions and ventilations at baseline. For their second simulations, control teams performed similarly except for reduced on-scene time, and experimental teams improved their chest compressions (P=0.03), pulmonary ventilations (P<0.01), and medication administration (P=0.02); changes in their performance of chest compression, defibrillation, airway, and transport tasks did not attain significance against control teams' changes. Experimental teams maintained performance improvements during reversed-role simulations. Simulation-based investigation into OHCA resuscitation revealed considerable variability and improvable deficiencies in small EMS teams. Goal-directed, automation-assisted OHCA management augmented select resuscitation bundle element performance without comprehensive improvement.

Combined Simulated Annealing and Genetic Algorithm Approach to Bus Network Design

NASA Astrophysics Data System (ADS)

Liu, Li; Olszewski, Piotr; Goh, Pong-Chai

A new method - combined simulated annealing (SA) and genetic algorithm (GA) approach is proposed to solve the problem of bus route design and frequency setting for a given road network with fixed bus stop locations and fixed travel demand. The method involves two steps: a set of candidate routes is generated first and then the best subset of these routes is selected by the combined SA and GA procedure. SA is the main process to search for a better solution to minimize the total system cost, comprising user and operator costs. GA is used as a sub-process to generate new solutions. Bus demand assignment on two alternative paths is performed at the solution evaluation stage. The method was implemented on four theoretical grid networks of different size and a benchmark network. Several GA operators (crossover and mutation) were utilized and tested for their effectiveness. The results show that the proposed method can efficiently converge to the optimal solution on a small network but computation time increases significantly with network size. The method can also be used for other transport operation management problems.

Optimal design of minimum mean-square error noise reduction algorithms using the simulated annealing technique.

PubMed

Bai, Mingsian R; Hsieh, Ping-Ju; Hur, Kur-Nan

2009-02-01

The performance of the minimum mean-square error noise reduction (MMSE-NR) algorithm in conjunction with time-recursive averaging (TRA) for noise estimation is found to be very sensitive to the choice of two recursion parameters. To address this problem in a more systematic manner, this paper proposes an optimization method to efficiently search the optimal parameters of the MMSE-TRA-NR algorithms. The objective function is based on a regression model, whereas the optimization process is carried out with the simulated annealing algorithm that is well suited for problems with many local optima. Another NR algorithm proposed in the paper employs linear prediction coding as a preprocessor for extracting the correlated portion of human speech. Objective and subjective tests were undertaken to compare the optimized MMSE-TRA-NR algorithm with several conventional NR algorithms. The results of subjective tests were processed by using analysis of variance to justify the statistic significance. A post hoc test, Tukey's Honestly Significant Difference, was conducted to further assess the pairwise difference between the NR algorithms.

An adaptive evolutionary multi-objective approach based on simulated annealing.

PubMed

Li, H; Landa-Silva, D

2011-01-01

A multi-objective optimization problem can be solved by decomposing it into one or more single objective subproblems in some multi-objective metaheuristic algorithms. Each subproblem corresponds to one weighted aggregation function. For example, MOEA/D is an evolutionary multi-objective optimization (EMO) algorithm that attempts to optimize multiple subproblems simultaneously by evolving a population of solutions. However, the performance of MOEA/D highly depends on the initial setting and diversity of the weight vectors. In this paper, we present an improved version of MOEA/D, called EMOSA, which incorporates an advanced local search technique (simulated annealing) and adapts the search directions (weight vectors) corresponding to various subproblems. In EMOSA, the weight vector of each subproblem is adaptively modified at the lowest temperature in order to diversify the search toward the unexplored parts of the Pareto-optimal front. Our computational results show that EMOSA outperforms six other well established multi-objective metaheuristic algorithms on both the (constrained) multi-objective knapsack problem and the (unconstrained) multi-objective traveling salesman problem. Moreover, the effects of the main algorithmic components and parameter sensitivities on the search performance of EMOSA are experimentally investigated.

Reaction of amorphous/crystalline SiOC/Fe interfaces by thermal annealing

DOE PAGES

Su, Qing; Zhernenkov, Mikhail; Ding, Hepeng; ...

2017-06-12

The development of revolutionary new alloys and composites is crucial to meeting materials requirements for next generation nuclear reactors. The newly developed amorphous silicon oxycarbide (SiOC) and crystalline Fe composite system has shown radiation tolerance over a wide range of temperatures. To advance understanding of this new composite, we investigate the structure and thermal stability of the interface between amorphous SiOC and crystalline Fe by combining various experimental techniques and simulation methods. We show that the SiOC/Fe interface is thermally stable up to at least 400 °C. When the annealing temperature reaches 600 °C, an intermixed region forms at thismore » interface. This region appears to be a crystalline phase that forms an incoherent interface with the Fe layer. Density functional theory (DFT) Molecular dynamics (MD) is performed on the homogeneous SiFeOC phase to study the early stages of 2 formation of the intermixed layer. Both experimental and simulation results suggest this phase has the fayalite crystal structure. As a result, the physical processes involved in the formation of the intermixed region are discussed.« less

Stochastic and Deterministic Crystal Structure Solution Methods in GSAS-II: Monte Carlo/Simulated Annealing Versus Charge Flipping

DOE PAGES

Von Dreele, Robert

2017-08-29

One of the goals in developing GSAS-II was to expand from the capabilities of the original General Structure Analysis System (GSAS) which largely encompassed just structure refinement and post refinement analysis. GSAS-II has been written almost entirely in Python loaded with graphics, GUI and mathematical packages (matplotlib, pyOpenGL, wxpython, numpy and scipy). Thus, GSAS-II has a fully developed modern GUI as well as extensive graphical display of data and results. However, the structure and operation of Python has required new approaches to many of the algorithms used in crystal structure analysis. The extensions beyond GSAS include image calibration/integration as wellmore » as peak fitting and unit cell indexing for powder data which are precursors for structure solution. Structure solution within GSAS-II begins with either Pawley or LeBail extracted structure factors from powder data or those measured in a single crystal experiment. Both charge flipping and Monte Carlo-Simulated Annealing techniques are available; the former can be applied to (3+1) incommensurate structures as well as conventional 3D structures.« less

Optoelectronic analogs of self-programming neural nets - Architecture and methodologies for implementing fast stochastic learning by simulated annealing

NASA Technical Reports Server (NTRS)

Farhat, Nabil H.

1987-01-01

Self-organization and learning is a distinctive feature of neural nets and processors that sets them apart from conventional approaches to signal processing. It leads to self-programmability which alleviates the problem of programming complexity in artificial neural nets. In this paper architectures for partitioning an optoelectronic analog of a neural net into distinct layers with prescribed interconnectivity pattern to enable stochastic learning by simulated annealing in the context of a Boltzmann machine are presented. Stochastic learning is of interest because of its relevance to the role of noise in biological neural nets. Practical considerations and methodologies for appreciably accelerating stochastic learning in such a multilayered net are described. These include the use of parallel optical computing of the global energy of the net, the use of fast nonvolatile programmable spatial light modulators to realize fast plasticity, optical generation of random number arrays, and an adaptive noisy thresholding scheme that also makes stochastic learning more biologically plausible. The findings reported predict optoelectronic chips that can be used in the realization of optical learning machines.

Stochastic Evolutionary Algorithms for Planning Robot Paths

NASA Technical Reports Server (NTRS)

Fink, Wolfgang; Aghazarian, Hrand; Huntsberger, Terrance; Terrile, Richard

2006-01-01

A computer program implements stochastic evolutionary algorithms for planning and optimizing collision-free paths for robots and their jointed limbs. Stochastic evolutionary algorithms can be made to produce acceptably close approximations to exact, optimal solutions for path-planning problems while often demanding much less computation than do exhaustive-search and deterministic inverse-kinematics algorithms that have been used previously for this purpose. Hence, the present software is better suited for application aboard robots having limited computing capabilities (see figure). The stochastic aspect lies in the use of simulated annealing to (1) prevent trapping of an optimization algorithm in local minima of an energy-like error measure by which the fitness of a trial solution is evaluated while (2) ensuring that the entire multidimensional configuration and parameter space of the path-planning problem is sampled efficiently with respect to both robot joint angles and computation time. Simulated annealing is an established technique for avoiding local minima in multidimensional optimization problems, but has not, until now, been applied to planning collision-free robot paths by use of low-power computers.

Two distinct crystallization processes in supercooled liquid

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

Tane, Masakazu, E-mail: mtane@sanken.osaka-u.ac.jp; Kimizuka, Hajime; Ichitsubo, Tetsu

2016-05-21

Using molecular dynamics simulations we show that two distinct crystallization processes, depending on the temperature at which crystallization occurs, appear in a supercooled liquid. As a model for glass-forming materials, an Al{sub 2}O{sub 3} model system, in which both the glass transition and crystallization from the supercooled liquid can be well reproduced, is employed. Simulations in the framework of an isothermal-isobaric ensemble indicate that the calculated time-temperature-transformation curve for the crystallization to γ(defect spinel)-Al{sub 2}O{sub 3} exhibited a typical nose shape, as experimentally observed in various glass materials. During annealing above the nose temperature, the structure of the supercooled liquidmore » does not change before the crystallization, because of the high atomic mobility (material transport). Thus, the crystallization is governed by the abrupt crystal nucleation, which results in the formation of a stable crystal structure. In contrast, during annealing below the nose temperature, the structure of the supercooled liquid gradually changes before the crystallization, and the formed crystal structure is less stable than that formed above the nose temperature, because of the restricted material transport.« less

Selecting Magnet Laminations Recipes Using the Meth-od of Sim-u-la-ted Annealing

NASA Astrophysics Data System (ADS)

Russell, A. D.; Baiod, R.; Brown, B. C.; Harding, D. J.; Martin, P. S.

1997-05-01

The Fermilab Main Injector project is building 344 dipoles using more than 7000 tons of steel. Budget and logistical constraints required that steel production, lamination stamping and magnet fabrication proceed in parallel. There were significant run-to-run variations in the magnetic properties of the steel (Martin, P.S., et al., Variations in the Steel Properties and the Excitation Characteristics of FMI Dipoles, this conference). The large lamination size (>0.5 m coil opening) resulted in variations of gap height due to differences in stress relief in the steel after stamping. To minimize magnet-to-magnet strength and field shape variations the laminations were shuffled based on the available magnetic and mechanical data and assigned to magnets using a computer program based on the method of simulated annealing. The lamination sets selected by the program have produced magnets which easily satisfy the design requirements. Variations of the average magnet gap are an order of magnitude smaller than the variations in lamination gaps. This paper discusses observed gap variations, the program structure and the strength uniformity results.

Simulated annealing two-point ray tracing

NASA Astrophysics Data System (ADS)

Velis, Danilo R.; Ulrych, Tadeusz J.

We present a new method for solving the two-point seismic ray tracing problem based on Fermat's principle. The algorithm overcomes some well known difficulties that arise in standard ray shooting and bending methods. Problems related to: (1) the selection of new take-off angles, and (2) local minima in multipathing cases, are overcome by using an efficient simulated annealing (SA) algorithm. At each iteration, the ray is propagated from the source by solving a standard initial value problem. The last portion of the raypath is then forced to pass through the receiver. Using SA, the total traveltime is then globally minimized by obtaining the initial conditions that produce the absolute minimum path. The procedure is suitable for tracing rays through 2D complex structures, although it can be extended to deal with 3D velocity media. Not only direct waves, but also reflected and head-waves can be incorporated in the scheme. One important advantage is its simplicity, in as much as any available or user-preferred initial value solver system can be used. A number of clarifying examples of multipathing in 2D media are examined.

Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking.

PubMed

Sasse, Alexander; de Vries, Sjoerd J; Schindler, Christina E M; de Beauchêne, Isaure Chauvot; Zacharias, Martin

2017-01-01

Protein-protein docking protocols aim to predict the structures of protein-protein complexes based on the structure of individual partners. Docking protocols usually include several steps of sampling, clustering, refinement and re-scoring. The scoring step is one of the bottlenecks in the performance of many state-of-the-art protocols. The performance of scoring functions depends on the quality of the generated structures and its coupling to the sampling algorithm. A tool kit, GRADSCOPT (GRid Accelerated Directly SCoring OPTimizing), was designed to allow rapid development and optimization of different knowledge-based scoring potentials for specific objectives in protein-protein docking. Different atomistic and coarse-grained potentials can be created by a grid-accelerated directly scoring dependent Monte-Carlo annealing or by a linear regression optimization. We demonstrate that the scoring functions generated by our approach are similar to or even outperform state-of-the-art scoring functions for predicting near-native solutions. Of additional importance, we find that potentials specifically trained to identify the native bound complex perform rather poorly on identifying acceptable or medium quality (near-native) solutions. In contrast, atomistic long-range contact potentials can increase the average fraction of near-native poses by up to a factor 2.5 in the best scored 1% decoys (compared to existing scoring), emphasizing the need of specific docking potentials for different steps in the docking protocol.

Engineering on-chip nanoporous gold material libraries via precision photothermal treatment

NASA Astrophysics Data System (ADS)

Chapman, Christopher A. R.; Wang, Ling; Biener, Juergen; Seker, Erkin; Biener, Monika M.; Matthews, Manyalibo J.

2015-12-01

Libraries of nanostructured materials on a single chip are a promising platform for high throughput and combinatorial studies of structure-property relationships in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material specifically suited for such studies because of its self-similar thermally induced coarsening behavior. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Here, laser micro-processing offers an attractive solution to this problem by providing a means to apply energy with high spatial and temporal resolution. In the present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and thermal conductivity of the supporting substrate on the local np-Au film temperatures during photothermal annealing. Based on these results we discuss the mechanisms by which the np-Au network is coarsened. Thermal transport simulations predict that continuous-wave mode laser irradiation of np-Au thin films on a silicon substrate supports the widest range of morphologies that can be created through photothermal annealing of np-Au. Using the guidance provided by simulations, we successfully fabricate an on-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in the parallel study of structure-property relationships.Libraries of nanostructured materials on a single chip are a promising platform for high throughput and combinatorial studies of structure-property relationships in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material specifically suited for such studies because of its self-similar thermally induced coarsening behavior. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Here, laser micro-processing offers an attractive solution to this problem by providing a means to apply energy with high spatial and temporal resolution. In the present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and thermal conductivity of the supporting substrate on the local np-Au film temperatures during photothermal annealing. Based on these results we discuss the mechanisms by which the np-Au network is coarsened. Thermal transport simulations predict that continuous-wave mode laser irradiation of np-Au thin films on a silicon substrate supports the widest range of morphologies that can be created through photothermal annealing of np-Au. Using the guidance provided by simulations, we successfully fabricate an on-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in the parallel study of structure-property relationships. Electronic supplementary information (ESI) available: Details of sample preparation, fabrication of material libraries, as well as further analysis and supporting scanning electron micrographs can be found in ESI. See DOI: 10.1039/c5nr04580k

Strength determination of brittle materials as curved monolithic structures.

PubMed

Hooi, P; Addison, O; Fleming, G J P

2014-04-01

The dental literature is replete with "crunch the crown" monotonic load-to-failure studies of all-ceramic materials despite fracture behavior being dominated by the indenter contact surface. Load-to-failure data provide no information on stress patterns, and comparisons among studies are impossible owing to variable testing protocols. We investigated the influence of nonplanar geometries on the maximum principal stress of curved discs tested in biaxial flexure in the absence of analytical solutions. Radii of curvature analogous to elements of complex dental geometries and a finite element analysis method were integrated with experimental testing as a surrogate solution to calculate the maximum principal stress at failure. We employed soda-lime glass discs, a planar control (group P, n = 20), with curvature applied to the remaining discs by slump forming to different radii of curvature (30, 20, 15, and 10 mm; groups R30-R10). The mean deflection (group P) and radii of curvature obtained on slumping (groups R30-R10) were determined by profilometry before and after annealing and surface treatment protocols. Finite element analysis used the biaxial flexure load-to-failure data to determine the maximum principal stress at failure. Mean maximum principal stresses and load to failure were analyzed with one-way analyses of variance and post hoc Tukey tests (α = 0.05). The measured radii of curvature differed significantly among groups, and the radii of curvature were not influenced by annealing. Significant increases in the mean load to failure were observed as the radius of curvature was reduced. The maximum principal stress did not demonstrate sensitivity to radius of curvature. The findings highlight the sensitivity of failure load to specimen shape. The data also support the synergistic use of bespoke computational analysis with conventional mechanical testing and highlight a solution to complications with complex specimen geometries.

Development of a Highly Sensitive Nested-PCR Procedure Using a Single Closed Tube for Detection of Erwinia amylovora in Asymptomatic Plant Material

PubMed Central

Llop, Pablo; Bonaterra, Anna; Peñalver, Javier; López, María M.

2000-01-01

A novel method, which involves a nested PCR in a single closed tube, was developed for the sensitive detection of Erwinia amylovora in plant material. The external and internal primer pairs used had different annealing temperatures and directed the amplification of a specific DNA fragment from plasmid pEA29. The procedure involved two consecutive PCRs, the first of which was performed at a higher annealing temperature that allowed amplification only by the external primer pair. Using pure cultures of E. amylovora, the sensitivity of the nested PCR in one tube was similar to that of a standard nested PCR in two tubes. The specificity and sensitivity were greater than those of standard PCR procedures that used a single primer pair. The presence of inhibitors in plant material, very common in E. amylovora hosts, is overcome with this system in combination with a simple DNA extraction protocol because it eliminates many of the inhibitory compounds. In addition, it needs a very small sample volume (1 μl of DNA extracted). With 83 samples of naturally infected material, this method achieved better results than any other PCR technique: standard PCR detected 55% of positive samples, two-tube nested PCR detected 71% of positive samples, and nested PCR in a single closed tube detected 78% of positive samples. When analyzing asymptomatic plant material, the number of positive samples detected by the developed nested PCR was also the highest, compared with the PCR protocols indicated previously (17, 20, and 25% of 251 samples analyzed, respectively). This method is proposed for the detection of endophytic and epiphytic populations of E. amylovora in epidemiological studies and for routine use in quarantine surveys, due to its high sensitivity, specificity, speed, and simplicity. PMID:10788384

Performance of Stochastic Targeted Blood Glucose Control Protocol by virtual trials in the Malaysian intensive care unit.

PubMed

Jamaludin, Ummu K; M Suhaimi, Fatanah; Abdul Razak, Normy Norfiza; Md Ralib, Azrina; Mat Nor, Mohd Basri; Pretty, Christopher G; Humaidi, Luqman

2018-08-01

Blood glucose variability is common in healthcare and it is not related or influenced by diabetes mellitus. To minimise the risk of high blood glucose in critically ill patients, Stochastic Targeted Blood Glucose Control Protocol is used in intensive care unit at hospitals worldwide. Thus, this study focuses on the performance of stochastic modelling protocol in comparison to the current blood glucose management protocols in the Malaysian intensive care unit. Also, this study is to assess the effectiveness of Stochastic Targeted Blood Glucose Control Protocol when it is applied to a cohort of diabetic patients. Retrospective data from 210 patients were obtained from a general hospital in Malaysia from May 2014 until June 2015, where 123 patients were having comorbid diabetes mellitus. The comparison of blood glucose control protocol performance between both protocol simulations was conducted through blood glucose fitted with physiological modelling on top of virtual trial simulations, mean calculation of simulation error and several graphical comparisons using stochastic modelling. Stochastic Targeted Blood Glucose Control Protocol reduces hyperglycaemia by 16% in diabetic and 9% in nondiabetic cohorts. The protocol helps to control blood glucose level in the targeted range of 4.0-10.0 mmol/L for 71.8% in diabetic and 82.7% in nondiabetic cohorts, besides minimising the treatment hour up to 71 h for 123 diabetic patients and 39 h for 87 nondiabetic patients. It is concluded that Stochastic Targeted Blood Glucose Control Protocol is good in reducing hyperglycaemia as compared to the current blood glucose management protocol in the Malaysian intensive care unit. Hence, the current Malaysian intensive care unit protocols need to be modified to enhance their performance, especially in the integration of insulin and nutrition intervention in decreasing the hyperglycaemia incidences. Improvement in Stochastic Targeted Blood Glucose Control Protocol in terms of u en model is also a must to adapt with the diabetic cohort. Copyright © 2018 Elsevier B.V. All rights reserved.

Simulation improves procedural protocol adherence during central venous catheter placement: a randomized-controlled trial

PubMed Central

Peltan, Ithan D.; Shiga, Takashi; Gordon, James A.; Currier, Paul F.

2015-01-01

Background Simulation training may improve proficiency at and reduces complications from central venous catheter (CVC) placement, but the scope of simulation’s effect remains unclear. This randomized controlled trial evaluated the effects of a pragmatic CVC simulation program on procedural protocol adherence, technical skill, and patient outcomes. Methods Internal medicine interns were randomized to standard training for CVC insertion or standard training plus simulation-based mastery training. Standard training involved a lecture, a video-based online module, and instruction by the supervising physician during actual CVC insertions. Intervention-group subjects additionally underwent supervised training on a venous access simulator until they demonstrated procedural competence. Raters evaluated interns’ performance during internal jugular CVC placement on actual patients in the medical intensive care unit. Generalized estimating equations were used to account for outcome clustering within trainees. Results We observed 52 interns place 87 CVCs. Simulation-trained interns exhibited better adherence to prescribed procedural technique than interns who received only standard training (p=0.024). There were no significant differences detected in first-attempt or overall cannulation success rates, mean needle passes, global assessment scores or complication rates. Conclusions Simulation training added to standard training improved protocol adherence during CVC insertion by novice practitioners. This study may have been too small to detect meaningful differences in venous cannulation proficiency and other clinical outcomes, highlighting the difficulty of patient-centered simulation research in settings where poor outcomes are rare. For high-performing systems, where protocol deviations may provide an important proxy for rare procedural complications, simulation may improve CVC insertion quality and safety. PMID:26154250

Au nanostructure arrays for plasmonic applications: annealed island films versus nanoimprint lithography

NASA Astrophysics Data System (ADS)

Lopatynskyi, Andrii M.; Lytvyn, Vitalii K.; Nazarenko, Volodymyr I.; Guo, L. Jay; Lucas, Brandon D.; Chegel, Volodymyr I.

2015-03-01

This paper attempts to compare the main features of random and highly ordered gold nanostructure arrays (NSA) prepared by thermally annealed island film and nanoimprint lithography (NIL) techniques, respectively. Each substrate possesses different morphology in terms of plasmonic enhancement. Both methods allow such important features as spectral tuning of plasmon resonance position depending on size and shape of nanostructures; however, the time and cost is quite different. The respective comparison was performed experimentally and theoretically for a number of samples with different geometrical parameters. Spectral characteristics of fabricated NSA exhibited an expressed plasmon peak in the range from 576 to 809 nm for thermally annealed samples and from 606 to 783 nm for samples prepared by NIL. Modelling of the optical response for nanostructures with typical shapes associated with these techniques (parallelepiped for NIL and semi-ellipsoid for annealed island films) was performed using finite-difference time-domain calculations. Mathematical simulations have indicated the dependence of electric field enhancement on the shape and size of the nanoparticles. As an important point, the distribution of electric field at so-called `hot spots' was considered. Parallelepiped-shaped nanoparticles were shown to yield maximal enhancement values by an order of magnitude greater than their semi-ellipsoid-shaped counterparts; however, both nanoparticle shapes have demonstrated comparable effective electrical field enhancement values. Optimized Au nanostructures with equivalent diameters ranging from 85 to 143 nm and height equal to 35 nm were obtained for both techniques, resulting in the largest electrical field enhancement. The application of island film thermal annealing method for nanochips fabrication can be considered as a possible cost-effective platform for various surface-enhanced spectroscopies; while the NIL-fabricated NSA looks like more effective for sensing of small-size objects.

Study on the effect of Cd-diffusion annealing on the electrical properties of CdZnTe

NASA Astrophysics Data System (ADS)

Wanwan, Li; Zechun, Cao; Bin, Zhang; Feng, Zhan; Hongtao, Liu; Wenbin, Sang; Jiahua, Min; Kang, Sun

2006-06-01

In order to meet the requirements for the device design of radiation detectors, CdZnTe (or Cd 1-xZn xTe) crystals grown by Vertical Bridgman Method often need subsequent annealing to increase their resistivity. The nature of this treatment is a diffusion process. Thus, it is meaningful to relate the change of resistivity to the diffusion parameters. A model correlating resistivity and conduction type of CdZnTe with the main diffusion parameter—diffusion coefficient—is put forward in this paper. Combining the model with the analysis of our experimental data, DCd=1.464×10 -10, 1.085×10 -11 and 4.167×10 -13 cm 2/s are the values of Cd self-diffusion coefficient in Cd 0.9Zn 0.1Te at 1073, 973 and 873 K, respectively. The data coincide closely with the Cd self-diffusion coefficient in CdTe provided by different authors [E.D. Jones, N.M. Stewart, Self-diffusion of cadmium in cadmium telluride, J. Crystal Growth 84 (1987) 289-294; P.M. Borsenberger, D.A. Stevenson, J. Phys. Chem. Solids 29 (1968) 1277; R.C. Whelan, D. Shaw, in: D.G. Thomas (Ed.), II -VI Semiconductor Compounds, Benjamin, New York, 1967, p. 451]. With the data, the effects of annealing time on the change of resistivity and conduction type for Cd 0.9Zn 0.1Te wafers, which are annealed in saturated Cd vapor at 1073, 973 and 873 K, were simulated, and good consistency was found. This work suggests an alternative way to obtain the diffusion coefficient in semiconductor materials and also enables ones to analyze the diffusion process quantitatively and predict the annealing results.

Solving a Higgs optimization problem with quantum annealing for machine learning.

PubMed

Mott, Alex; Job, Joshua; Vlimant, Jean-Roch; Lidar, Daniel; Spiropulu, Maria

2017-10-18

The discovery of Higgs-boson decays in a background of standard-model processes was assisted by machine learning methods. The classifiers used to separate signals such as these from background are trained using highly unerring but not completely perfect simulations of the physical processes involved, often resulting in incorrect labelling of background processes or signals (label noise) and systematic errors. Here we use quantum and classical annealing (probabilistic techniques for approximating the global maximum or minimum of a given function) to solve a Higgs-signal-versus-background machine learning optimization problem, mapped to a problem of finding the ground state of a corresponding Ising spin model. We build a set of weak classifiers based on the kinematic observables of the Higgs decay photons, which we then use to construct a strong classifier. This strong classifier is highly resilient against overtraining and against errors in the correlations of the physical observables in the training data. We show that the resulting quantum and classical annealing-based classifier systems perform comparably to the state-of-the-art machine learning methods that are currently used in particle physics. However, in contrast to these methods, the annealing-based classifiers are simple functions of directly interpretable experimental parameters with clear physical meaning. The annealer-trained classifiers use the excited states in the vicinity of the ground state and demonstrate some advantage over traditional machine learning methods for small training datasets. Given the relative simplicity of the algorithm and its robustness to error, this technique may find application in other areas of experimental particle physics, such as real-time decision making in event-selection problems and classification in neutrino physics.

In Situ Apparatus to Study Gas-Metal Reactions and Wettability at High Temperatures for Hot-Dip Galvanizing Applications

NASA Astrophysics Data System (ADS)

Koltsov, A.; Cornu, M.-J.; Scheid, J.

2018-02-01

The understanding of gas-metal reactions and related surface wettability at high temperatures is often limited due to the lack of in situ surface characterization. Ex situ transfers at low temperature between annealing furnace, wettability device, and analytical tools induce noticeable changes of surface composition distinct from the reality of the phenomena.Therefore, a high temperature wettability device was designed in order to allow in situ sample surface characterization by x-rays photoelectron spectroscopy after gas/metal and liquid metal/solid metal surface reactions. Such airless characterization rules out any contamination and oxidation of surfaces and reveals their real composition after heat treatment and chemical reaction. The device consists of two connected reactors, respectively, dedicated to annealing treatments and wettability measurements. Heat treatments are performed in an infrared lamp furnace in a well-controlled atmosphere conditions designed to reproduce gas-metal reactions occurring during the industrial recrystallization annealing of steels. Wetting experiments are carried out in dispensed drop configuration with the precise control of the deposited droplets kinetic energies. The spreading of drops is followed by a high-speed CCD video camera at 500-2000 frames/s in order to reach information at very low contact time. First trials have started to simulate phenomena occurring during recrystallization annealing and hot-dip galvanizing on polished pure Fe and FeAl8 wt.% samples. The results demonstrate real surface chemistry of steel samples after annealing when they are put in contact with liquid zinc alloy bath during hot-dip galvanizing. The wetting results are compared to literature data and coupled with the characterization of interfacial layers by FEG-Auger. It is fair to conclude that the results show the real interest of such in situ experimental setup for interfacial chemistry studies.

Solving a Higgs optimization problem with quantum annealing for machine learning

NASA Astrophysics Data System (ADS)

Mott, Alex; Job, Joshua; Vlimant, Jean-Roch; Lidar, Daniel; Spiropulu, Maria

2017-10-01

The discovery of Higgs-boson decays in a background of standard-model processes was assisted by machine learning methods. The classifiers used to separate signals such as these from background are trained using highly unerring but not completely perfect simulations of the physical processes involved, often resulting in incorrect labelling of background processes or signals (label noise) and systematic errors. Here we use quantum and classical annealing (probabilistic techniques for approximating the global maximum or minimum of a given function) to solve a Higgs-signal-versus-background machine learning optimization problem, mapped to a problem of finding the ground state of a corresponding Ising spin model. We build a set of weak classifiers based on the kinematic observables of the Higgs decay photons, which we then use to construct a strong classifier. This strong classifier is highly resilient against overtraining and against errors in the correlations of the physical observables in the training data. We show that the resulting quantum and classical annealing-based classifier systems perform comparably to the state-of-the-art machine learning methods that are currently used in particle physics. However, in contrast to these methods, the annealing-based classifiers are simple functions of directly interpretable experimental parameters with clear physical meaning. The annealer-trained classifiers use the excited states in the vicinity of the ground state and demonstrate some advantage over traditional machine learning methods for small training datasets. Given the relative simplicity of the algorithm and its robustness to error, this technique may find application in other areas of experimental particle physics, such as real-time decision making in event-selection problems and classification in neutrino physics.

Finite-key security analyses on passive decoy-state QKD protocols with different unstable sources

PubMed Central

Song, Ting-Ting; Qin, Su-Juan; Wen, Qiao-Yan; Wang, Yu-Kun; Jia, Heng-Yue

2015-01-01

In quantum communication, passive decoy-state QKD protocols can eliminate many side channels, but the protocols without any finite-key analyses are not suitable for in practice. The finite-key securities of passive decoy-state (PDS) QKD protocols with two different unstable sources, type-II parametric down-convention (PDC) and phase randomized weak coherent pulses (WCPs), are analyzed in our paper. According to the PDS QKD protocols, we establish an optimizing programming respectively and obtain the lower bounds of finite-key rates. Under some reasonable values of quantum setup parameters, the lower bounds of finite-key rates are simulated. The simulation results show that at different transmission distances, the affections of different fluctuations on key rates are different. Moreover, the PDS QKD protocol with an unstable PDC source can resist more intensity fluctuations and more statistical fluctuation. PMID:26471947

Protocol Support for a New Satellite-Based Airspace Communication Network

NASA Technical Reports Server (NTRS)

Shang, Yadong; Hadjitheodosiou, Michael; Baras, John

2004-01-01

We recommend suitable transport protocols for an aeronautical network supporting Internet and data services via satellite. We study the characteristics of an aeronautical satellite hybrid network and focus on the problems that cause dramatically degraded performance of the Transport Protocol. We discuss various extensions to standard TCP that alleviate some of these performance problems. Through simulation, we identify those TCP implementations that can be expected to perform well. Based on the observation that it is difficult for an end-to-end solution to solve these problems effectively, we propose a new TCP-splitting protocol, termed Aeronautical Transport Control Protocol (AeroTCP). The main idea of this protocol is to use a fixed window for flow control and one duplicated acknowledgement (ACK) for fast recovery. Our simulation results show that AeroTCP can maintain higher utilization for the satellite link than end-to-end TCP, especially in high BER environment.

Physiological responses to simulated firefighter exercise protocols in varying environments.

PubMed

Horn, Gavin P; Kesler, Richard M; Motl, Robert W; Hsiao-Wecksler, Elizabeth T; Klaren, Rachel E; Ensari, Ipek; Petrucci, Matthew N; Fernhall, Bo; Rosengren, Karl S

2015-01-01

For decades, research to quantify the effects of firefighting activities and personal protective equipment on physiology and biomechanics has been conducted in a variety of testing environments. It is unknown if these different environments provide similar information and comparable responses. A novel Firefighting Activities Station, which simulates four common fireground tasks, is presented for use with an environmental chamber in a controlled laboratory setting. Nineteen firefighters completed three different exercise protocols following common research practices. Simulated firefighting activities conducted in an environmental chamber or live-fire structures elicited similar physiological responses (max heart rate: 190.1 vs 188.0 bpm, core temperature response: 0.047°C/min vs 0.043°C/min) and accelerometry counts. However, the response to a treadmill protocol commonly used in laboratory settings resulted in significantly lower heart rate (178.4 vs 188.0 bpm), core temperature response (0.037°C/min vs 0.043°C/min) and physical activity counts compared with firefighting activities in the burn building. Practitioner Summary: We introduce a new approach for simulating realistic firefighting activities in a controlled laboratory environment for ergonomics assessment of fire service equipment and personnel. Physiological responses to this proposed protocol more closely replicate those from live-fire activities than a traditional treadmill protocol and are simple to replicate and standardise.

iSAFT Protocol Validation Platform for On-Board Data Networks

NASA Astrophysics Data System (ADS)

Tavoularis, Antonis; Kollias, Vangelis; Marinis, Kostas

2014-08-01

iSAFT is an integrated powerful HW/SW environmentfor the simulation, validation & monitoring of satellite/spacecraft on-board data networks supporting simultaneously a wide range of protocols (RMAP, PTP, CCSDS Space Packet, TM/TC, CANopen, etc.) and network interfaces (SpaceWire, ECSS MIL-STD-1553, ECSS CAN). It is based on over 20 years of TELETEL's experience in the area of protocol validation in the telecommunications and aeronautical sectors, and it has been fully re-engineered in cooperation of TELETEL with ESA & space Primes, to comply with space on-board industrial validation requirements (ECSS, EGSE, AIT, AIV, etc.). iSAFT is highly modular and expandable to support new network interfaces & protocols and it is based on the powerful iSAFT graphical tool chain (Protocol Analyser / Recorder, TestRunner, Device Simulator, Traffic Generator, etc.).

Using and comparing metaheuristic algorithms for optimizing bidding strategy viewpoint of profit maximization of generators

NASA Astrophysics Data System (ADS)

Mousavi, Seyed Hosein; Nazemi, Ali; Hafezalkotob, Ashkan

2015-03-01

With the formation of the competitive electricity markets in the world, optimization of bidding strategies has become one of the main discussions in studies related to market designing. Market design is challenged by multiple objectives that need to be satisfied. The solution of those multi-objective problems is searched often over the combined strategy space, and thus requires the simultaneous optimization of multiple parameters. The problem is formulated analytically using the Nash equilibrium concept for games composed of large numbers of players having discrete and large strategy spaces. The solution methodology is based on a characterization of Nash equilibrium in terms of minima of a function and relies on a metaheuristic optimization approach to find these minima. This paper presents some metaheuristic algorithms to simulate how generators bid in the spot electricity market viewpoint of their profit maximization according to the other generators' strategies, such as genetic algorithm (GA), simulated annealing (SA) and hybrid simulated annealing genetic algorithm (HSAGA) and compares their results. As both GA and SA are generic search methods, HSAGA is also a generic search method. The model based on the actual data is implemented in a peak hour of Tehran's wholesale spot market in 2012. The results of the simulations show that GA outperforms SA and HSAGA on computing time, number of function evaluation and computing stability, as well as the results of calculated Nash equilibriums by GA are less various and different from each other than the other algorithms.

Scalable Online Network Modeling and Simulation

DTIC Science & Technology

2005-08-01

ONLINE NETWORK MODELING AND SIMULATION 6. AUTHOR(S) Boleslaw Szymanski , Shivkumar Kalyanaraman, Biplab Sikdar and Christopher Carothers 5...performance for a wide range of parameter values (parameter sensitivity), understanding of protocol stability and dynamics, and studying feature ...a wide range of parameter values (parameter sensitivity), understanding of protocol stability and dynamics, and studying feature interactions

Safe bunker designing for the 18 MV Varian 2100 Clinac: a comparison between Monte Carlo simulation based upon data and new protocol recommendations

PubMed Central

Beigi, Manije; Afarande, Fatemeh; Ghiasi, Hosein

2016-01-01

Aim The aim of this study was to compare two bunkers designed by only protocols recommendations and Monte Carlo (MC) based upon data derived for an 18 MV Varian 2100Clinac accelerator. Background High energy radiation therapy is associated with fast and thermal photoneutrons. Adequate shielding against the contaminant neutron has been recommended by IAEA and NCRP new protocols. Materials and methods The latest protocols released by the IAEA (safety report No. 47) and NCRP report No. 151 were used for the bunker designing calculations. MC method based upon data was also derived. Two bunkers using protocols and MC upon data were designed and discussed. Results From designed door's thickness, the door designed by the MC simulation and Wu–McGinley analytical method was closer in both BPE and lead thickness. In the case of the primary and secondary barriers, MC simulation resulted in 440.11 mm for the ordinary concrete, total concrete thickness of 1709 mm was required. Calculating the same parameters value with the recommended analytical methods resulted in 1762 mm for the required thickness using 445 mm as recommended by TVL for the concrete. Additionally, for the secondary barrier the thickness of 752.05 mm was obtained. Conclusion Our results showed MC simulation and the followed protocols recommendations in dose calculation are in good agreement in the radiation contamination dose calculation. Difference between the two analytical and MC simulation methods revealed that the application of only one method for the bunker design may lead to underestimation or overestimation in dose and shielding calculations. PMID:26900357

Using Simulations to Investigate Decision Making in Airline Operations

NASA Technical Reports Server (NTRS)

Bruce, Peter J.; Gray, Judy H.

2003-01-01

This paper examines a range of methods to collect data for the investigation of decision-making in airline Operations Control Centres (OCCs). A study was conducted of 52 controllers in five OCCs of both domestic and international airlines in the Asia-Pacific region. A range of methods was used including: surveys, interviews, observations, simulations, and think-aloud protocol. The paper compares and evaluates the suitability of these techniques for gathering data and provides recommendations on the application of simulations. Keywords Data Collection, Decision-Making, Research Methods, Simulation, Think-Aloud Protocol.

ShareSync: A Solution for Deterministic Data Sharing over Ethernet

NASA Technical Reports Server (NTRS)

Dunn, Daniel J., II; Koons, William A.; Kennedy, Richard D.; Davis, Philip A.

2007-01-01

As part of upgrading the Contact Dynamics Simulation Laboratory (CDSL) at the NASA Marshall Space Flight Center (MSFC), a simple, cost effective method was needed to communicate data among the networked simulation machines and I/O controllers used to run the facility. To fill this need and similar applicable situations, a generic protocol was developed, called ShareSync. ShareSync is a lightweight, real-time, publish-subscribe Ethernet protocol for simple and deterministic data sharing across diverse machines and operating systems. ShareSync provides a simple Application Programming Interface (API) for simulation programmers to incorporate into their code. The protocol is compatible with virtually all Ethernet-capable machines, is flexible enough to support a variety of applications, is fast enough to provide soft real-time determinism, and is a low-cost resource for distributed simulation development, deployment, and maintenance. The first design cycle iteration of ShareSync has been completed, and the protocol has undergone several testing procedures including endurance and benchmarking tests and approaches the 2001ts data synchronization design goal for the CDSL.

The Behavior of TCP and Its Extensions in Space

NASA Technical Reports Server (NTRS)

Wang, Ruhai; Horan, Stephen

2001-01-01

The performance of Transmission Control Protocol (TCP) in space has been examined from the observations of simulation and experimental tests for several years at National Aeronautics and Space Administration (NASA), Department of Defense (DoD) and universities. At New Mexico State University (NMSU), we have been concentrating on studying the performance of two protocol suites: the file transfer protocol (ftp) running over Transmission Control Protocol/Internet Protocol (TCP/IP) stack and the file protocol (fp) running over the Space Communications Protocol Standards (SCPS)-Transport Protocol (TP) developed under the Consultative Committee for Space Data Systems (CCSDS) standards process. SCPS-TP is considered to be TCP's extensions for space communications. This dissertation experimentally studies the behavior of TCP and SCPS-TP by running the protocol suites over both the Space-to-Ground Link Simulator (SGLS) test-bed and realistic satellite link. The study concentrates on comparing protocol behavior by plotting the averaged file transfer times for different experimental configurations and analyzing them using Statistical Analysis System (SAS) based procedures. The effects of different link delays and various Bit-Error-Rates (BERS) on each protocol performance are also studied and linear regression models are built for experiments over SGLS test-bed to reflect the relationships between the file transfer time and various transmission conditions.

Hafnium transistor process design for neural interfacing.

PubMed

Parent, David W; Basham, Eric J

2009-01-01

A design methodology is presented that uses 1-D process simulations of Metal Insulator Semiconductor (MIS) structures to design the threshold voltage of hafnium oxide based transistors used for neural recording. The methodology is comprised of 1-D analytical equations for threshold voltage specification, and doping profiles, and 1-D MIS Technical Computer Aided Design (TCAD) to design a process to implement a specific threshold voltage, which minimized simulation time. The process was then verified with a 2-D process/electrical TCAD simulation. Hafnium oxide films (HfO) were grown and characterized for dielectric constant and fixed oxide charge for various annealing temperatures, two important design variables in threshold voltage design.

Comparison between phase field simulations and experimental data from intragranular bubble growth in UO{sub 2}

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

Tonks, M. R.; Biner, S. B.; Mille, P. C.

2013-07-01

In this work, we used the phase field method to simulate the post-irradiation annealing of UO{sub 2} described in the experimental work by Kashibe et al., 1993 [1]. The simulations were carried out in 2D and 3D using the MARMOT FEM-based phase-field modeling framework. The 2-D results compared fairly well with the experiments, in spite of the assumptions made in the model. The 3-D results compare even more favorably to experiments, indicating that diffusion in all three directions must be considered to accurate represent the bubble growth. (authors)

Advertisement-Based Energy Efficient Medium Access Protocols for Wireless Sensor Networks

NASA Astrophysics Data System (ADS)

Ray, Surjya Sarathi

One of the main challenges that prevents the large-scale deployment of Wireless Sensor Networks (WSNs) is providing the applications with the required quality of service (QoS) given the sensor nodes' limited energy supplies. WSNs are an important tool in supporting applications ranging from environmental and industrial monitoring, to battlefield surveillance and traffic control, among others. Most of these applications require sensors to function for long periods of time without human intervention and without battery replacement. Therefore, energy conservation is one of the main goals for protocols for WSNs. Energy conservation can be performed in different layers of the protocol stack. In particular, as the medium access control (MAC) layer can access and control the radio directly, large energy savings is possible through intelligent MAC protocol design. To maximize the network lifetime, MAC protocols for WSNs aim to minimize idle listening of the sensor nodes, packet collisions, and overhearing. Several approaches such as duty cycling and low power listening have been proposed at the MAC layer to achieve energy efficiency. In this thesis, I explore the possibility of further energy savings through the advertisement of data packets in the MAC layer. In the first part of my research, I propose Advertisement-MAC or ADV-MAC, a new MAC protocol for WSNs that utilizes the concept of advertising for data contention. This technique lets nodes listen dynamically to any desired transmission and sleep during transmissions not of interest. This minimizes the energy lost in idle listening and overhearing while maintaining an adaptive duty cycle to handle variable loads. Additionally, ADV-MAC enables energy efficient MAC-level multicasting. An analytical model for the packet delivery ratio and the energy consumption of the protocol is also proposed. The analytical model is verified with simulations and is used to choose an optimal value of the advertisement period. Simulations show that the optimized ADV-MAC provides substantial energy gains (50% to 70% less than other MAC protocols for WSNs such as T-MAC and S-MAC for the scenarios investigated) while faring as well as T-MAC in terms of packet delivery ratio and latency. Although ADV-MAC provides substantial energy gains over S-MAC and T-MAC, it is not optimal in terms of energy savings because contention is done twice -- once in the Advertisement Period and once in the Data Period. In the next part of my research, the second contention in the Data Period is eliminated and the advantages of contention-based and TDMA-based protocols are combined to form Advertisement based Time-division Multiple Access (ATMA), a distributed TDMA-based MAC protocol for WSNs. ATMA utilizes the bursty nature of the traffic to prevent energy waste through advertisements and reservations for data slots. Extensive simulations and qualitative analysis show that with bursty traffic, ATMA outperforms contention-based protocols (S-MAC, T-MAC and ADV-MAC), a TDMA based protocol (TRAMA) and hybrid protocols (Z-MAC and IEEE 802.15.4). ATMA provides energy reductions of up to 80%, while providing the best packet delivery ratio (close to 100%) and latency among all the investigated protocols. Simulations alone cannot reflect many of the challenges faced by real implementations of MAC protocols, such as clock-drift, synchronization, imperfect physical layers, and irregular interference from other transmissions. Such issues may cripple a protocol that otherwise performs very well in software simulations. Hence, to validate my research, I conclude with a hardware implementation of the ATMA protocol on SORA (Software Radio), developed by Microsoft Research Asia. SORA is a reprogrammable Software Defined Radio (SDR) platform that satisfies the throughput and timing requirements of modern wireless protocols while utilizing the rich general purpose PC development environment. Experimental results obtained from the hardware implementation of ATMA closely mirror the simulation results obtained for a single hop network with 4 nodes.

Design and development of compact monitoring system for disaster remote health centres.

PubMed

Santhi, S; Sadasivam, G S

2015-02-01

To enhance speedy communication between the patient and the doctor through newly proposed routing protocol at the mobile node. The proposed model is applied for a telemedicine application during disaster recovery management. In this paper, Energy Efficient Link Stability Routing Protocol (EELSRP) has been developed by simulation and real time. This framework is designed for the immediate healing of affected persons in remote areas, especially at the time of the disaster where there is no hospital proximity. In case of disasters, there might be an outbreak of infectious diseases. In such cases, the patient's medical record is also transferred by the field operator from disaster place to the hospital to facilitate the identification of the disease-causing agent and to prescribe the necessary medication. The heterogeneous networking framework provides reliable, energy efficientand speedy communication between the patient and the doctor using the proposed routing protocol at the mobile node. The performance of the simulation and real time versions of the Energy Efficient Link Stability Routing Protocol (EELSRP) protocol has been analyzed. Experimental results prove the efficiency of the real-time version of EESLRP protocol. The packet delivery ratio and throughput of the real time version of EELSRP protocol is increased by 3% and 10%, respectively, when compared to the simulated version of EELSRP. The end-to-end delay and energy consumption are reduced by 10% and 2% in the real time version of EELSRP.

Analyzing the effect of routing protocols on media access control protocols in radio networks

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

Barrett, C. L.; Drozda, M.; Marathe, A.

2002-01-01

We study the effect of routing protocols on the performance of media access control (MAC) protocols in wireless radio networks. Three well known MAC protocols: 802.11, CSMA, and MACA are considered. Similarly three recently proposed routing protocols: AODV, DSR and LAR scheme 1 are considered. The experimental analysis was carried out using GloMoSim: a tool for simulating wireless networks. The main focus of our experiments was to study how the routing protocols affect the performance of the MAC protocols when the underlying network and traffic parameters are varied. The performance of the protocols was measured w.r.t. five important parameters: (i)more » number of received packets, (ii) average latency of each packet, (iii) throughput (iv) long term fairness and (v) number of control packets at the MAC layer level. Our results show that combinations of routing and MAC protocols yield varying performance under varying network topology and traffic situations. The result has an important implication; no combination of routing protocol and MAC protocol is the best over all situations. Also, the performance analysis of protocols at a given level in the protocol stack needs to be studied not locally in isolation but as a part of the complete protocol stack. A novel aspect of our work is the use of statistical technique, ANOVA (Analysis of Variance) to characterize the effect of routing protocols on MAC protocols. This technique is of independent interest and can be utilized in several other simulation and empirical studies.« less

Research on a Queue Scheduling Algorithm in Wireless Communications Network

NASA Astrophysics Data System (ADS)

Yang, Wenchuan; Hu, Yuanmei; Zhou, Qiancai

This paper proposes a protocol QS-CT, Queue Scheduling Mechanism based on Multiple Access in Ad hoc net work, which adds queue scheduling mechanism to RTS-CTS-DATA using multiple access protocol. By endowing different queues different scheduling mechanisms, it makes networks access to the channel much more fairly and effectively, and greatly enhances the performance. In order to observe the final performance of the network with QS-CT protocol, we simulate it and compare it with MACA/C-T without QS-CT protocol. Contrast to MACA/C-T, the simulation result shows that QS-CT has greatly improved the throughput, delay, rate of packets' loss and other key indicators.

Hafnium oxide films for application as gate dielectrics

NASA Astrophysics Data System (ADS)

Hsu, Shuo-Lin

The deposition and characterization of HfO2 films for potential application as a high-kappa gate dielectric in MOS devices has been investigated. DC magnetron reactive sputtering was utilized to prepare the HfO2 films. Structural, chemical, and electrical analyses were performed to characterize the various physical, chemical and electrical properties of the sputtered HfO2 films. The sputtered HfO2 films were annealed to simulate the dopant activation process used in semiconductor processing, and to study the thermal stability of the high-kappa, films. The changes in the film properties due to the annealing are also discussed in this work. Glancing angle XRD was used to analyse the atomic scale structure of the films. The as deposited films exhibit an amorphous, regardless of the film thickness. During post-deposition annealing, the thicker films crystallized at lower temperature (< 600°C), and ultra-thin (5.8 nm) film crystallized at higher temperature (600--720°C). The crystalline phase which formed depended on the thickness of the films. The low temperature phase (monoclinic) formed in the 10--20 nm annealed films, and high temperature phase (tetragonal) formed in the ultra-thin annealed HfO2 film. TEM cross-section studies of as deposited samples show that an interfacial layer (< 1nm) exists between HfO2/Si for all film thicknesses. The interfacial layer grows thicker during heat treatment, and grows more rapidly when grain boundaries are present. XPS surface analysis shows the as deposited films are fully oxidized with an excess of oxygen. Interfacial chemistry analysis indicated that the interfacial layer is a silicon-rich silicate layer, which tends to transform to silica-like layer during heat treatment. I-V measurements show the leakage current density of the Al/as deposited-HfO 2/Si MOS diode is of the order of 10-3 A/cm 2, two orders of magnitude lower than that of a ZrO2 film with similar physical thickness. Carrier transport is dominated by Schottky emission at lower electric fields, and by Frenkel-Poole emission in the higher electric field region. After annealing, the leakage current density decreases significantly as the structure remains amorphous structure. It is suggested that this decrease is assorted with the densification and defect healing which accures when the porous as-deposited amorphous structure is annealed. The leakage current density increases of the HfO2 layer crystallizes on annealing, which is attributed to the presence of grain boundaries. C-V measurements of the as deposited film shows typical C-V characteristics, with negligible hystersis, a small flat band voltage shift, but great frequency dispersion. The relative permittivity of HfO2/interfacial layer stack obtained from the capacitance at accumulation is 15, which corresponds to an EOT (equivalent oxide thickness) = 1.66 nm. After annealing, the frequency dispersion is greatly enhanced, and the C-V curve is shifted toward the negative voltage. Reliability tests show that the HfO2 films which remain amorphous after annealing possess superior resistance to constant voltage stress and ambient aging. This study concluded that the sputtered HfO 2 films exhibit an amorphous as deposited. Postdeposition annealing alters the crystallinity, interfacial properties, and electrical characteristics. The HfO2 films which remain amorphous structure after annealing possess the best electrical properties.

Influence of voids distribution on the deformation behavior of nanocrystalline palladium

NASA Astrophysics Data System (ADS)

Bachurin, D. V.

2018-07-01

Uniaxial deformation of three-dimensional nanocrystalline palladium containing porosity in the form of voids was investigated by means of molecular dynamics method. Simulations were performed at temperature of 300 K and at a constant strain rate of 108s-1. Two cases of voids distribution were considered: random and at triple or quadrupole junctions. It has been revealed that both the voids distribution and subsequent annealing at elevated temperature influence the deformation behavior of nanocrystalline palladium. In particular, the presence of voids at grain junctions results in a reduction of the Young's modulus and more pronounced softening effect during plastic deformation. The subsequent annealing evokes shrinkage of voids and strengthening effect. Contribution of grain boundary accommodation processes into both elastic and plastic deformation of nanocrystalline materials is discussed.

Traffic Adaptive Energy Efficient and Low Latency Medium Access Control for Wireless Sensor Networks

NASA Astrophysics Data System (ADS)

Yadav, Rajesh; Varma, Shirshu; Malaviya, N.

2008-05-01

Medium access control for wireless sensor networks has been a very active research area in the recent years. The traditional wireless medium access control protocol such as IEEE 802.11 is not suitable for the sensor network application because these are battery powered. The recharging of these sensor nodes is expensive and also not possible. The most of the literature in the medium access for the sensor network focuses on the energy efficiency. The proposed MAC protocol solves the energy inefficiency caused by idle listening, control packet overhead and overhearing taking nodes latency into consideration based on the network traffic. Simulation experiments have been performed to demonstrate the effectiveness of the proposed approach. The validation of the simulation results of the proposed MAC has been done by comparing it with the analytical model. This protocol has been simulated in Network Simulator ns-2.

Programmable multi-node quantum network design and simulation

NASA Astrophysics Data System (ADS)

Dasari, Venkat R.; Sadlier, Ronald J.; Prout, Ryan; Williams, Brian P.; Humble, Travis S.

2016-05-01

Software-defined networking offers a device-agnostic programmable framework to encode new network functions. Externally centralized control plane intelligence allows programmers to write network applications and to build functional network designs. OpenFlow is a key protocol widely adopted to build programmable networks because of its programmability, flexibility and ability to interconnect heterogeneous network devices. We simulate the functional topology of a multi-node quantum network that uses programmable network principles to manage quantum metadata for protocols such as teleportation, superdense coding, and quantum key distribution. We first show how the OpenFlow protocol can manage the quantum metadata needed to control the quantum channel. We then use numerical simulation to demonstrate robust programmability of a quantum switch via the OpenFlow network controller while executing an application of superdense coding. We describe the software framework implemented to carry out these simulations and we discuss near-term efforts to realize these applications.

Conservative parallel simulation of priority class queueing networks

NASA Technical Reports Server (NTRS)

Nicol, David

1992-01-01

A conservative synchronization protocol is described for the parallel simulation of queueing networks having C job priority classes, where a job's class is fixed. This problem has long vexed designers of conservative synchronization protocols because of its seemingly poor ability to compute lookahead: the time of the next departure. For, a job in service having low priority can be preempted at any time by an arrival having higher priority and an arbitrarily small service time. The solution is to skew the event generation activity so that the events for higher priority jobs are generated farther ahead in simulated time than lower priority jobs. Thus, when a lower priority job enters service for the first time, all the higher priority jobs that may preempt it are already known and the job's departure time can be exactly predicted. Finally, the protocol was analyzed and it was demonstrated that good performance can be expected on the simulation of large queueing networks.

Conservative parallel simulation of priority class queueing networks

NASA Technical Reports Server (NTRS)

Nicol, David M.

1990-01-01

A conservative synchronization protocol is described for the parallel simulation of queueing networks having C job priority classes, where a job's class is fixed. This problem has long vexed designers of conservative synchronization protocols because of its seemingly poor ability to compute lookahead: the time of the next departure. For, a job in service having low priority can be preempted at any time by an arrival having higher priority and an arbitrarily small service time. The solution is to skew the event generation activity so that the events for higher priority jobs are generated farther ahead in simulated time than lower priority jobs. Thus, when a lower priority job enters service for the first time, all the higher priority jobs that may preempt it are already known and the job's departure time can be exactly predicted. Finally, the protocol was analyzed and it was demonstrated that good performance can be expected on the simulation of large queueing networks.

Self-consistent simulation of CdTe solar cells with active defects

DOE PAGES

Brinkman, Daniel; Guo, Da; Akis, Richard; ...

2015-07-21

We demonstrate a self-consistent numerical scheme for simulating an electronic device which contains active defects. As a specific case, we consider copper defects in cadmium telluride solar cells. The presence of copper has been shown experimentally to play a crucial role in predicting device performance. The primary source of this copper is migration away from the back contact during annealing, which likely occurs predominantly along grain boundaries. We introduce a mathematical scheme for simulating this effect in 2D and explain the numerical implementation of the system. Lastly, we will give numerical results comparing our results to known 1D simulations tomore » demonstrate the accuracy of the solver and then show results unique to the 2D case.« less

Memory versus irreversibility in the thermal densification of amorphous glasses

NASA Astrophysics Data System (ADS)

Ovadyahu, Z.

2017-06-01

We report on dynamic effects associated with thermally annealing amorphous indium-oxide films. In this process, the resistance of a given sample may decrease by several orders of magnitude at room temperatures, while its amorphous structure is preserved. The main effect of the process is densification, i.e., increased system density. The study includes the evolution of the system resistivity during and after the thermal treatment, the changes in the conductance noise, and the accompanying changes in the optical properties. The sample resistance is used to monitor the system dynamics during the annealing period as well as the relaxation that ensues after its termination. These reveal slow processes that fit well with a stretched-exponential law, a behavior that is commonly observed in structural glasses. There is an intriguing similarity between these effects and those obtained in high-pressure densification experiments. Both protocols exhibit the "slow spring-back" effect, a familiar response of memory foams. A heuristic picture based on a modified Lennard-Jones potential for the effective interparticle interaction is argued to qualitatively account for these densification-rarefaction phenomena in amorphous materials, whether affected by thermal treatment or by application of high pressure.

Strain Relaxation in Si{sub 1-x}Ge{sub x} Thin Films on Si(100) Substrates: Modeling and Comparisons with Experiments

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

Kolluri, K; Zepeda-Ruiz, L A; Murthy, C S

2005-03-22

Strained semiconductor thin films grown epitaxially on semiconductor substrates of different composition, such as Si{sub 1-x}Ge{sub x}/Si, are becoming increasingly important in modern microelectronic technologies. In this paper, we report a hierarchical computational approach for analysis of dislocation formation, glide motion, multiplication, and annihilation in Si{sub 1-x}Ge{sub x} epitaxial thin films on Si substrates. Specifically, a condition is developed for determining the critical film thickness with respect to misfit dislocation generation as a function of overall film composition, film compositional grading, and (compliant) substrate thickness. In addition, the kinetics of strain relaxation in the epitaxial film during growth or thermalmore » annealing (including post-implantation annealing) is analyzed using a properly parameterized dislocation mean-field theoretical model, which describes plastic deformation dynamics due to threading dislocation propagation. The theoretical results for Si{sub 1-x}Ge{sub x} epitaxial thin films grown on Si (100) substrates are compared with experimental measurements and are used to discuss film growth and thermal processing protocols toward optimizing the mechanical response of the epitaxial film.« less

Study on the Microstructure, Mechanical Properties and Corrosion Behavior of Mg-Zn-Ca Alloy Wire for Biomaterial Application

NASA Astrophysics Data System (ADS)

Zheng, Maobo; Xu, Guangquan; Liu, Debao; Zhao, Yue; Ning, Baoqun; Chen, Minfang

2018-03-01

Due to their excellent biocompatibility and biodegradability, magnesium alloy wires have attracted much attention for biomaterial applications including orthopedic K-wires and sutures in wound closure. In this study, Mg-3Zn-0.2Ca alloy wires were prepared by cold drawing combined with proper intermediate annealing process. Microstructures, texture, mechanical properties and corrosion behavior of Mg-3Zn-0.2Ca alloy wire in a simulated body fluid were investigated. The results showed that the secondary phase and average grain size of the Mg-3Zn-0.2Ca alloy were refined in comparison with the as-extruded alloy and a strong (0002)<10-10>//DD basal fiber texture system was formed after multi-pass cold drawing. After the annealing, most of the basal planes were tilted to the drawing direction (DD) by about 35°, presenting the characteristics of random texture, and the texture intensity decreased. The as-annealed wire shows good mechanical properties with the ultimate tensile strength (UTS), yield strength (YS) and elongation of 253 ± 8.5 MPa, 212 ± 11.3 MPa and 9.2 ± 0.9%, respectively. Electrochemical and hydrogen evolution measurements showed that the corrosion resistance of the Mg-3Zn-0.2Ca alloy wire was improved after the annealing. The immersion test indicated that the Mg-3Zn-0.2Ca wire exhibited uniform corrosion behavior during the initial period of immersion, but then exhibited local corrosion behavior.

Inverted Apatite (U-Th)/He and Fission-track Dates from the Rae craton, Baffin Island, Canada and Implications for Apatite Radiation Damage-He Diffusivity Models

NASA Astrophysics Data System (ADS)

Ault, A. K.; Reiners, P. W.; Thomson, S. N.; Miller, G. H.

2015-12-01

Coupled apatite (U-Th)/He and fission-track (AFT) thermochronology data from the same sample can be used to decipher complex low temperature thermal histories and evaluate compatibility between these two methods. Existing apatite He damage-diffusivity models parameterize radiation damage annealing as fission-track annealing and yield inverted apatite He and AFT dates for samples with prolonged residence in the He partial retention zone. Apatite chemistry also impacts radiation damage and fission-track annealing, temperature sensitivity, and dates in both systems. We present inverted apatite He and AFT dates from the Rae craton, Baffin Island, Canada, that cannot be explained by apatite chemistry or existing damage-diffusivity and fission track models. Apatite He dates from 34 individual analyses from 6 samples range from 237 ± 44 Ma to 511 ± 25 Ma and collectively define a positive date-eU relationship. AFT dates from these same samples are 238 ± 15 Ma to 350 ± 20 Ma. These dates and associated track length data are inversely correlated and define the left segment of a boomerang diagram. Three of the six samples with 20-90 ppm eU apatite grains yield apatite He and AFT dates inverted by 300 million years. These samples have average apatite Cl chemistry of ≤0.02 wt.%, with no correlation between Cl content and Dpar. Thermal history simulations using geologic constraints, an apatite He radiation damage accumulation and annealing model, apatite He dates with the range of eU values, and AFT date and track length data, do not yield any viable time-temperature paths. Apatite He and AFT data modeled separately predict thermal histories with Paleozoic-Mesozoic peaks reheating temperatures differing by ≥15 °C. By modifying the parameter controlling damage annealing (Rmr0) from the canonical 0.83 to 0.5-0.6, forward models reproduce the apatite He date-eU correlation and AFT dates with a common thermal history. Results imply apatite radiation damage anneals at higher temperatures than fission-track damage and the impact on coupled apatite He and AFT dates is magnified for protracted cooling histories. Further experimental and field-based tests are important for refining radiation damage and fission-track annealing parameters for accurate interpretation of apatite He- and AFT-derived thermal histories.

2-D Ultrasound Sparse Arrays Multidepth Radiation Optimization Using Simulated Annealing and Spiral-Array Inspired Energy Functions.

PubMed

Roux, Emmanuel; Ramalli, Alessandro; Tortoli, Piero; Cachard, Christian; Robini, Marc C; Liebgott, Herve

2016-12-01

Full matrix arrays are excellent tools for 3-D ultrasound imaging, but the required number of active elements is too high to be individually controlled by an equal number of scanner channels. The number of active elements is significantly reduced by the sparse array techniques, but the position of the remaining elements must be carefully optimized. This issue is faced here by introducing novel energy functions in the simulated annealing (SA) algorithm. At each iteration step of the optimization process, one element is freely translated and the associated radiated pattern is simulated. To control the pressure field behavior at multiple depths, three energy functions inspired by the pressure field radiated by a Blackman-tapered spiral array are introduced. Such energy functions aim at limiting the main lobe width while lowering the side lobe and grating lobe levels at multiple depths. Numerical optimization results illustrate the influence of the number of iterations, pressure measurement points, and depths, as well as the influence of the energy function definition on the optimized layout. It is also shown that performance close to or even better than the one provided by a spiral array, here assumed as reference, may be obtained. The finite-time convergence properties of SA allow the duration of the optimization process to be set in advance.

Simplified Models for Accelerated Structural Prediction of Conjugated Semiconducting Polymers

DOE PAGES

Henry, Michael M.; Jones, Matthew L.; Oosterhout, Stefan D.; ...

2017-11-08

We perform molecular dynamics simulations of poly(benzodithiophene-thienopyrrolodione) (BDT-TPD) oligomers in order to evaluate the accuracy with which unoptimized molecular models can predict experimentally characterized morphologies. The predicted morphologies are characterized using simulated grazing-incidence X-ray scattering (GIXS) and compared to the experimental scattering patterns. We find that approximating the aromatic rings in BDT-TPD with rigid bodies, rather than combinations of bond, angle, and dihedral constraints, results in 14% lower computational cost and provides nearly equivalent structural predictions compared to the flexible model case. The predicted glass transition temperature of BDT-TPD (410 +/- 32 K) is found to be in agreement withmore » experiments. Predicted morphologies demonstrate short-range structural order due to stacking of the chain backbones (p-p stacking around 3.9 A), and long-range spatial correlations due to the self-organization of backbone stacks into 'ribbons' (lamellar ordering around 20.9 A), representing the best-to-date computational predictions of structure of complex conjugated oligomers. We find that expensive simulated annealing schedules are not needed to predict experimental structures here, with instantaneous quenches providing nearly equivalent predictions at a fraction of the computational cost of annealing. We therefore suggest utilizing rigid bodies and fast cooling schedules for high-throughput screening studies of semiflexible polymers and oligomers to utilize their significant computational benefits where appropriate.« less

Simplified Models for Accelerated Structural Prediction of Conjugated Semiconducting Polymers

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

Henry, Michael M.; Jones, Matthew L.; Oosterhout, Stefan D.

We perform molecular dynamics simulations of poly(benzodithiophene-thienopyrrolodione) (BDT-TPD) oligomers in order to evaluate the accuracy with which unoptimized molecular models can predict experimentally characterized morphologies. The predicted morphologies are characterized using simulated grazing-incidence X-ray scattering (GIXS) and compared to the experimental scattering patterns. We find that approximating the aromatic rings in BDT-TPD with rigid bodies, rather than combinations of bond, angle, and dihedral constraints, results in 14% lower computational cost and provides nearly equivalent structural predictions compared to the flexible model case. The predicted glass transition temperature of BDT-TPD (410 +/- 32 K) is found to be in agreement withmore » experiments. Predicted morphologies demonstrate short-range structural order due to stacking of the chain backbones (p-p stacking around 3.9 A), and long-range spatial correlations due to the self-organization of backbone stacks into 'ribbons' (lamellar ordering around 20.9 A), representing the best-to-date computational predictions of structure of complex conjugated oligomers. We find that expensive simulated annealing schedules are not needed to predict experimental structures here, with instantaneous quenches providing nearly equivalent predictions at a fraction of the computational cost of annealing. We therefore suggest utilizing rigid bodies and fast cooling schedules for high-throughput screening studies of semiflexible polymers and oligomers to utilize their significant computational benefits where appropriate.« less

A Simulated Annealing based Optimization Algorithm for Automatic Variogram Model Fitting

NASA Astrophysics Data System (ADS)

Soltani-Mohammadi, Saeed; Safa, Mohammad

2016-09-01

Fitting a theoretical model to an experimental variogram is an important issue in geostatistical studies because if the variogram model parameters are tainted with uncertainty, the latter will spread in the results of estimations and simulations. Although the most popular fitting method is fitting by eye, in some cases use is made of the automatic fitting method on the basis of putting together the geostatistical principles and optimization techniques to: 1) provide a basic model to improve fitting by eye, 2) fit a model to a large number of experimental variograms in a short time, and 3) incorporate the variogram related uncertainty in the model fitting. Effort has been made in this paper to improve the quality of the fitted model by improving the popular objective function (weighted least squares) in the automatic fitting. Also, since the variogram model function (£) and number of structures (m) too affect the model quality, a program has been provided in the MATLAB software that can present optimum nested variogram models using the simulated annealing method. Finally, to select the most desirable model from among the single/multi-structured fitted models, use has been made of the cross-validation method, and the best model has been introduced to the user as the output. In order to check the capability of the proposed objective function and the procedure, 3 case studies have been presented.

Energetics and kinetics of primary charge separation in bacterial photosynthesis.

PubMed

LeBard, David N; Kapko, Vitaliy; Matyushov, Dmitry V

2008-08-21

We report the results of molecular dynamics (MD) simulations and formal modeling of the free-energy surfaces and reaction rates of primary charge separation in the reaction center of Rhodobacter sphaeroides. Two simulation protocols were used to produce MD trajectories. Standard force-field potentials were employed in the first protocol. In the second protocol, the special pair was made polarizable to reproduce a high polarizability of its photoexcited state observed by Stark spectroscopy. The charge distribution between covalent and charge-transfer states of the special pair was dynamically adjusted during the simulation run. We found from both protocols that the breadth of electrostatic fluctuations of the protein/water environment far exceeds previous estimates, resulting in about 1.6 eV reorganization energy of electron transfer in the first protocol and 2.5 eV in the second protocol. Most of these electrostatic fluctuations become dynamically frozen on the time scale of primary charge separation, resulting in much smaller solvation contributions to the activation barrier. While water dominates solvation thermodynamics on long observation times, protein emerges as the major thermal bath coupled to electron transfer on the picosecond time of the reaction. Marcus parabolas were obtained for the free-energy surfaces of electron transfer by using the first protocol, while a highly asymmetric surface was obtained in the second protocol. A nonergodic formulation of the diffusion-reaction electron-transfer kinetics has allowed us to reproduce the experimental results for both the temperature dependence of the rate and the nonexponential decay of the population of the photoexcited special pair.

Microseismic response characteristics modeling and locating of underground water supply pipe leak

NASA Astrophysics Data System (ADS)

Wang, J.; Liu, J.

2015-12-01

In traditional methods of pipeline leak location, geophones must be located on the pipe wall. If the exact location of the pipeline is unknown, the leaks cannot be identified accurately. To solve this problem, taking into account the characteristics of the pipeline leak, we propose a continuous random seismic source model and construct geological models to investigate the proposed method for locating underground pipeline leaks. Based on two dimensional (2D) viscoacoustic equations and the staggered grid finite-difference (FD) algorithm, the microseismic wave field generated by a leaking pipe is modeled. Cross-correlation analysis and the simulated annealing (SA) algorithm were utilized to obtain the time difference and the leak location. We also analyze and discuss the effect of the number of recorded traces, the survey layout, and the offset and interval of the traces on the accuracy of the estimated location. The preliminary results of the simulation and data field experiment indicate that (1) a continuous random source can realistically represent the leak microseismic wave field in a simulation using 2D visco-acoustic equations and a staggered grid FD algorithm. (2) The cross-correlation method is effective for calculating the time difference of the direct wave relative to the reference trace. However, outside the refraction blind zone, the accuracy of the time difference is reduced by the effects of the refracted wave. (3) The acquisition method of time difference based on the microseismic theory and SA algorithm has a great potential for locating leaks from underground pipelines from an array located on the ground surface. Keywords: Viscoacoustic finite-difference simulation; continuous random source; simulated annealing algorithm; pipeline leak location

A novel protocol for dispatcher assisted CPR improves CPR quality and motivation among rescuers-A randomized controlled simulation study.

PubMed

Rasmussen, Stinne Eika; Nebsbjerg, Mette Amalie; Krogh, Lise Qvirin; Bjørnshave, Katrine; Krogh, Kristian; Povlsen, Jonas Agerlund; Riddervold, Ingunn Skogstad; Grøfte, Thorbjørn; Kirkegaard, Hans; Løfgren, Bo

2017-01-01

Emergency dispatchers use protocols to instruct bystanders in cardiopulmonary resuscitation (CPR). Studies changing one element in the dispatcher's protocol report improved CPR quality. Whether several changes interact is unknown and the effect of combining multiple changes previously reported to improve CPR quality into one protocol remains to be investigated. We hypothesize that a novel dispatch protocol, combining multiple beneficial elements improves CPR quality compared with a standard protocol. A novel dispatch protocol was designed including wording on chest compressions, using a metronome, regular encouragements and a 10-s rest each minute. In a simulated cardiac arrest scenario, laypersons were randomized to perform single-rescuer CPR guided with the novel or the standard protocol. a composite endpoint of time to first compression, hand position, compression depth and rate and hands-off time (maximum score: 22 points). Afterwards participants answered a questionnaire evaluating the dispatcher assistance. The novel protocol (n=61) improved CPR quality score compared with the standard protocol (n=64) (mean (SD): 18.6 (1.4)) points vs. 17.5 (1.7) points, p<0.001. The novel protocol resulted in deeper chest compressions (mean (SD): 58 (12)mm vs. 52 (13)mm, p=0.02) and improved rate of correct hand position (61% vs. 36%, p=0.01) compared with the standard protocol. In both protocols hands-off time was short. The novel protocol improved motivation among rescuers compared with the standard protocol (p=0.002). Participants guided with a standard dispatch protocol performed high quality CPR. A novel bundle of care protocol improved CPR quality score and motivation among rescuers. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The mechanical properties and microstructures of vanadium bearing high strength dual phase steels processed with continuous galvanizing line simulations

NASA Astrophysics Data System (ADS)

Gong, Yu

For galvanized or galvannealed steels to be commercially successful, they must exhibit several attributes: (i) easy and inexpensive processing in the hot mill, cold mill and on the coating line, (ii) high strength with good formability and spot weldability, and (iii) good corrosion resistance. At the beginning of this thesis, compositions with a common base but containing various additions of V or Nb with or without high N were designed and subjected to Gleeble simulations of different galvanizing(GI), galvannealing(GA) and supercooling processing. The results revealed the phase balance was strongly influenced by the different microalloying additions, while the strengths of each phase were somewhat less affected. Our research revealed that the amount of austenite formed during intercritical annealing can be strongly influenced by the annealing temperature and the pre-annealing conditions of the hot band (coiling temperature) and cold band (% cold reduction). In the late part of this thesis, the base composition was a low carbon steel which would exhibit good spot weldability. To this steel were added two levels of Cr and Mo for strengthening the ferrite and increasing the hardenability of intercritically formed austenite. Also, these steels were produced with and without the addition of vanadium in an effort to further increase the strength. Since earlier studies revealed a relationship between the nature of the starting cold rolled microstructure and the response to CGL processing, the variables of hot band coiling temperature and level of cold reduction prior to annealing were also studied. Finally, in an effort to increase strength and ductility of both the final sheet (general formability) and the sheared edges of cold punched holes (local formability), a new thermal path was developed that replaced the conventional GI ferrite-martensite microstructure with a new ferrite-martensite-tempered martensite and retained austenite microstructure. The new microstructure exhibited a somewhat lower strength but much high general and local formabilities. In this thesis, both the physical and mechanical metallurgy of these steels and processes will be discussed. This research has shown that simple compositions and processes can result in DP steels with so-called Generation III properties.

Software Modules for the Proximity-1 Space Link Interleaved Time Synchronization (PITS) Protocol

NASA Technical Reports Server (NTRS)

Woo, Simon S.; Veregge, John R.; Gao, Jay L.; Clare, Loren P.; Mills, David

2012-01-01

The Proximity-1 Space Link Interleaved Time Synchronization (PITS) protocol provides time distribution and synchronization services for space systems. A software prototype implementation of the PITS algorithm has been developed that also provides the test harness to evaluate the key functionalities of PITS with simulated data source and sink. PITS integrates time synchronization functionality into the link layer of the CCSDS Proximity-1 Space Link Protocol. The software prototype implements the network packet format, data structures, and transmit- and receive-timestamp function for a time server and a client. The software also simulates the transmit and receive-time stamp exchanges via UDP (User Datagram Protocol) socket between a time server and a time client, and produces relative time offsets and delay estimates.

Design Science Research toward Designing/Prototyping a Repeatable Model for Testing Location Management (LM) Algorithms for Wireless Networking

ERIC Educational Resources Information Center

Peacock, Christopher

2012-01-01

The purpose of this research effort was to develop a model that provides repeatable Location Management (LM) testing using a network simulation tool, QualNet version 5.1 (2011). The model will provide current and future protocol developers a framework to simulate stable protocol environments for development. This study used the Design Science…

Building America House Simulation Protocols

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

Hendron, Robert; Engebrecht, Cheryn

2010-09-01

The House Simulation Protocol document was developed to track and manage progress toward Building America's multi-year, average whole-building energy reduction research goals for new construction and existing homes, using a consistent analytical reference point. This report summarizes the guidelines for developing and reporting these analytical results in a consistent and meaningful manner for all home energy uses using standard operating conditions.

Pathway for recovery of photo-degraded polymer solar cells by post degradation thermal anneal

DOE PAGES

Bhattacharya, J.; Joshi, P. H.; Biswas, Rana; ...

2017-02-16

The photo-degradation of polymer solar cells is a critical challenge preventing its commercial deployment. We experimentally fabricate organic solar cells and characterize their degradation under solar simulators in an environmental chamber under nitrogen flow, without exposure to oxygen and moisture. We have developed a thermally stable inverted organic solar cell architecture in which light induced degradation of device characteristics can be reversibly annealed to the pristine values. The stable inverted cells utilized MoO x layers that are thermally treated immediately after their deposition on the organic layer, and before metal cathode deposition. Organic solar cells that are photo-degraded in themore » presence of oxygen, however show irreversible degradation that cannot be thermally recovered. The decrease of organic solar cell characteristics correlates with increases in mid-gap electronic states, measured using capacitance spectroscopy and dark current. It is likely the photo-induced defect states caused by local H motion from the alkyl chains to the aromatic backbone, can be reversibly annealed at elevated temperatures after photo-degradation. Finally, our results provide a pathway for improving the stability of organic photovoltaics.« less

Microstructure and Property Modifications of Cold Rolled IF Steel by Local Laser Annealing

NASA Astrophysics Data System (ADS)

Hallberg, Håkan; Adamski, Frédéric; Baïz, Sarah; Castelnau, Olivier

2017-10-01

Laser annealing experiments are performed on cold rolled IF steel whereby highly localized microstructure and property modification are achieved. The microstructure is seen to develop by strongly heterogeneous recrystallization to provide steep gradients, across the submillimeter scale, of grain size and crystallographic texture. Hardness mapping by microindentation is used to reveal the corresponding gradients in macroscopic properties. A 2D level set model of the microstructure development is established as a tool to further optimize the method and to investigate, for example, the development of grain size variations due to the strong and transient thermal gradient. Particular focus is given to the evolution of the beneficial γ-fiber texture during laser annealing. The simulations indicate that the influence of selective growth based on anisotropic grain boundary properties only has a minor effect on texture evolution compared to heterogeneous stored energy, temperature variations, and nucleation conditions. It is also shown that although the α-fiber has an initial frequency advantage, the higher probability of γ-nucleation, in combination with a higher stored energy driving force in this fiber, promotes a stronger presence of the γ-fiber as also observed in experiments.

Synthesis of graphene and graphene nanostructures by ion implantation and pulsed laser annealing

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

Wang, Xiaotie; Rudawski, Nicholas G.; Appleton, Bill R.

2016-07-14

In this paper, we report a systematic study that shows how the numerous processing parameters associated with ion implantation (II) and pulsed laser annealing (PLA) can be manipulated to control the quantity and quality of graphene (G), few-layer graphene (FLG), and other carbon nanostructures selectively synthesized in crystalline SiC (c-SiC). Controlled implantations of Si{sup −} plus C{sup −} and Au{sup +} ions in c-SiC showed that both the thickness of the amorphous layer formed by ion damage and the doping effect of the implanted Au enhance the formation of G and FLG during PLA. The relative contributions of the amorphousmore » and doping effects were studied separately, and thermal simulation calculations were used to estimate surface temperatures and to help understand the phase changes occurring during PLA. In addition to the amorphous layer thickness and catalytic doping effects, other enhancement effects were found to depend on other ion species, the annealing environment, PLA fluence and number of pulses, and even laser frequency. Optimum II and PLA conditions are identified and possible mechanisms for selective synthesis of G, FLG, and carbon nanostructures are discussed.« less

Growth and Surface Modification of LaFeO3 Thin Films Induced By Reductive Annealing

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

Flynn, Brendan T.; Zhang, Hongliang; Shutthanandan, V.

2015-03-01

The electronic and ionic conductivity of perovskite oxides has enabled their use in diverse applications such as automotive exhaust catalysts, solid oxide fuel cell cathodes, and visible light photocatalysts. The redox chemistry at the surface of perovskite oxides is largely dependent on the oxidation state of the metal cations as well as the oxide surface stoichiometry. In this study, LaFeO3 (LFO) thin films grown on yttria-stabilized zirconia (YSZ) was characterized using both bulk and surface sensitive techniques. A combination of in situ reflection high energy electron diffraction (RHEED), x-ray diffraction (XRD), transmission electron microscopy (TEM) and Rutherford backscattering spectrometry (RBS)more » demonstrated that the film is highly oriented and stoichiometric. The film was annealed in an ultra-high vacuum chamber to simulate reducing conditions and studied by angle-resolved x-ray photoelectron spectroscopy (XPS). Iron was found to exist as Fe(0), Fe(II), and Fe(III) depending on the annealing conditions and the depth within the film. A decrease in the concentration of surface oxygen species was correlated with iron reduction. These results should help guide and enhance the design of perovskite materials for catalysts.« less

Long-term fuel retention and release in JET ITER-Like Wall at ITER-relevant baking temperatures

NASA Astrophysics Data System (ADS)

Heinola, K.; Likonen, J.; Ahlgren, T.; Brezinsek, S.; De Temmerman, G.; Jepu, I.; Matthews, G. F.; Pitts, R. A.; Widdowson, A.; Contributors, JET

2017-08-01

The fuel outgassing efficiency from plasma-facing components exposed in JET-ILW has been studied at ITER-relevant baking temperatures. Samples retrieved from the W divertor and Be main chamber were annealed at 350 and 240 °C, respectively. Annealing was performed with thermal desoprtion spectrometry (TDS) for 0, 5 and 15 h to study the deuterium removal effectiveness at the nominal baking temperatures. The remained fraction was determined by emptying the samples fully of deuterium by heating W and Be samples up to 1000 and 775 °C,respectively. Results showed the deposits in the divertor having an increasing effect to the remaining retention at temperatures above baking. Highest remaining fractions 54 and 87 % were observed with deposit thicknesses of 10 and 40 μm, respectively. Substantially high fractions were obtained in the main chamber samples from the deposit-free erosion zone of the limiter midplane, in which the dominant fuel retention mechanism is via implantation: 15 h annealing resulted in retained deuterium higher than 90 % . TDS results from the divertor were simulated with TMAP7 calculations. The spectra were modelled with three deuterium activation energies resulting in good agreement with the experiments.

Pathway for recovery of photo-degraded polymer solar cells by post degradation thermal anneal

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

Bhattacharya, J.; Joshi, P. H.; Biswas, Rana

The photo-degradation of polymer solar cells is a critical challenge preventing its commercial deployment. We experimentally fabricate organic solar cells and characterize their degradation under solar simulators in an environmental chamber under nitrogen flow, without exposure to oxygen and moisture. We have developed a thermally stable inverted organic solar cell architecture in which light induced degradation of device characteristics can be reversibly annealed to the pristine values. The stable inverted cells utilized MoO x layers that are thermally treated immediately after their deposition on the organic layer, and before metal cathode deposition. Organic solar cells that are photo-degraded in themore » presence of oxygen, however show irreversible degradation that cannot be thermally recovered. The decrease of organic solar cell characteristics correlates with increases in mid-gap electronic states, measured using capacitance spectroscopy and dark current. It is likely the photo-induced defect states caused by local H motion from the alkyl chains to the aromatic backbone, can be reversibly annealed at elevated temperatures after photo-degradation. Finally, our results provide a pathway for improving the stability of organic photovoltaics.« less

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing.

PubMed

Lee, Juyong; Lee, Jinhyuk; Sasaki, Takeshi N; Sasai, Masaki; Seok, Chaok; Lee, Jooyoung

2011-08-01

Ab initio protein structure prediction is a challenging problem that requires both an accurate energetic representation of a protein structure and an efficient conformational sampling method for successful protein modeling. In this article, we present an ab initio structure prediction method which combines a recently suggested novel way of fragment assembly, dynamic fragment assembly (DFA) and conformational space annealing (CSA) algorithm. In DFA, model structures are scored by continuous functions constructed based on short- and long-range structural restraint information from a fragment library. Here, DFA is represented by the full-atom model by CHARMM with the addition of the empirical potential of DFIRE. The relative contributions between various energy terms are optimized using linear programming. The conformational sampling was carried out with CSA algorithm, which can find low energy conformations more efficiently than simulated annealing used in the existing DFA study. The newly introduced DFA energy function and CSA sampling algorithm are implemented into CHARMM. Test results on 30 small single-domain proteins and 13 template-free modeling targets of the 8th Critical Assessment of protein Structure Prediction show that the current method provides comparable and complementary prediction results to existing top methods. Copyright © 2011 Wiley-Liss, Inc.

Characterization of the probabilistic traveling salesman problem.

PubMed

Bowler, Neill E; Fink, Thomas M A; Ball, Robin C

2003-09-01

We show that stochastic annealing can be successfully applied to gain new results on the probabilistic traveling salesman problem. The probabilistic "traveling salesman" must decide on an a priori order in which to visit n cities (randomly distributed over a unit square) before learning that some cities can be omitted. We find the optimized average length of the pruned tour follows E(L(pruned))=sqrt[np](0.872-0.105p)f(np), where p is the probability of a city needing to be visited, and f(np)-->1 as np--> infinity. The average length of the a priori tour (before omitting any cities) is found to follow E(L(a priori))=sqrt[n/p]beta(p), where beta(p)=1/[1.25-0.82 ln(p)] is measured for 0.05< or =p< or =0.6. Scaling arguments and indirect measurements suggest that beta(p) tends towards a constant for p<0.03. Our stochastic annealing algorithm is based on limited sampling of the pruned tour lengths, exploiting the sampling error to provide the analog of thermal fluctuations in simulated (thermal) annealing. The method has general application to the optimization of functions whose cost to evaluate rises with the precision required.

PROTOCOL TO EVALUATE THE MOISTURE DURABILITY OF ENERGY-EFFICIENT WALLS

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

Boudreaux, Philip R; Pallin, Simon B; Hun, Diana E

Walls account for about 8% of the energy used in residential buildings. This energy penalty can be reduced with higher insulation levels and increased airtightness. However, these measures can compromise the moisture durability and long-term performance of wall assemblies because they can lead to lower moisture tolerance due to reduced drying potential. To avert these problems, a moisture durability protocol was developed to evaluate the probability that an energy-efficient wall design will experience mold growth. This protocol examines the effects of moisture sources in walls through a combination of simulations and lab experiments, uses the mold growth index as themore » moisture durability indicator, and is based on a probabilistic approach that utilizes stochastically varying input parameters. The simulation tools used include a new validated method for taking into account the effects of air leakage in wall assemblies This paper provides an overview of the developed protocol, discussion of the probabilistic simulation approach and describes results from the evaluation of two wall assemblies in Climate Zones 2, 4, and 6. The protocol will be used to supply builders with wall designs that are energy efficient, moisture durable and cost-effective.« less

Direction based Hazard Routing Protocol (DHRP) for disseminating road hazard information using road side infrastructures in VANETs.

PubMed

Berlin, M A; Anand, Sheila

2014-01-01

This paper presents Direction based Hazard Routing Protocol (DHRP) for disseminating information about fixed road hazards such as road blocks, tree fall, boulders on road, snow pile up, landslide, road maintenance work and other obstacles to the vehicles approaching the hazardous location. The proposed work focuses on dissemination of hazard messages on highways with sparse traffic. The vehicle coming across the hazard would report the presence of the hazard. It is proposed to use Road Side fixed infrastructure Units for reliable and timely delivery of hazard messages to vehicles. The vehicles can then take appropriate safety action to avoid the hazardous location. The proposed protocol has been implemented and tested using SUMO simulator to generate road traffic and NS 2.33 network simulator to analyze the performance of DHRP. The performance of the proposed protocol was also compared with simple flooding protocol and the results are presented.

Phase 1 Free Air CO2 Enrichment Model-Data Synthesis (FACE-MDS): Model Output Data (2015)

DOE Data Explorer

Walker, A. P.; De Kauwe, M. G.; Medlyn, B. E.; Zaehle, S.; Asao, S.; Dietze, M.; El-Masri, B.; Hanson, P. J.; Hickler, T.; Jain, A.; Luo, Y.; Parton, W. J.; Prentice, I. C.; Ricciuto, D. M.; Thornton, P. E.; Wang, S.; Wang, Y -P; Warlind, D.; Weng, E.; Oren, R.; Norby, R. J.

2015-01-01

These datasets comprise the model output from phase 1 of the FACE-MDS. These include simulations of the Duke and Oak Ridge experiments and also idealised long-term (300 year) simulations at both sites (please see the modelling protocol for details). Included as part of this dataset are modelling and output protocols. The model datasets are formatted according to the output protocols. Phase 1 datasets are reproduced here for posterity and reproducibility although the model output for the experimental period have been somewhat superseded by the Phase 2 datasets.

A Stochastic Point Cloud Sampling Method for Multi-Template Protein Comparative Modeling.

PubMed

Li, Jilong; Cheng, Jianlin

2016-05-10

Generating tertiary structural models for a target protein from the known structure of its homologous template proteins and their pairwise sequence alignment is a key step in protein comparative modeling. Here, we developed a new stochastic point cloud sampling method, called MTMG, for multi-template protein model generation. The method first superposes the backbones of template structures, and the Cα atoms of the superposed templates form a point cloud for each position of a target protein, which are represented by a three-dimensional multivariate normal distribution. MTMG stochastically resamples the positions for Cα atoms of the residues whose positions are uncertain from the distribution, and accepts or rejects new position according to a simulated annealing protocol, which effectively removes atomic clashes commonly encountered in multi-template comparative modeling. We benchmarked MTMG on 1,033 sequence alignments generated for CASP9, CASP10 and CASP11 targets, respectively. Using multiple templates with MTMG improves the GDT-TS score and TM-score of structural models by 2.96-6.37% and 2.42-5.19% on the three datasets over using single templates. MTMG's performance was comparable to Modeller in terms of GDT-TS score, TM-score, and GDT-HA score, while the average RMSD was improved by a new sampling approach. The MTMG software is freely available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/mtmg.html.

A Stochastic Point Cloud Sampling Method for Multi-Template Protein Comparative Modeling

PubMed Central

Li, Jilong; Cheng, Jianlin

2016-01-01

Generating tertiary structural models for a target protein from the known structure of its homologous template proteins and their pairwise sequence alignment is a key step in protein comparative modeling. Here, we developed a new stochastic point cloud sampling method, called MTMG, for multi-template protein model generation. The method first superposes the backbones of template structures, and the Cα atoms of the superposed templates form a point cloud for each position of a target protein, which are represented by a three-dimensional multivariate normal distribution. MTMG stochastically resamples the positions for Cα atoms of the residues whose positions are uncertain from the distribution, and accepts or rejects new position according to a simulated annealing protocol, which effectively removes atomic clashes commonly encountered in multi-template comparative modeling. We benchmarked MTMG on 1,033 sequence alignments generated for CASP9, CASP10 and CASP11 targets, respectively. Using multiple templates with MTMG improves the GDT-TS score and TM-score of structural models by 2.96–6.37% and 2.42–5.19% on the three datasets over using single templates. MTMG’s performance was comparable to Modeller in terms of GDT-TS score, TM-score, and GDT-HA score, while the average RMSD was improved by a new sampling approach. The MTMG software is freely available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/mtmg.html. PMID:27161489

Quantum chemical molecular dynamics simulation of single-walled carbon nanotube cap nucleation on an iron particle.

PubMed

Ohta, Yasuhito; Okamoto, Yoshiko; Page, Alister J; Irle, Stephan; Morokuma, Keiji

2009-11-24

The atomic scale details of single-walled carbon nanotube (SWNT) nucleation on metal catalyst particles are elusive to experimental observations. Computer simulation of metal-catalyzed SWNT nucleation is a challenging topic but potentially of great importance to understand the factors affecting SWNT diameters, chirality, and growth efficiency. In this work, we use nonequilibrium density functional tight-binding molecular dynamics simulations and report nucleation of sp(2)-carbon cap structures on an iron particle consisting of 38 atoms. One C(2) molecule was placed every 1.0 ps around an Fe(38) cluster for 30 ps, after which a further 410 ps of annealing simulation without carbon supply was performed. We find that sp(2)-carbon network nucleation and annealing processes occur in three sequential and repetitive stages: (A) polyyne chains on the metal surface react with each other to evolve into a Y-shaped polyyne junction, which preferentially form a five-membered ring as a nucleus; (B) polyyne chains on the first five-membered ring form an additional fused five- or six-membered ring; and (C) pentagon-to-hexagon self-healing rearrangement takes place with the help of short-lived polyyne chains, stabilized by the mobile metal atoms. The observed nucleation process resembles the formation of a fullerene cage. However, the metal particle plays a key role in differentiating the nucleation process from fullerene cage formation, most importantly by keeping the growing cap structure from closing into a fullerene cage and by keeping the carbon edge "alive" for the addition of new carbon material.

Surface structure and stability of partially hydroxylated silica surfaces

DOE PAGES

Rimsza, J. M.; Jones, R. E.; Criscenti, L. J.

2017-04-04

Surface energies of silicates influence crack propagation during brittle fracture and decrease with surface relaxation caused by annealing and hydroxylation. Molecular-level simulations are particularly suited for the investigation of surface processes. In this work, classical MD simulations of silica surfaces are performed with two force fields (ClayFF and ReaxFF) to investigate the effect of force field reactivity on surface structure and energy as a function of surface hydroxylation. An unhydroxylated fracture surface energy of 5.1 J/m 2 is calculated with the ClayFF force field, and 2.0 J/m 2 is calculated for the ReaxFF force field. The ClayFF surface energies aremore » consistent with the experimental results from double cantilever beam fracture tests (4.5 J/m 2), whereas ReaxFF underestimated these surface energies. Surface relaxation via annealing and hydroxylation was performed by creating a low-energy equilibrium surface. Annealing condensed neighboring siloxane bonds increased the surface connectivity, and decreased the surface energies by 0.2 J/m 2 for ClayFF and 0.8 J/m 2 for ReaxFF. Posthydroxylation surface energies decreased further to 4.6 J/m 2 with the ClayFF force field and to 0.2 J/m 2 with the ReaxFF force field. Experimental equilibrium surface energies are ~0.35 J/m 2, consistent with the ReaxFF force field. Although neither force field was capable of replicating both the fracture and equilibrium surface energies reported from experiment, each was consistent with one of these conditions. Furthermore, future computational investigations that rely on accurate surface energy values should consider the surface state of the system and select the appropriate force field.« less

Annealed Importance Sampling Reversible Jump MCMC algorithms

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

Karagiannis, Georgios; Andrieu, Christophe

2013-03-20

It will soon be 20 years since reversible jump Markov chain Monte Carlo (RJ-MCMC) algorithms have been proposed. They have significantly extended the scope of Markov chain Monte Carlo simulation methods, offering the promise to be able to routinely tackle transdimensional sampling problems, as encountered in Bayesian model selection problems for example, in a principled and flexible fashion. Their practical efficient implementation, however, still remains a challenge. A particular difficulty encountered in practice is in the choice of the dimension matching variables (both their nature and their distribution) and the reversible transformations which allow one to define the one-to-one mappingsmore » underpinning the design of these algorithms. Indeed, even seemingly sensible choices can lead to algorithms with very poor performance. The focus of this paper is the development and performance evaluation of a method, annealed importance sampling RJ-MCMC (aisRJ), which addresses this problem by mitigating the sensitivity of RJ-MCMC algorithms to the aforementioned poor design. As we shall see the algorithm can be understood as being an “exact approximation” of an idealized MCMC algorithm that would sample from the model probabilities directly in a model selection set-up. Such an idealized algorithm may have good theoretical convergence properties, but typically cannot be implemented, and our algorithms can approximate the performance of such idealized algorithms to an arbitrary degree while not introducing any bias for any degree of approximation. Our approach combines the dimension matching ideas of RJ-MCMC with annealed importance sampling and its Markov chain Monte Carlo implementation. We illustrate the performance of the algorithm with numerical simulations which indicate that, although the approach may at first appear computationally involved, it is in fact competitive.« less

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

Rimsza, J. M.; Jones, R. E.; Criscenti, L. J.

Surface energies of silicates influence crack propagation during brittle fracture and decrease with surface relaxation caused by annealing and hydroxylation. Molecular-level simulations are particularly suited for the investigation of surface processes. In this work, classical MD simulations of silica surfaces are performed with two force fields (ClayFF and ReaxFF) to investigate the effect of force field reactivity on surface structure and energy as a function of surface hydroxylation. An unhydroxylated fracture surface energy of 5.1 J/m 2 is calculated with the ClayFF force field, and 2.0 J/m 2 is calculated for the ReaxFF force field. The ClayFF surface energies aremore » consistent with the experimental results from double cantilever beam fracture tests (4.5 J/m 2), whereas ReaxFF underestimated these surface energies. Surface relaxation via annealing and hydroxylation was performed by creating a low-energy equilibrium surface. Annealing condensed neighboring siloxane bonds increased the surface connectivity, and decreased the surface energies by 0.2 J/m 2 for ClayFF and 0.8 J/m 2 for ReaxFF. Posthydroxylation surface energies decreased further to 4.6 J/m 2 with the ClayFF force field and to 0.2 J/m 2 with the ReaxFF force field. Experimental equilibrium surface energies are ~0.35 J/m 2, consistent with the ReaxFF force field. Although neither force field was capable of replicating both the fracture and equilibrium surface energies reported from experiment, each was consistent with one of these conditions. Furthermore, future computational investigations that rely on accurate surface energy values should consider the surface state of the system and select the appropriate force field.« less

Discrete Optimization of Electronic Hyperpolarizabilities in a Chemical Subspace

DTIC Science & Technology

2009-05-01

molecular design. Methods for optimization in discrete spaces have been studied extensively and recently reviewed ( 5). Optimization methods include...integer programming, as in branch-and-bound techniques (including dead-end elimination [ 6]), simulated annealing ( 7), and genetic algorithms ( 8...These algorithms have found renewed interest and application in molecular and materials design (9- 12) . Recently, new approaches have been

Comprehensive Model of Single Particle Pulverized Coal Combustion Extended to Oxy-Coal Conditions

DOE PAGES

Holland, Troy; Fletcher, Thomas H.

2017-02-22

Oxy-fired coal combustion is a promising potential carbon capture technology. Predictive CFD simulations are valuable tools in evaluating and deploying oxy-fuel and other carbon capture technologies either as retrofit technologies or for new construction. But, accurate predictive simulations require physically realistic submodels with low computational requirements. In particular, comprehensive char oxidation and gasification models have been developed that describe multiple reaction and diffusion processes. Our work extends a comprehensive char conversion code (CCK), which treats surface oxidation and gasification reactions as well as processes such as film diffusion, pore diffusion, ash encapsulation, and annealing. In this work several submodels inmore » the CCK code were updated with more realistic physics or otherwise extended to function in oxy-coal conditions. Improved submodels include the annealing model, the swelling model, the mode of burning parameter, and the kinetic model, as well as the addition of the chemical percolation devolatilization (CPD) model. We compare our results of the char combustion model to oxy-coal data, and further compared to parallel data sets near conventional conditions. A potential method to apply the detailed code in CFD work is given.« less

Comprehensive Model of Single Particle Pulverized Coal Combustion Extended to Oxy-Coal Conditions

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

Holland, Troy; Fletcher, Thomas H.

Oxy-fired coal combustion is a promising potential carbon capture technology. Predictive CFD simulations are valuable tools in evaluating and deploying oxy-fuel and other carbon capture technologies either as retrofit technologies or for new construction. But, accurate predictive simulations require physically realistic submodels with low computational requirements. In particular, comprehensive char oxidation and gasification models have been developed that describe multiple reaction and diffusion processes. Our work extends a comprehensive char conversion code (CCK), which treats surface oxidation and gasification reactions as well as processes such as film diffusion, pore diffusion, ash encapsulation, and annealing. In this work several submodels inmore » the CCK code were updated with more realistic physics or otherwise extended to function in oxy-coal conditions. Improved submodels include the annealing model, the swelling model, the mode of burning parameter, and the kinetic model, as well as the addition of the chemical percolation devolatilization (CPD) model. We compare our results of the char combustion model to oxy-coal data, and further compared to parallel data sets near conventional conditions. A potential method to apply the detailed code in CFD work is given.« less

Heterostructured ZnFe2O4/Fe2TiO5/TiO2 Composite Nanotube Arrays with an Improved Photocatalysis Degradation Efficiency Under Simulated Sunlight Irradiation

NASA Astrophysics Data System (ADS)

Xiong, Kun; Wang, Kunzhou; Chen, Lin; Wang, Xinqing; Fan, Qingbo; Courtois, Jérémie; Liu, Yuliang; Tuo, Xianguo; Yan, Minhao

2018-03-01

To improve the visible light absorption and photocatalytic activity of titanium dioxide nanotube arrays (TONTAs), ZnFe2O4 (ZFO) nanocrystals were perfused into pristine TONTA pipelines using a novel bias voltage-assisted perfusion method. ZFO nanocrystals were well anchored on the inner walls of the pristine TONTAs when the ZFO suspensions (0.025 mg mL-1) were kept under a 60 V bias voltage for 1 h. After annealing at 750 °C for 2 h, the heterostructured ZFO/Fe2TiO5 (FTO)/TiO2 composite nanotube arrays were successfully obtained. Furthermore, Fe3+ was reduced to Fe2+ when solid solution reactions occurred at the interface of ZFO and the pristine TONTAs. Introducing ZFO significantly enhanced the visible light absorption of the ZFO/FTO/TONTAs relative to that of the annealed TONTAs. The coexistence of type I and staggered type II band alignment in the ZFO/FTO/TONTAs facilitated the separation of photogenerated electrons and holes, thereby improving the efficiency of the ZFO/FTO/TONTAs for photocatalytic degradation of methylene blue when irradiated with simulated sunlight. [Figure not available: see fulltext.