Bayesian ensemble refinement by replica simulations and reweighting.

PubMed

Hummer, Gerhard; Köfinger, Jürgen

2015-12-28

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.

Design of replica bit line control circuit to optimize power for SRAM

NASA Astrophysics Data System (ADS)

Pengjun, Wang; Keji, Zhou; Huihong, Zhang; Daohui, Gong

2016-12-01

A design of a replica bit line control circuit to optimize power for SRAM is proposed. The proposed design overcomes the limitations of the traditional replica bit line control circuit, which cannot shut off the word line in time. In the novel design, the delay of word line enable and disable paths are balanced. Thus, the word line can be opened and shut off in time. Moreover, the chip select signal is decomposed, which prevents feedback oscillations caused by the replica bit line and the replica word line. As a result, the switch power caused by unnecessary discharging of the bit line is reduced. A 2-kb SRAM is fully custom designed in an SMIC 65-nm CMOS process. The traditional replica bit line control circuit and the new replica bit line control circuit are used in the designed SRAM, and their performances are compared with each other. The experimental results show that at a supply voltage of 1.2 V, the switch power consumption of the memory array can be reduced by 53.7%. Project supported by the Zhejiang Provincial Natural Science Foundation of China (No. LQ14F040001), the National Natural Science Foundation of China (Nos. 61274132, 61234002, 61474068), and the K. C. Wong Magna Fund in Ningbo University.

Bayesian ensemble refinement by replica simulations and reweighting

NASA Astrophysics Data System (ADS)

Hummer, Gerhard; Köfinger, Jürgen

2015-12-01

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations

PubMed Central

Henriksen, Niel M.; Roe, Daniel R.; Cheatham, Thomas E.

2013-01-01

Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 microseconds of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations. PMID:23477537

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.

PubMed

Henriksen, Niel M; Roe, Daniel R; Cheatham, Thomas E

2013-04-18

Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example, by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 μs of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations.

Neurovascular Modeling: Small-Batch Manufacturing of Silicone Vascular Replicas

PubMed Central

Chueh, J.Y.; Wakhloo, A.K.; Gounis, M.J.

2009-01-01

BACKGROUND AND PURPOSE Realistic, population based cerebrovascular replicas are required for the development of neuroendovascular devices. The objective of this work was to develop an efficient methodology for manufacturing realistic cerebrovascular replicas. MATERIALS AND METHODS Brain MR angiography data from 20 patients were acquired. The centerline of the vasculature was calculated, and geometric parameters were measured to describe quantitatively the internal carotid artery (ICA) siphon. A representative model was created on the basis of the quantitative measurements. Using this virtual model, we designed a mold with core-shell structure and converted it into a physical object by fused-deposit manufacturing. Vascular replicas were created by injection molding of different silicones. Mechanical properties, including the stiffness and luminal coefficient of friction, were measured. RESULTS The average diameter, length, and curvature of the ICA siphon were 4.15 ± 0.09 mm, 22.60 ± 0.79 mm, and 0.34 ± 0.02 mm-1 (average ± standard error of the mean), respectively. From these image datasets, we created a median virtual model, which was transformed into a physical replica by an efficient batch-manufacturing process. The coefficient of friction of the luminal surface of the replica was reduced by up to 55% by using liquid silicone rubber coatings. The modulus ranged from 0.67 to 1.15 MPa compared with 0.42 MPa from human postmortem studies, depending on the material used to make the replica. CONCLUSIONS Population-representative, smooth, and true-to-scale silicone arterial replicas with uniform wall thickness were successfully built for in vitro neurointerventional device-testing by using a batch-manufacturing process. PMID:19321626

Rapid prototyping to create vascular replicas from CT scan data: making tools to teach, rehearse, and choose treatment strategies.

PubMed

Knox, K; Kerber, Charles W; Singel, S A; Bailey, M J; Imbesi, S G

2005-05-01

Our goal was to develop and prove the accuracy of a system that would allow us to re-create live patient arterial pathology. Anatomically accurate replicas of blood vessels could allow physicians to teach and practice dangerous interventional techniques and might also be used to gather basic physiologic information. The preparation of replicas has, until now, depended on acquisition of fresh cadaver material. Using rapid prototyping, it should be able to replicate vascular pathology in a live patient. We obtained CT angiographic scan data from two patients with known arterial abnormalities. We took such data and, using proprietary software, created a 3D replica using a commercially available rapid prototyping machine. From the prototypes, using a lost wax technique, we created vessel replicas, placed those replicas in the CT scanner, then compared those images with the original scans. Comparison of the images made directly from the patient and from the replica showed that with each step, the relationships were maintained, remaining within 3% of the original, but some smoothing occurred in the final computer manipulation. From routinely obtainable CT angiographic data, it is possible to create accurate replicas of human vascular pathology with the aid of commercially available stereolithography equipment. Visual analysis of the images appeared to be as important as the measurements. With 64 and 128 slice detector scanners becoming available, acquisition times fall enough that we should be able to model rapidly moving structures such as the aortic root. (c) 2005 Wiley-Liss, Inc.

A Novel General Chemistry Laboratory: Creation of Biomimetic Superhydrophobic Surfaces through Replica Molding

ERIC Educational Resources Information Center

Verbanic, Samuel; Brady, Owen; Sanda, Ahmed; Gustafson, Carolina; Donhauser, Zachary J.

2014-01-01

Biomimetic replicas of superhydrophobic lotus and taro leaf surfaces can be made using polydimethylsiloxane. These replicas faithfully reproduce the microstructures of the leaves' surface and can be analyzed using contact angle goniometry, self-cleaning experiments, and optical microscopy. These simple and adaptable experiments were used to…

Flexible Nonstick Replica Mold for Transfer Printing of Ag Ink.

PubMed

Lee, Bong Kuk; Yu, Han Young; Kim, Yarkyeon; Yoon, Yong Sun; Jang, Won Ik; Do, Lee-Mi; Park, Ji-Ho; Park, Jaehoon

2016-03-01

We report the fabrication of flexible replica molds for transfer printing of Ag ink on a rigid glass substrate. As mold precursors, acrylic mixtures were prepared from silsesquioxane-based materials, silicone acrylate, poly(propylene glycol) diacrylate, 3,3,4,4,5,5,6,6,7,7,8,8, 9,9,10,10,10-heptadecafluorodecyl methacrylate, and photoinitiator. By using these materials, the replica molds were fabricated from a silicon master onto a flexible substrate by means of UV-assisted molding process at room temperature. The wettability of Ag ink decreased with increase in the water contact angle of replica molds. On the other hand, the transfer rate of Ag ink onto adhesive-modified substrates increased with increase in the water contact angle of replica molds. Transferred patterns were found to be thermally stable on the photocurable adhesive layer, whereas Ag-ink patterns transferred on non-photocurable adhesives were distorted by thermal treatment. We believe that these characteristics of replica molds and adhesives offer a new strategy for the development of the transfer printing of solution-based ink materials.

Shaping ability of reciproc and TF adaptive systems in severely curved canals of rapid microCT-based prototyping molar replicas.

PubMed

Ordinola-Zapata, Ronald; Bramante, Clovis Monteiro; Duarte, Marco Antonio Húngaro; Cavenago, Bruno Cavalini; Jaramillo, David; Versiani, Marco Aurélio

2014-01-01

To evaluate the shaping ability of Reciproc and Twisted-File Adaptive systems in rapid prototyping replicas. Two mandibular molars showing S-shaped and 62-degree curvatures in the mesial root were scanned by using a microcomputed tomography (μCT) system. The data were exported in the stereolitograhic format and 20 samples of each molar were printed at 16 µm resolution. The mesial canals of 10 replicas of each specimen were prepared with each system. Transportation was measured by overlapping radiographs taken before and after preparation and resin thickness after instrumentation was measured by μCT. Both systems maintained the original shape of the apical third in both anatomies (P>0.05). Overall, considering the resin thickness in the 62-degree replicas, no statistical difference was found between the systems (P>0.05). In the S-shaped curvature replica, Reciproc significantly decreased the thickness of the resin walls in comparison with TF Adaptive. The evaluated systems were able to maintain the original shape at the apical third of severely curved mesial canals of molar replicas.

Accelerating the Convergence of Replica Exchange Simulations Using Gibbs Sampling and Adaptive Temperature Sets

DOE PAGES

Vogel, Thomas; Perez, Danny

2015-08-28

We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of relevant states through the whole ensemble of replicas. This mechanism depends on the knowledge of global thermodynamic functions which are measured during the simulation and not coupled to the heat bath temperatures driving the individual simulations. Therefore, this setup also allows for a continuous adaptation of the temperature set. In this paper, we will review the new scheme and demonstrate its capability. Furthermore, themore » method is particularly useful for the fast and reliable estimation of the microcanonical temperature T(U) or, equivalently, of the density of states g(U) over a wide range of energies.« less

Efficiency of exchange schemes in replica exchange

NASA Astrophysics Data System (ADS)

Lingenheil, Martin; Denschlag, Robert; Mathias, Gerald; Tavan, Paul

2009-08-01

In replica exchange simulations a fast diffusion of the replicas through the temperature space maximizes the efficiency of the statistical sampling. Here, we compare the diffusion speed as measured by the round trip rates for four exchange algorithms. We find different efficiency profiles with optimal average acceptance probabilities ranging from 8% to 41%. The best performance is determined by benchmark simulations for the most widely used algorithm, which alternately tries to exchange all even and all odd replica pairs. By analytical mathematics we show that the excellent performance of this exchange scheme is due to the high diffusivity of the underlying random walk.

Replica-based Crack Inspection

NASA Technical Reports Server (NTRS)

Newman, John A.; Smith, Stephen W.; Piascik, R. S.; Willard, Scott A.; Dawicke, David S.

2007-01-01

A surface replica-based crack inspection method has recently been developed for use in Space Shuttle main engine (SSME) hydrogen feedline flowliners. These flowliners exist to ensure favorable flow of liquid hydrogen over gimble joint bellows, and consist of two rings each containing 38 elongated slots. In the summer of 2002, multiple cracks ranging from 0.1 inches to 0.6 inches long were discovered; each orbiter contained at least one cracked flowliner. These long cracks were repaired and eddy current inspections ensured that no cracks longer than 0.075 inches were present. However, subsequent fracture-mechanics review of flight rationale required detection of smaller cracks, and was the driving force for development of higher-resolution inspection method. Acetate tape surface replicas have been used for decades to detect and monitor small cracks. However, acetate tape replicas have primarily been limited to laboratory specimens because complexities involved in making these replicas - requiring acetate tape to be dissolved with acetone - are not well suited for a crack inspection tool. More recently developed silicon-based replicas are better suited for use as a crack detection tool. A commercially available silicon-based replica product has been determined to be acceptable for use in SSME hydrogen feedlines. A method has been developed using this product and a scanning electron microscope for analysis, which can find cracks as small as 0.005 inches and other features (e.g., pits, scratches, tool marks, etc.) as small as 0.001 inches. The resolution of this method has been validated with dozens of cracks generated in a laboratory setting and this method has been used to locate 55 cracks (ranging in size from 0.040 inches to 0.004 inches) on space flight hardware. These cracks were removed by polishing away the cracked material and a second round of replicas confirmed the repair.

Shaping ability of Reciproc and TF Adaptive systems in severely curved canals of rapid microCT-based prototyping molar replicas

PubMed Central

ORDINOLA-ZAPATA, Ronald; BRAMANTE, Clovis Monteiro; DUARTE, Marco Antonio Húngaro; CAVENAGO, Bruno Cavalini; JARAMILLO, David; VERSIANI, Marco Aurélio

2014-01-01

Objective: To evaluate the shaping ability of Reciproc and Twisted-File Adaptive systems in rapid prototyping replicas. Material and Methods: Two mandibular molars showing S-shaped and 62-degree curvatures in the mesial root were scanned by using a microcomputed tomography (μCT) system. The data were exported in the stereolitograhic format and 20 samples of each molar were printed at 16 µm resolution. The mesial canals of 10 replicas of each specimen were prepared with each system. Transportation was measured by overlapping radiographs taken before and after preparation and resin thickness after instrumentation was measured by μCT. Results: Both systems maintained the original shape of the apical third in both anatomies (P>0.05). Overall, considering the resin thickness in the 62-degree replicas, no statistical difference was found between the systems (P>0.05). In the S-shaped curvature replica, Reciproc significantly decreased the thickness of the resin walls in comparison with TF Adaptive. Conclusions: The evaluated systems were able to maintain the original shape at the apical third of severely curved mesial canals of molar replicas. PMID:24918662

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

PubMed

Ostermeir, Katja; Zacharias, Martin

2014-12-01

Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations. © 2014 Wiley Periodicals, Inc.

Development of isothermal-isobaric replica-permutation method for molecular dynamics and Monte Carlo simulations and its application to reveal temperature and pressure dependence of folded, misfolded, and unfolded states of chignolin

NASA Astrophysics Data System (ADS)

Yamauchi, Masataka; Okumura, Hisashi

2017-11-01

We developed a two-dimensional replica-permutation molecular dynamics method in the isothermal-isobaric ensemble. The replica-permutation method is a better alternative to the replica-exchange method. It was originally developed in the canonical ensemble. This method employs the Suwa-Todo algorithm, instead of the Metropolis algorithm, to perform permutations of temperatures and pressures among more than two replicas so that the rejection ratio can be minimized. We showed that the isothermal-isobaric replica-permutation method performs better sampling efficiency than the isothermal-isobaric replica-exchange method and infinite swapping method. We applied this method to a β-hairpin mini protein, chignolin. In this simulation, we observed not only the folded state but also the misfolded state. We calculated the temperature and pressure dependence of the fractions on the folded, misfolded, and unfolded states. Differences in partial molar enthalpy, internal energy, entropy, partial molar volume, and heat capacity were also determined and agreed well with experimental data. We observed a new phenomenon that misfolded chignolin becomes more stable under high-pressure conditions. We also revealed this mechanism of the stability as follows: TYR2 and TRP9 side chains cover the hydrogen bonds that form a β-hairpin structure. The hydrogen bonds are protected from the water molecules that approach the protein as the pressure increases.

Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics.

PubMed

Galvelis, Raimondas; Re, Suyong; Sugita, Yuji

2017-05-09

Molecular dynamics (MD) simulation of a N-glycan in solution is challenging because of high-energy barriers of the glycosidic linkages, functional group rotational barriers, and numerous intra- and intermolecular hydrogen bonds. In this study, we apply different enhanced conformational sampling approaches, namely, metadynamics (MTD), the replica-exchange MD (REMD), and the recently proposed replica state exchange MTD (RSE-MTD), to a N-glycan in solution and compare the conformational sampling efficiencies of the approaches. MTD helps to cross the high-energy barrier along the ω angle by utilizing a bias potential, but it cannot enhance sampling of the other degrees of freedom. REMD ensures moderate-energy barrier crossings by exchanging temperatures between replicas, while it hardly crosses the barriers along ω. In contrast, RSE-MTD succeeds to cross the high-energy barrier along ω as well as to enhance sampling of the other degrees of freedom. We tested two RSE-MTD schemes: in one scheme, 64 replicas were simulated with the bias potential along ω at different temperatures, while simulations of four replicas were performed with the bias potentials for different CVs at 300 K. In both schemes, one unbiased replica at 300 K was included to compute conformational properties of the glycan. The conformational sampling of the former is better than the other enhanced sampling methods, while the latter shows reasonable performance without spending large computational resources. The latter scheme is likely to be useful when a N-glycan-attached protein is simulated.

Calculation of absolute protein-ligand binding free energy using distributed replica sampling.

PubMed

Rodinger, Tomas; Howell, P Lynne; Pomès, Régis

2008-10-21

Distributed replica sampling [T. Rodinger et al., J. Chem. Theory Comput. 2, 725 (2006)] is a simple and general scheme for Boltzmann sampling of conformational space by computer simulation in which multiple replicas of the system undergo a random walk in reaction coordinate or temperature space. Individual replicas are linked through a generalized Hamiltonian containing an extra potential energy term or bias which depends on the distribution of all replicas, thus enforcing the desired sampling distribution along the coordinate or parameter of interest regardless of free energy barriers. In contrast to replica exchange methods, efficient implementation of the algorithm does not require synchronicity of the individual simulations. The algorithm is inherently suited for large-scale simulations using shared or heterogeneous computing platforms such as a distributed network. In this work, we build on our original algorithm by introducing Boltzmann-weighted jumping, which allows moves of a larger magnitude and thus enhances sampling efficiency along the reaction coordinate. The approach is demonstrated using a realistic and biologically relevant application; we calculate the standard binding free energy of benzene to the L99A mutant of T4 lysozyme. Distributed replica sampling is used in conjunction with thermodynamic integration to compute the potential of mean force for extracting the ligand from protein and solvent along a nonphysical spatial coordinate. Dynamic treatment of the reaction coordinate leads to faster statistical convergence of the potential of mean force than a conventional static coordinate, which suffers from slow transitions on a rugged potential energy surface.

Calculation of absolute protein-ligand binding free energy using distributed replica sampling

NASA Astrophysics Data System (ADS)

Rodinger, Tomas; Howell, P. Lynne; Pomès, Régis

2008-10-01

Distributed replica sampling [T. Rodinger et al., J. Chem. Theory Comput. 2, 725 (2006)] is a simple and general scheme for Boltzmann sampling of conformational space by computer simulation in which multiple replicas of the system undergo a random walk in reaction coordinate or temperature space. Individual replicas are linked through a generalized Hamiltonian containing an extra potential energy term or bias which depends on the distribution of all replicas, thus enforcing the desired sampling distribution along the coordinate or parameter of interest regardless of free energy barriers. In contrast to replica exchange methods, efficient implementation of the algorithm does not require synchronicity of the individual simulations. The algorithm is inherently suited for large-scale simulations using shared or heterogeneous computing platforms such as a distributed network. In this work, we build on our original algorithm by introducing Boltzmann-weighted jumping, which allows moves of a larger magnitude and thus enhances sampling efficiency along the reaction coordinate. The approach is demonstrated using a realistic and biologically relevant application; we calculate the standard binding free energy of benzene to the L99A mutant of T4 lysozyme. Distributed replica sampling is used in conjunction with thermodynamic integration to compute the potential of mean force for extracting the ligand from protein and solvent along a nonphysical spatial coordinate. Dynamic treatment of the reaction coordinate leads to faster statistical convergence of the potential of mean force than a conventional static coordinate, which suffers from slow transitions on a rugged potential energy surface.

Shape-preserving transformations of organic matter and compositions thereof

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

Kaehr, Bryan J.; Meyer, Kristin; Townson, Jason L.

The present invention relates to methods of transforming organic matter into organic-inorganic composites, inorganic replicas, or conductive replicas. Organic matter, such as biological cells and tissue and organs, can be converted into such composites and replicas using the methods described herein. In particular, such methods transform organic matter (into inorganic, organic-inorganic, or conductive constructs), while simultaneously preserving microscopic and/or macroscopic structural detail.

Approximate message passing for nonconvex sparse regularization with stability and asymptotic analysis

NASA Astrophysics Data System (ADS)

Sakata, Ayaka; Xu, Yingying

2018-03-01

We analyse a linear regression problem with nonconvex regularization called smoothly clipped absolute deviation (SCAD) under an overcomplete Gaussian basis for Gaussian random data. We propose an approximate message passing (AMP) algorithm considering nonconvex regularization, namely SCAD-AMP, and analytically show that the stability condition corresponds to the de Almeida-Thouless condition in spin glass literature. Through asymptotic analysis, we show the correspondence between the density evolution of SCAD-AMP and the replica symmetric (RS) solution. Numerical experiments confirm that for a sufficiently large system size, SCAD-AMP achieves the optimal performance predicted by the replica method. Through replica analysis, a phase transition between replica symmetric and replica symmetry breaking (RSB) region is found in the parameter space of SCAD. The appearance of the RS region for a nonconvex penalty is a significant advantage that indicates the region of smooth landscape of the optimization problem. Furthermore, we analytically show that the statistical representation performance of the SCAD penalty is better than that of \

Automated magnification calibration in transmission electron microscopy using Fourier analysis of replica images.

PubMed

van der Laak, Jeroen A W M; Dijkman, Henry B P M; Pahlplatz, Martin M M

2006-03-01

The magnification factor in transmission electron microscopy is not very precise, hampering for instance quantitative analysis of specimens. Calibration of the magnification is usually performed interactively using replica specimens, containing line or grating patterns with known spacing. In the present study, a procedure is described for automated magnification calibration using digital images of a line replica. This procedure is based on analysis of the power spectrum of Fourier transformed replica images, and is compared to interactive measurement in the same images. Images were used with magnification ranging from 1,000 x to 200,000 x. The automated procedure deviated on average 0.10% from interactive measurements. Especially for catalase replicas, the coefficient of variation of automated measurement was considerably smaller (average 0.28%) compared to that of interactive measurement (average 3.5%). In conclusion, calibration of the magnification in digital images from transmission electron microscopy may be performed automatically, using the procedure presented here, with high precision and accuracy.

Crystal Ball Replica

NASA Astrophysics Data System (ADS)

Ajamian, John

2016-09-01

The A2 collaboration of the Institute for Nuclear Physics of Johannes Gutenberg University performs research on (multiple) meson photoproduction and nucleon structure and dynamics using a high energy polarized photon beam at specific targets. Particles scattered from the target are detected in the Crystal Ball, or CB. The CB is composed of 672 NaI crystals that surround the target and can analyze particle type and energy of ejected particles. Our project was to create a replica of the CB that could display what was happening in real time on a 3 Dimensional scale replica. Our replica was constructed to help explain the physics to the general public, be used as a tool when calibrating each of the 672 NaI crystals, and to better analyze the electron showering of particles coming from the target. This poster will focus on the hardware steps necessary to construct the replica and wire the 672 programmable LEDS in such a way that they can be mapped to correspond to the Crystal Ball elements. George Washington NSF Grant.

Application of Replica Technique and SEM in Accuracy Measurement of Ceramic Crowns

NASA Astrophysics Data System (ADS)

Trifkovic, B.; Budak, I.; Todorovic, A.; Hodolic, J.; Puskar, T.; Jevremovic, D.; Vukelic, D.

2012-01-01

The paper presents a comparative study of the measuring values of the marginal gap related to the ceramic crowns made by dental CAD/CAM system using the replica technique and SEM. The study was conducted using three experimental groups, which consisted of ceramic crowns manufactured by the Cerec CAD/CAM system. The scanning procedure was carried out using three specialized dental 3D digitization systems from the Cerec family - two types of extraoral optical scanning systems and an intraoral optical scanner. Measurements of the marginal gap were carried out using the replica technique and SEM. The comparison of aggregate values of the marginal gap using the replica technique showed a statistically significant difference between the systems. The measured values of marginal gaps of ceramic crowns using the replica technique were significantly lower compared to those measured by SEM. The results indicate that the choice of technique for measuring the accuracy of ceramic crowns influences the final results of investigation.

Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange.

PubMed

Kubitzki, Marcus B; de Groot, Bert L

2007-06-15

Today's standard molecular dynamics simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large number of degrees of freedom involved. Aiming at increased sampling efficiency, we present a novel simulation method combining the ideas of essential dynamics and REX. Unlike standard REX, in each replica only a selection of essential collective modes of a subsystem of interest (essential subspace) is coupled to a higher temperature, with the remainder of the system staying at a reference temperature, T(0). This selective excitation along with the replica framework permits efficient approximate ensemble-preserving conformational sampling and allows much larger temperature differences between replicas, thereby considerably enhancing sampling efficiency. Ensemble properties and sampling performance of the method are discussed using dialanine and guanylin test systems, with multi-microsecond molecular dynamics simulations of these test systems serving as references.

SRF Cavity Surface Topography Characterization Using Replica Techniques

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

C. Xu, M.J. Kelley, C.E. Reece

2012-07-01

To better understand the roll of topography on SRF cavity performance, we seek to obtain detailed topographic information from the curved practical cavity surfaces. Replicas taken from a cavity interior surface provide internal surface molds for fine Atomic Force Microscopy (AFM) and stylus profilometry. In this study, we confirm the replica resolution both on surface local defects such as grain boundary and etching pits and compare the surface uniform roughness with the aid of Power Spectral Density (PSD) where we can statistically obtain roughness parameters at different scales. A series of sampling locations are at the same magnetic field chosenmore » at the same latitude on a single cell cavity to confirm the uniformity. Another series of sampling locations at different magnetic field amplitudes are chosen for this replica on the same cavity for later power loss calculation. We also show that application of the replica followed by rinsing does not adversely affect the cavity performance.« less

Fractographic ceramic failure analysis using the replica technique

PubMed Central

Scherrer, Susanne S.; Quinn, Janet B.; Quinn, George D.; Anselm Wiskott, H. W.

2007-01-01

Objectives To demonstrate the effectiveness of in vivo replicas of fractured ceramic surfaces for descriptive fractography as applied to the analysis of clinical failures. Methods The fracture surface topography of partially failed veneering ceramic of a Procera Alumina molar and an In Ceram Zirconia premolar were examined utilizing gold-coated epoxy poured replicas viewed using scanning electron microscopy. The replicas were inspected for fractographic features such as hackle, wake hackle, twist hackle, compression curl and arrest lines for determination of the direction of crack propagation and location of the origin. Results For both veneering ceramics, replicas provided an excellent reproduction of the fractured surfaces. Fine details including all characteristic fracture features produced by the interaction of the advancing crack with the material's microstructure could be recognized. The observed features are indicators of the local direction of crack propagation and were used to trace the crack's progression back to its initial starting zone (the origin). Drawbacks of replicas such as artifacts (air bubbles) or imperfections resulting from inadequate epoxy pouring were noted but not critical for the overall analysis of the fractured surfaces. Significance The replica technique proved to be easy to use and allowed an excellent reproduction of failed ceramic surfaces. It should be applied before attempting to remove any failed part remaining in situ as the fracture surface may be damaged during this procedure. These two case studies are intended as an introduction for the clinical researcher in using qualitative (descriptive) fractography as a tool for understanding fracture processes in brittle restorative materials and, secondarily, to draw conclusions as to possible design inadequacies in failed restorations. PMID:17270267

Dynamical self-arrest in symmetric and asymmetric diblock copolymer melts using a replica approach within a local theory.

PubMed

Wu, Sangwook

2009-03-01

We investigate dynamical self-arrest in a diblock copolymer melt using a replica approach within a self-consistent local method based on dynamical mean-field theory (DMFT). The local replica approach effectively predicts (chiN)_{A} for dynamical self-arrest in a block copolymer melt for symmetric and asymmetric cases. We discuss the competition of the cubic and quartic interactions in the Landau free energy for a block copolymer melt in stabilizing a glassy state depending on the chain length. Our local replica theory provides a universal value for the dynamical self-arrest in block copolymer melts with (chiN)_{A} approximately 10.5+64N;{-3/10} for the symmetric case.

Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering

PubMed Central

2015-01-01

The lateral heterogeneity of cellular membranes plays an important role in many biological functions such as signaling and regulating membrane proteins. This heterogeneity can result from preferential interactions between membrane components or interactions with membrane proteins. One major difficulty in molecular dynamics simulations aimed at studying the membrane heterogeneity is that lipids diffuse slowly and collectively in bilayers, and therefore, it is difficult to reach equilibrium in lateral organization in bilayer mixtures. Here, we propose the use of the replica exchange with solute tempering (REST) approach to accelerate lateral relaxation in heterogeneous bilayers. REST is based on the replica exchange method but tempers only the solute, leaving the temperature of the solvent fixed. Since the number of replicas in REST scales approximately only with the degrees of freedom in the solute, REST enables us to enhance the configuration sampling of lipid bilayers with fewer replicas, in comparison with the temperature replica exchange molecular dynamics simulation (T-REMD) where the number of replicas scales with the degrees of freedom of the entire system. We apply the REST method to a cholesterol and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer mixture and find that the lateral distribution functions of all molecular pair types converge much faster than in the standard MD simulation. The relative diffusion rate between molecules in REST is, on average, an order of magnitude faster than in the standard MD simulation. Although REST was initially proposed to study protein folding and its efficiency in protein folding is still under debate, we find a unique application of REST to accelerate lateral equilibration in mixed lipid membranes and suggest a promising way to probe membrane lateral heterogeneity through molecular dynamics simulation. PMID:25328493

Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling.

PubMed

Rauscher, Sarah; Neale, Chris; Pomès, Régis

2009-10-13

Generalized-ensemble algorithms in temperature space have become popular tools to enhance conformational sampling in biomolecular simulations. A random walk in temperature leads to a corresponding random walk in potential energy, which can be used to cross over energetic barriers and overcome the problem of quasi-nonergodicity. In this paper, we introduce two novel methods: simulated tempering distributed replica sampling (STDR) and virtual replica exchange (VREX). These methods are designed to address the practical issues inherent in the replica exchange (RE), simulated tempering (ST), and serial replica exchange (SREM) algorithms. RE requires a large, dedicated, and homogeneous cluster of CPUs to function efficiently when applied to complex systems. ST and SREM both have the drawback of requiring extensive initial simulations, possibly adaptive, for the calculation of weight factors or potential energy distribution functions. STDR and VREX alleviate the need for lengthy initial simulations, and for synchronization and extensive communication between replicas. Both methods are therefore suitable for distributed or heterogeneous computing platforms. We perform an objective comparison of all five algorithms in terms of both implementation issues and sampling efficiency. We use disordered peptides in explicit water as test systems, for a total simulation time of over 42 μs. Efficiency is defined in terms of both structural convergence and temperature diffusion, and we show that these definitions of efficiency are in fact correlated. Importantly, we find that ST-based methods exhibit faster temperature diffusion and correspondingly faster convergence of structural properties compared to RE-based methods. Within the RE-based methods, VREX is superior to both SREM and RE. On the basis of our observations, we conclude that ST is ideal for simple systems, while STDR is well-suited for complex systems.

Axial displacement of abutments into implants and implant replicas, with the tapered cone-screw internal connection, as a function of tightening torque.

PubMed

Dailey, Bruno; Jordan, Laurence; Blind, Olivier; Tavernier, Bruno

2009-01-01

The passive fit of a superstructure on implant abutments is essential to success. One source of error when using a tapered cone-screw internal connection may be the difference between the tightening torque level applied to the abutments by the laboratory technician compared to that applied by the treating clinician. The purpose of this study was to measure the axial displacement of tapered cone-screw abutments into implants and their replicas as a function of the tightening torque level. Twenty tapered cone-screw abutments were selected. Two groups were created: 10 abutments were secured into 10 implants, and 10 abutments were secured into 10 corresponding implant replicas. Each abutment was tightened in increasing increments of 5 Ncm, from 0 Ncm to 45 Ncm, with a torque controller. The length of each sample was measured repeatedly with an Electronic Digital Micrometer. The mean axial displacement for the implant group and the replica group was calculated. The data were analyzed by the Mann-Whitney and Spearman tests. For both groups, there was always an axial displacement of the abutment upon each incremental application of torque. The mean axial displacement values varied between 7 and 12 microm for the implant group and between 6 and 21 microm for the replica group at each 5-Ncm increment. From 0 to 45 Ncm, the total mean axial displacement values were 89 microm for the implant group and 122 microm for the replica group. There was a continuous axial displacement of the abutments into implants and implant replicas when the applied torque was raised from 0 to 45 Ncm. Torque applied above the level recommended by the manufacturer increased the difference in displacement between the two groups.

Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering.

PubMed

Huang, Kun; García, Angel E

2014-10-14

The lateral heterogeneity of cellular membranes plays an important role in many biological functions such as signaling and regulating membrane proteins. This heterogeneity can result from preferential interactions between membrane components or interactions with membrane proteins. One major difficulty in molecular dynamics simulations aimed at studying the membrane heterogeneity is that lipids diffuse slowly and collectively in bilayers, and therefore, it is difficult to reach equilibrium in lateral organization in bilayer mixtures. Here, we propose the use of the replica exchange with solute tempering (REST) approach to accelerate lateral relaxation in heterogeneous bilayers. REST is based on the replica exchange method but tempers only the solute, leaving the temperature of the solvent fixed. Since the number of replicas in REST scales approximately only with the degrees of freedom in the solute, REST enables us to enhance the configuration sampling of lipid bilayers with fewer replicas, in comparison with the temperature replica exchange molecular dynamics simulation (T-REMD) where the number of replicas scales with the degrees of freedom of the entire system. We apply the REST method to a cholesterol and 1,2-dipalmitoyl- sn -glycero-3-phosphocholine (DPPC) bilayer mixture and find that the lateral distribution functions of all molecular pair types converge much faster than in the standard MD simulation. The relative diffusion rate between molecules in REST is, on average, an order of magnitude faster than in the standard MD simulation. Although REST was initially proposed to study protein folding and its efficiency in protein folding is still under debate, we find a unique application of REST to accelerate lateral equilibration in mixed lipid membranes and suggest a promising way to probe membrane lateral heterogeneity through molecular dynamics simulation.

Secrets of the Chinese magic mirror replica

NASA Astrophysics Data System (ADS)

Mak, Se-yuen; Yip, Din-yan

2001-03-01

We examine the structure of five Chinese magic mirror replicas using a special imaging technique developed by the authors. All mirrors are found to have a two-layered structure. The reflecting surface that gives rise to a projected magic pattern on the screen is hidden under a polished half-reflecting top layer. An alternative method of making the magic mirror using ancient technology has been proposed. Finally, we suggest a simple method of reconstructing a mirror replica in the laboratory.

Evidence of iridescence in TiO2 nanostructures. A probably photonic effect

NASA Astrophysics Data System (ADS)

Rey-Gonzalez, Rafael; Quiroz, Heiddy P.; Barrera-Patiño, Claudia; Dussan, Anderson; Grupo de Optica e Informacion Cuantica Collaboration; Grupo de Materiales Nanoestructutrados y sus Aplicaciones Collaboration

In this work, we present a study of optical properties of titanium dioxide nanotubes (TiO2). Nanotubes were obtained by electrochemical anodization method, using ethylene glycol solutions containing different amounts of water and fluoride. A complex structure is observed between nanotubes and Ti foils on surface when nanotubes are released from the sheet. These forms can be associated with replicas or marks in surface of the Ti foil. The optical response of replicas is studied by Uv-Vis spectrophotometry using white light and varying the angle of the incident light. Absorbance measurements reveal that these replicas exhibit a shift towards lower values of lambda when the angle of the incident light increases of 200 to 600. These changes may be associated with iridescent effects in this material. The concavity of the replicas in association with air could be generating photonic-like effects. Using a 2D model of replicas - air system, the photonic band structures are found through a plane wave approach. Correlations between photonic properties and iridescent effects are explored. Grupo de Optica e Informacion Cuantica.

Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space

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

Valentim, Alexandra; Rocha, Julio C. S.; Tsai, Shan-Ho

We considered a higher-dimensional extension for the replica-exchange Wang-Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of Wang-Landau and Replica-Exchange algorithms, and the one-dimensional version of this approach has been shown to be very efficient and to scale well, up to several thousands of computing cores. This approach allows us to split the parameter space of the system to be simulated into several pieces and still perform a random walk over the entire parameter range, ensuring the ergodicity of the simulation. Previous work, inmore » which a similar scheme of parallel simulation was implemented without using replica exchange and with a different way to combine the result from the pieces, led to discontinuities in the final density of states over the entire range of parameters. From our simulations, it appears that the replica-exchange Wang-Landau algorithm is able to overcome this diculty, allowing exploration of higher parameter phase space by keeping track of the joint density of states.« less

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.

PubMed

Mishra, Sushil Kumar; Kara, Mahmut; Zacharias, Martin; Koca, Jaroslav

2014-01-01

Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.

Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: a general algorithm and its extension for free energy calculation on rugged energy surface.

PubMed

Li, Hongzhi; Yang, Wei

2007-03-21

An approach is developed in the replica exchange framework to enhance conformational sampling for the quantum mechanical (QM) potential based molecular dynamics simulations. Importantly, with our enhanced sampling treatment, a decent convergence for electronic structure self-consistent-field calculation is robustly guaranteed, which is made possible in our replica exchange design by avoiding direct structure exchanges between the QM-related replicas and the activated (scaled by low scaling parameters or treated with high "effective temperatures") molecular mechanical (MM) replicas. Although the present approach represents one of the early efforts in the enhanced sampling developments specifically for quantum mechanical potentials, the QM-based simulations treated with the present technique can possess the similar sampling efficiency to the MM based simulations treated with the Hamiltonian replica exchange method (HREM). In the present paper, by combining this sampling method with one of our recent developments (the dual-topology alchemical HREM approach), we also introduce a method for the sampling enhanced QM-based free energy calculations.

Fish and robot dancing together: bluefin killifish females respond differently to the courtship of a robot with varying color morphs.

PubMed

Phamduy, P; Polverino, G; Fuller, R C; Porfiri, M

2014-09-01

The experimental integration of bioinspired robots in groups of social animals has become a valuable tool to understand the basis of social behavior and uncover the fundamental determinants of animal communication. In this study, we measured the preference of fertile female bluefin killifish (Lucania goodei) for robotic replicas whose aspect ratio, body size, motion pattern, and color morph were inspired by adult male killifish. The motion of the fish replica was controlled via a robotic platform, which simulated the typical courtship behavior observed in killifish males. The positional preferences of females were measured for three different color morphs (red, yellow, and blue). While variation in preference was high among females, females tend to spend more time in the vicinity of the yellow painted robot replicas. This preference may have emerged because the yellow robot replicas were very bright, particularly in the longer wavelengths (550–700 nm) compared to the red and blue replicas. These findings are in agreement with previous observations in mosquitofish and zebrafish on fish preference for artificially enhanced yellow pigmentation.

Disordered λ φ4+ρ φ6 Landau-Ginzburg model

NASA Astrophysics Data System (ADS)

Diaz, R. Acosta; Svaiter, N. F.; Krein, G.; Zarro, C. A. D.

2018-03-01

We discuss a disordered λ φ4+ρ φ6 Landau-Ginzburg model defined in a d -dimensional space. First we adopt the standard procedure of averaging the disorder-dependent free energy of the model. The dominant contribution to this quantity is represented by a series of the replica partition functions of the system. Next, using the replica-symmetry ansatz in the saddle-point equations, we prove that the average free energy represents a system with multiple ground states with different order parameters. For low temperatures we show the presence of metastable equilibrium states for some replica fields for a range of values of the physical parameters. Finally, going beyond the mean-field approximation, the one-loop renormalization of this model is performed, in the leading-order replica partition function.

Coupling of phonons with excitons bound to different donors and acceptors in hexagonal GaN

NASA Astrophysics Data System (ADS)

Korona, K. P.; Wysmoek, A.; Kuhl, J.; Kamiska, M.; Baranowski, J. M.; Look, D. C.; Park, S. S.

2006-06-01

Time-resolved measurements of GaN with different donors (oxygen or silicon) and acceptors (zinc or magnesium) showed pronounced bound exciton lines and their phonon replicas. The analysis included three phonon modes characteristic for the wurtzite (hexagonal) phase: A1(LO), E1(TO) and E2H. It was shown that relative amplitudes of replicas depended upon the chemical nature of the defects that the bind excitons. The replicas were stronger for acceptor- than for donor-related features. Huang-Rhys factors S = 0.06 +/- 0.02 and S = 0.025 +/- 0.01, were found for the A0X and the D0X LO replicas, respectively. A significant difference in phonon coupling to silicon and oxygen donor bound excitons has been observed.

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

Vogel, Thomas; Perez, Danny

We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of relevant states through the whole ensemble of replicas. This mechanism depends on the knowledge of global thermodynamic functions which are measured during the simulation and not coupled to the heat bath temperatures driving the individual simulations. Therefore, this setup also allows for a continuous adaptation of the temperature set. In this paper, we will review the new scheme and demonstrate its capability. Furthermore, themore » method is particularly useful for the fast and reliable estimation of the microcanonical temperature T(U) or, equivalently, of the density of states g(U) over a wide range of energies.« less

Self-assembly of block copolymers on topographically patterned polymeric substrates

DOEpatents

Russell, Thomas P.; Park, Soojin; Lee, Dong Hyun; Xu, Ting

2016-05-10

Highly-ordered block copolymer films are prepared by a method that includes forming a polymeric replica of a topographically patterned crystalline surface, forming a block copolymer film on the topographically patterned surface of the polymeric replica, and annealing the block copolymer film. The resulting structures can be used in a variety of different applications, including the fabrication of high density data storage media. The ability to use flexible polymers to form the polymeric replica facilitates industrial-scale processes utilizing the highly-ordered block copolymer films.

Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm.

PubMed

Zhou, Ruhong

2004-05-01

A highly parallel replica exchange method (REM) that couples with a newly developed molecular dynamics algorithm particle-particle particle-mesh Ewald (P3ME)/RESPA has been proposed for efficient sampling of protein folding free energy landscape. The algorithm is then applied to two separate protein systems, beta-hairpin and a designed protein Trp-cage. The all-atom OPLSAA force field with an explicit solvent model is used for both protein folding simulations. Up to 64 replicas of solvated protein systems are simulated in parallel over a wide range of temperatures. The combined trajectories in temperature and configurational space allow a replica to overcome free energy barriers present at low temperatures. These large scale simulations reveal detailed results on folding mechanisms, intermediate state structures, thermodynamic properties and the temperature dependences for both protein systems.

Sublattice parallel replica dynamics.

PubMed

Martínez, Enrique; Uberuaga, Blas P; Voter, Arthur F

2014-06-01

Exascale computing presents a challenge for the scientific community as new algorithms must be developed to take full advantage of the new computing paradigm. Atomistic simulation methods that offer full fidelity to the underlying potential, i.e., molecular dynamics (MD) and parallel replica dynamics, fail to use the whole machine speedup, leaving a region in time and sample size space that is unattainable with current algorithms. In this paper, we present an extension of the parallel replica dynamics algorithm [A. F. Voter, Phys. Rev. B 57, R13985 (1998)] by combining it with the synchronous sublattice approach of Shim and Amar [ and , Phys. Rev. B 71, 125432 (2005)], thereby exploiting event locality to improve the algorithm scalability. This algorithm is based on a domain decomposition in which events happen independently in different regions in the sample. We develop an analytical expression for the speedup given by this sublattice parallel replica dynamics algorithm and compare it with parallel MD and traditional parallel replica dynamics. We demonstrate how this algorithm, which introduces a slight additional approximation of event locality, enables the study of physical systems unreachable with traditional methodologies and promises to better utilize the resources of current high performance and future exascale computers.

Localization-Free Detection of Replica Node Attacks in Wireless Sensor Networks Using Similarity Estimation with Group Deployment Knowledge

PubMed Central

Ding, Chao; Yang, Lijun; Wu, Meng

2017-01-01

Due to the unattended nature and poor security guarantee of the wireless sensor networks (WSNs), adversaries can easily make replicas of compromised nodes, and place them throughout the network to launch various types of attacks. Such an attack is dangerous because it enables the adversaries to control large numbers of nodes and extend the damage of attacks to most of the network with quite limited cost. To stop the node replica attack, we propose a location similarity-based detection scheme using deployment knowledge. Compared with prior solutions, our scheme provides extra functionalities that prevent replicas from generating false location claims without deploying resource-consuming localization techniques on the resource-constraint sensor nodes. We evaluate the security performance of our proposal under different attack strategies through heuristic analysis, and show that our scheme achieves secure and robust replica detection by increasing the cost of node replication. Additionally, we evaluate the impact of network environment on the proposed scheme through theoretic analysis and simulation experiments, and indicate that our scheme achieves effectiveness and efficiency with substantially lower communication, computational, and storage overhead than prior works under different situations and attack strategies. PMID:28098846

Multiple cues produced by a robotic fish modulate aggressive behaviour in Siamese fighting fishes.

PubMed

Romano, Donato; Benelli, Giovanni; Donati, Elisa; Remorini, Damiano; Canale, Angelo; Stefanini, Cesare

2017-07-05

The use of robotics to establish social interactions between animals and robots, represents an elegant and innovative method to investigate animal behaviour. However, robots are still underused to investigate high complex and flexible behaviours, such as aggression. Here, Betta splendens was tested as model system to shed light on the effect of a robotic fish eliciting aggression. We evaluated how multiple signal systems, including a light stimulus, affect aggressive responses in B. splendens. Furthermore, we conducted experiments to estimate if aggressive responses were triggered by the biomimetic shape of fish replica, or whether any intruder object was effective as well. Male fishes showed longer and higher aggressive displays as puzzled stimuli from the fish replica increased. When the fish replica emitted its full sequence of cues, the intensity of aggression exceeded even that produced by real fish opponents. Fish replica shape was necessary for conspecific opponent perception, evoking significant aggressive responses. Overall, this study highlights that the efficacy of an artificial opponent eliciting aggressive behaviour in fish can be boosted by exposure to multiple signals. Optimizing the cue combination delivered by the robotic fish replica may be helpful to predict escalating levels of aggression.

Localization-Free Detection of Replica Node Attacks in Wireless Sensor Networks Using Similarity Estimation with Group Deployment Knowledge.

PubMed

Ding, Chao; Yang, Lijun; Wu, Meng

2017-01-15

Due to the unattended nature and poor security guarantee of the wireless sensor networks (WSNs), adversaries can easily make replicas of compromised nodes, and place them throughout the network to launch various types of attacks. Such an attack is dangerous because it enables the adversaries to control large numbers of nodes and extend the damage of attacks to most of the network with quite limited cost. To stop the node replica attack, we propose a location similarity-based detection scheme using deployment knowledge. Compared with prior solutions, our scheme provides extra functionalities that prevent replicas from generating false location claims without deploying resource-consuming localization techniques on the resource-constraint sensor nodes. We evaluate the security performance of our proposal under different attack strategies through heuristic analysis, and show that our scheme achieves secure and robust replica detection by increasing the cost of node replication. Additionally, we evaluate the impact of network environment on the proposed scheme through theoretic analysis and simulation experiments, and indicate that our scheme achieves effectiveness and efficiency with substantially lower communication, computational, and storage overhead than prior works under different situations and attack strategies.

Portfolio optimization problem with nonidentical variances of asset returns using statistical mechanical informatics.

PubMed

Shinzato, Takashi

2016-12-01

The portfolio optimization problem in which the variances of the return rates of assets are not identical is analyzed in this paper using the methodology of statistical mechanical informatics, specifically, replica analysis. We defined two characteristic quantities of an optimal portfolio, namely, minimal investment risk and investment concentration, in order to solve the portfolio optimization problem and analytically determined their asymptotical behaviors using replica analysis. Numerical experiments were also performed, and a comparison between the results of our simulation and those obtained via replica analysis validated our proposed method.

Portfolio optimization problem with nonidentical variances of asset returns using statistical mechanical informatics

NASA Astrophysics Data System (ADS)

Shinzato, Takashi

2016-12-01

The portfolio optimization problem in which the variances of the return rates of assets are not identical is analyzed in this paper using the methodology of statistical mechanical informatics, specifically, replica analysis. We defined two characteristic quantities of an optimal portfolio, namely, minimal investment risk and investment concentration, in order to solve the portfolio optimization problem and analytically determined their asymptotical behaviors using replica analysis. Numerical experiments were also performed, and a comparison between the results of our simulation and those obtained via replica analysis validated our proposed method.

A digital approach to fabricating an abutment replica to control cement volume in a cement-retained implant prosthesis.

PubMed

Lee, Ju-Hyoung; Park, In-Sook; Sohn, Dong-Seok

2016-07-01

If a cement-retained implant prosthesis is placed on an abutment, excess cement should be minimized or removed to prevent periimplant inflammation. Various methods for fabricating an abutment replica have been introduced to maintain tissue health and reduce clean-up time. The purpose of this article is to present an alternative technique for fabricating an abutment replica with computer-aided design/computer-aided manufacturing (CAD/CAM) technology. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Physical mapping of complex genomes

DOEpatents

Evans, G.A.

1993-06-15

A method for the simultaneous identification of overlapping cosmid clones among multiple cosmid clones and the use of the method for mapping complex genomes are provided. A library of cosmid clones that contains the DNA to be mapped is constructed and arranged in a manner such that individual clones can be identified and replicas of the arranged clones prepared. In preferred embodiments, the clones are arranged in a two dimensional matrix. In such embodiments, the cosmid clones in a row are pooled, mixed probes complementary to the ends of the DNA inserts in the pooled clones are synthesized, hybridized to a first replica of the library. Hybridizing clones, which include the pooled row, are identified. A second portion of clones is prepared by pooling cosmid clones that correspond to a column in the matrix. The second pool thereby includes one clone from the first portion pooled clones. This common clone is located on the replica at the intersection of the column and row. Mixed probes complementary to the ends of the DNA inserts in the second pooled portion of clones are prepared and hybridized to a second replica of the library. The hybridization pattern on the first and second replicas of the library are compared and cross-hybridizing clones, other than the clones in the pooled column and row, that hybridize to identical clones in the first and second replicas are identified. These clones necessarily include DNA inserts that overlap with the DNA insert in the common clone located at the intersection of the pooled row and pooled column. The DNA in the entire library may be mapped by pooling the clones in each of the rows and columns of the matrix, preparing mixed end-specific probes and hybridizing the probes from each row or column to a replica of the library. Since all clones in the library are located at the intersection of a column and a row, the overlapping clones for all clones in the library may be identified and a physical map constructed.

Replica Resummation of the Baker-Campbell-Hausdorff Series

NASA Astrophysics Data System (ADS)

Vajna, Szabolcs; Klobas, Katja; Prosen, Tomaž; Polkovnikov, Anatoli

2018-05-01

We developed a novel perturbative expansion based on the replica trick for the Floquet Hamiltonian governing the dynamics of periodically kicked systems where the kick strength is the small parameter. The expansion is formally equivalent to an infinite resummation of the Baker-Campbell-Hausdorff series in the undriven (nonperturbed) Hamiltonian, while considering terms up to a finite order in the kick strength. As an application of the replica expansion, we analyze an Ising spin 1 /2 chain periodically kicked with a magnetic field with a strength h , which has both longitudinal and transverse components. We demonstrate that even away from the regime of high frequency driving, if there is heating, its rate is nonperturbative in the kick strength, bounded from above by a stretched exponential: e-const h-1 /2 . This guarantees the existence of a very long prethermal regime, where the dynamics is governed by the Floquet Hamiltonian obtained from the replica expansion.

Microlens fabrication by replica molding of frozen laser-printed droplets

NASA Astrophysics Data System (ADS)

Surdo, Salvatore; Diaspro, Alberto; Duocastella, Martí

2017-10-01

In this work, we synergistically combine laser-induced forward transfer (LIFT) and replica molding for the fabrication of microlenses with control of their geometry and size independent of the material or substrate used. Our approach is based on a multistep process in which liquid microdroplets of an aqueous solution are first printed on a substrate by LIFT. Following a freezing step, the microdroplets are used as a master to fabricate a polydimethylsiloxane (PDMS) mold. A subsequent replica molding step enables the creation of microlenses and microlens arrays on arbitrary selected substrates and by using different curable polymers. Thus, our method combines the rapid fabrication capabilities of LIFT and the perfectively smooth surface quality of the generated microdroplets, with the advantages of replica molding in terms of parallelization and materials flexibility. We demonstrate our strategy by generating microlenses of different photocurable polymers and by characterizing their optical and morphological properties.

Toward mass producible ordered bulk heterojunction organic photovoltaic devices.

PubMed

Kim, Taeyong; Yoon, Hyunsik; Song, Hyung-Jun; Haberkorn, Niko; Cho, Younghyun; Sung, Seung Hyun; Lee, Chang Hee; Char, Kookheon; Theato, Patrick

2012-12-13

A strategy to fabricate nanostructured poly(3-hexylthiophene) (P3HT) films for organic photovoltaic (OPV) cells by a direct transfer method from a reusable soft replica mold is presented. The flexible polyfluoropolyether (PFPE) replica mold allows low-pressure and low- temperature process condition for the successful transfer of nanostructured P3HT films onto PEDOT/PSS-coated ITO substrates. To reduce the fabrication cost of masters in large area, we employed well-ordered anodic aluminum oxide (AAO) as a template. Also, we provide a method to fabricate reversed nanostructures by exploiting the self-replication of replica molds. The concept of the transfer method in low temperature with a flexible and reusable replica mold obtained from an AAO template will be a firm foundation for a low-cost fabrication process of ordered OPVs. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Replica Fourier Tansforms on Ultrametric Trees, and Block-Diagonalizing Multi-Replica Matrices

NASA Astrophysics Data System (ADS)

de Dominicis, C.; Carlucci, D. M.; Temesvári, T.

1997-01-01

The analysis of objects living on ultrametric trees, in particular the block-diagonalization of 4-replica matrices M^{α β;γ^δ}, is shown to be dramatically simplified through the introduction of properly chosen operations on those objects. These are the Replica Fourier Transforms on ultrametric trees. Those transformations are defined and used in the present work. On montre que l'analyse d'objets vivant sur un arbre ultramétrique, en particulier, la diagonalisation par blocs d'une matrice M^{α β;γ^δ} dépendant de 4-répliques, se simplifie de façon dramatique si l'on introduit les opérations appropriées sur ces objets. Ce sont les Transformées de Fourier de Répliques sur un arbre ultramétrique. Ces transformations sont définies et utilisées dans le présent travail.

Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems

PubMed Central

Huang, Xuhui; Hagen, Morten; Kim, Byungchan; Friesner, Richard A.; Zhou, Ruhong; Berne, B. J.

2009-01-01

We apply the recently developed replica exchange with solute tempering (REST) to three large solvated peptide systems: an α-helix, a β-hairpin, and a TrpCage, with these peptides defined as the “central group”. We find that our original implementation of REST is not always more efficient than the replica exchange method (REM). Specifically, we find that exchanges between folded (F) and unfolded (U) conformations with vastly different structural energies are greatly reduced by the nonappearance of the water self-interaction energy in the replica exchange acceptance probabilities. REST, however, is expected to remain useful for a large class of systems for which the energy gap between the two states is not large, such as weakly bound protein–ligand complexes. Alternatively, a shell of water molecules can be incorporated into the central group, as discussed in the original paper. PMID:17439169

Coulomb replica-exchange method: handling electrostatic attractive and repulsive forces for biomolecules.

PubMed

Itoh, Satoru G; Okumura, Hisashi

2013-03-30

We propose a new type of the Hamiltonian replica-exchange method (REM) for molecular dynamics (MD) and Monte Carlo simulations, which we refer to as the Coulomb REM (CREM). In this method, electrostatic charge parameters in the Coulomb interactions are exchanged among replicas while temperatures are exchanged in the usual REM. By varying the atom charges, the CREM overcomes free-energy barriers and realizes more efficient sampling in the conformational space than the REM. Furthermore, this method requires only a smaller number of replicas because only the atom charges of solute molecules are used as exchanged parameters. We performed Coulomb replica-exchange MD simulations of an alanine dipeptide in explicit water solvent and compared the results with those of the conventional canonical, replica exchange, and van der Waals REMs. Two force fields of AMBER parm99 and AMBER parm99SB were used. As a result, the CREM sampled all local-minimum free-energy states more frequently than the other methods for both force fields. Moreover, the Coulomb, van der Waals, and usual REMs were applied to a fragment of an amyloid-β peptide (Aβ) in explicit water solvent to compare the sampling efficiency of these methods for a larger system. The CREM sampled structures of the Aβ fragment more efficiently than the other methods. We obtained β-helix, α-helix, 3(10)-helix, β-hairpin, and β-sheet structures as stable structures and deduced pathways of conformational transitions among these structures from a free-energy landscape. Copyright © 2012 Wiley Periodicals, Inc.

Gamma-ray dosimetry measurements of the Little Boy replica

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

Plassmann, E.A.; Pederson, R.A.

1984-01-01

We present the current status of our gamma-ray dosimetry results for the Little Boy replica. Both Geiger-Mueller and thermoluminescent detectors were used in the measurements. Future work is needed to test assumptions made in data analysis.

Creating technical heritage object replicas in a virtual environment

NASA Astrophysics Data System (ADS)

Egorova, Olga; Shcherbinin, Dmitry

2016-03-01

The paper presents innovative informatics methods for creating virtual technical heritage replicas, which are of significant scientific and practical importance not only to researchers but to the public in general. By performing 3D modeling and animation of aircrafts, spaceships, architectural-engineering buildings, and other technical objects, the process of learning is achieved while promoting the preservation of the replicas for future generations. Modern approaches based on the wide usage of computer technologies attract a greater number of young people to explore the history of science and technology and renew their interest in the field of mechanical engineering.

A genetic algorithm for replica server placement

NASA Astrophysics Data System (ADS)

Eslami, Ghazaleh; Toroghi Haghighat, Abolfazl

2012-01-01

Modern distribution systems use replication to improve communication delay experienced by their clients. Some techniques have been developed for web server replica placement. One of the previous studies was Greedy algorithm proposed by Qiu et al, that needs knowledge about network topology. In This paper, first we introduce a genetic algorithm for web server replica placement. Second, we compare our algorithm with Greedy algorithm proposed by Qiu et al, and Optimum algorithm. We found that our approach can achieve better results than Greedy algorithm proposed by Qiu et al but it's computational time is more than Greedy algorithm.

A genetic algorithm for replica server placement

NASA Astrophysics Data System (ADS)

Eslami, Ghazaleh; Toroghi Haghighat, Abolfazl

2011-12-01

Modern distribution systems use replication to improve communication delay experienced by their clients. Some techniques have been developed for web server replica placement. One of the previous studies was Greedy algorithm proposed by Qiu et al, that needs knowledge about network topology. In This paper, first we introduce a genetic algorithm for web server replica placement. Second, we compare our algorithm with Greedy algorithm proposed by Qiu et al, and Optimum algorithm. We found that our approach can achieve better results than Greedy algorithm proposed by Qiu et al but it's computational time is more than Greedy algorithm.

Communication: Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering

NASA Astrophysics Data System (ADS)

Arefi, Hadi H.; Yamamoto, Takeshi

2017-12-01

Conventional molecular-dynamics (cMD) simulation has a well-known limitation in accessible time and length scales, and thus various enhanced sampling techniques have been proposed to alleviate the problem. In this paper, we explore the utility of replica exchange with solute tempering (REST) (i.e., a variant of Hamiltonian replica exchange methods) to simulate the self-assembly of a supramolecular polymer in explicit solvent and compare the performance with temperature-based replica exchange MD (T-REMD) as well as cMD. As a test system, we consider a relatively simple all-atom model of supramolecular polymerization (namely, benzene-1,3,5-tricarboxamides in methylcyclohexane solvent). Our results show that both REST and T-REMD are able to predict highly ordered polymer structures with helical H-bonding patterns, in contrast to cMD which completely fails to obtain such a structure for the present model. At the same time, we have also experienced some technical challenge (i.e., aggregation-dispersion transition and the resulting bottleneck for replica traversal), which is illustrated numerically. Since the computational cost of REST scales more moderately than T-REMD, we expect that REST will be useful for studying the self-assembly of larger systems in solution with enhanced rearrangement of monomers.

Connexin composition in apposed gap junction hemiplaques revealed by matched double-replica freeze-fracture replica immunogold labeling.

PubMed

Rash, John E; Kamasawa, Naomi; Davidson, Kimberly G V; Yasumura, Thomas; Pereda, Alberto E; Nagy, James I

2012-06-01

Despite the combination of light-microscopic immunocytochemistry, histochemical mRNA detection techniques and protein reporter systems, progress in identifying the protein composition of neuronal versus glial gap junctions, determination of the differential localization of their constituent connexin proteins in two apposing membranes and understanding human neurological diseases caused by connexin mutations has been problematic due to ambiguities introduced in the cellular and subcellular assignment of connexins. Misassignments occurred primarily because membranes and their constituent proteins are below the limit of resolution of light microscopic imaging techniques. Currently, only serial thin-section transmission electron microscopy and freeze-fracture replica immunogold labeling have sufficient resolution to assign connexin proteins to either or both sides of gap junction plaques. However, freeze-fracture replica immunogold labeling has been limited because conventional freeze fracturing allows retrieval of only one of the two membrane fracture faces within a gap junction, making it difficult to identify connexin coupling partners in hemiplaques removed by fracturing. We now summarize progress in ascertaining the connexin composition of two coupled hemiplaques using matched double-replicas that are labeled simultaneously for multiple connexins. This approach allows unambiguous identification of connexins and determination of the membrane "sidedness" and the identities of connexin coupling partners in homotypic and heterotypic gap junctions of vertebrate neurons.

Validation of newly developed physical laparoscopy simulator in transabdominal preperitoneal (TAPP) inguinal hernia repair.

PubMed

Nishihara, Yuichi; Isobe, Yoh; Kitagawa, Yuko

2017-12-01

A realistic simulator for transabdominal preperitoneal (TAPP) inguinal hernia repair would enhance surgeons' training experience before they enter the operating theater. The purpose of this study was to create a novel physical simulator for TAPP inguinal hernia repair and obtain surgeons' opinions regarding its efficacy. Our novel TAPP inguinal hernia repair simulator consists of a physical laparoscopy simulator and a handmade organ replica model. The physical laparoscopy simulator was created by three-dimensional (3D) printing technology, and it represents the trunk of the human body and the bendability of the abdominal wall under pneumoperitoneal pressure. The organ replica model was manually created by assembling materials. The TAPP inguinal hernia repair simulator allows for the performance of all procedures required in TAPP inguinal hernia repair. Fifteen general surgeons performed TAPP inguinal hernia repair using our simulator. Their opinions were scored on a 5-point Likert scale. All participants strongly agreed that the 3D-printed physical simulator and organ replica model were highly useful for TAPP inguinal hernia repair training (median, 5 points) and TAPP inguinal hernia repair education (median, 5 points). They felt that the simulator would be effective for TAPP inguinal hernia repair training before entering the operating theater. All surgeons considered that this simulator should be introduced in the residency curriculum. We successfully created a physical simulator for TAPP inguinal hernia repair training using 3D printing technology and a handmade organ replica model created with inexpensive, readily accessible materials. Preoperative TAPP inguinal hernia repair training using this simulator and organ replica model may be of benefit in the training of all surgeons. All general surgeons involved in the present study felt that this simulator and organ replica model should be used in their residency curriculum.

Efficient Round-Trip Time Optimization for Replica-Exchange Enveloping Distribution Sampling (RE-EDS).

PubMed

Sidler, Dominik; Cristòfol-Clough, Michael; Riniker, Sereina

2017-06-13

Replica-exchange enveloping distribution sampling (RE-EDS) allows the efficient estimation of free-energy differences between multiple end-states from a single molecular dynamics (MD) simulation. In EDS, a reference state is sampled, which can be tuned by two types of parameters, i.e., smoothness parameters(s) and energy offsets, such that all end-states are sufficiently sampled. However, the choice of these parameters is not trivial. Replica exchange (RE) or parallel tempering is a widely applied technique to enhance sampling. By combining EDS with the RE technique, the parameter choice problem could be simplified and the challenge shifted toward an optimal distribution of the replicas in the smoothness-parameter space. The choice of a certain replica distribution can alter the sampling efficiency significantly. In this work, global round-trip time optimization (GRTO) algorithms are tested for the use in RE-EDS simulations. In addition, a local round-trip time optimization (LRTO) algorithm is proposed for systems with slowly adapting environments, where a reliable estimate for the round-trip time is challenging to obtain. The optimization algorithms were applied to RE-EDS simulations of a system of nine small-molecule inhibitors of phenylethanolamine N-methyltransferase (PNMT). The energy offsets were determined using our recently proposed parallel energy-offset (PEOE) estimation scheme. While the multistate GRTO algorithm yielded the best replica distribution for the ligands in water, the multistate LRTO algorithm was found to be the method of choice for the ligands in complex with PNMT. With this, the 36 alchemical free-energy differences between the nine ligands were calculated successfully from a single RE-EDS simulation 10 ns in length. Thus, RE-EDS presents an efficient method for the estimation of relative binding free energies.

A dynamic replication management strategy in distributed GIS

NASA Astrophysics Data System (ADS)

Pan, Shaoming; Xiong, Lian; Xu, Zhengquan; Chong, Yanwen; Meng, Qingxiang

2018-03-01

Replication strategy is one of effective solutions to meet the requirement of service response time by preparing data in advance to avoid the delay of reading data from disks. This paper presents a brand-new method to create copies considering the selection of replicas set, the number of copies for each replica and the placement strategy of all copies. First, the popularities of all data are computed considering both the historical access records and the timeliness of the records. Then, replica set can be selected based on their recent popularities. Also, an enhanced Q-value scheme is proposed to assign the number of copies for each replica. Finally, a reasonable copies placement strategy is designed to meet the requirement of load balance. In addition, we present several experiments that compare the proposed method with techniques that use other replication management strategies. The results show that the proposed model has better performance than other algorithms in all respects. Moreover, the experiments based on different parameters also demonstrated the effectiveness and adaptability of the proposed algorithm.

Replica molding-based nanopatterning of tribocharge on elastomer with application to electrohydrodynamic nanolithography

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

Li, Qiang; Peer, Akshit; Cho, In Ho

Replica molding often induces tribocharge on elastomers. To date, this phenomenon has been studied only on untextured elastomer surfaces even though replica molding is an effective method for their nanotexturing. Here we show that on elastomer surfaces nanotextured through replica molding the induced tribocharge also becomes patterned at nanoscale in close correlation with the nanotexture. Here, by applying Kelvin probe microscopy, electrohydrodynamic lithography, and electrostatic analysis to our model nanostructure, poly(dimethylsiloxane) nanocup arrays replicated from a polycarbonate nanocone array, we reveal that the induced tribocharge is highly localized within the nanocup, especially around its rim. Through finite element analysis, wemore » also find that the rim sustains the strongest friction during the demolding process. From these findings, we identify the demolding-induced friction as the main factor governing the tribocharge’s nanoscale distribution pattern. Finally, by incorporating the resulting annular tribocharge into electrohydrodynamic lithography, we also accomplish facile realization of nanovolcanos with 10 nm-scale craters.« less

Electronically transparent graphene replicas of diatoms: a new technique for the investigation of frustule morphology

PubMed Central

Pan, Zhengwei; Lerch, Sarah J. L.; Xu, Liang; Li, Xufan; Chuang, Yen-Jun; Howe, Jane Y.; Mahurin, Shannon M.; Dai, Sheng; Hildebrand, Mark

2014-01-01

The morphogenesis of the silica cell walls (called frustules) of unicellular algae known as diatoms is one of the most intriguing mysteries of the diatoms. To study frustule morphogenesis, optical, electron and atomic force microscopy has been extensively used to reveal the frustule morphology. However, since silica frustules are opaque, past observations were limited to outer and fracture surfaces, restricting observations of interior structures. Here we show that opaque silica frustules can be converted into electronically transparent graphene replicas, fabricated using chemical vapor deposition of methane. Chemical vapor deposition creates a continuous graphene coating preserving the frustule's shape and fine, complicated internal features. Subsequent dissolution of the silica with hydrofluoric acid yields a free-standing replica of the internal and external native frustule morphologies. Electron microscopy renders these graphene replicas highly transparent, revealing previously unobserved, complex, three-dimensional, interior frustule structures, which lend new insights into the investigation of frustule morphogenesis. PMID:25135739

Replica molding-based nanopatterning of tribocharge on elastomer with application to electrohydrodynamic nanolithography

DOE PAGES

Li, Qiang; Peer, Akshit; Cho, In Ho; ...

2018-03-02

Replica molding often induces tribocharge on elastomers. To date, this phenomenon has been studied only on untextured elastomer surfaces even though replica molding is an effective method for their nanotexturing. Here we show that on elastomer surfaces nanotextured through replica molding the induced tribocharge also becomes patterned at nanoscale in close correlation with the nanotexture. Here, by applying Kelvin probe microscopy, electrohydrodynamic lithography, and electrostatic analysis to our model nanostructure, poly(dimethylsiloxane) nanocup arrays replicated from a polycarbonate nanocone array, we reveal that the induced tribocharge is highly localized within the nanocup, especially around its rim. Through finite element analysis, wemore » also find that the rim sustains the strongest friction during the demolding process. From these findings, we identify the demolding-induced friction as the main factor governing the tribocharge’s nanoscale distribution pattern. Finally, by incorporating the resulting annular tribocharge into electrohydrodynamic lithography, we also accomplish facile realization of nanovolcanos with 10 nm-scale craters.« less

Czechoslovak Replica X-Ray Mirrors for Astronomical Applications

NASA Astrophysics Data System (ADS)

Hudec, R.; Valnicek, B.

Imaging X-ray mirrors has been developed in Czechoslovakia since 1970 by a way of two different replica technologies based on galvanoplastics and reactoplastics as a natural part of Czechoslovak X-ray astronomy program. Until now about 30 mirros with diameters between 1.7 and 24 cm were manufactured. Seven mirrors were flown in space experiments. The new technology used since 1981 allows to produce light-weight X-ray mirrors at relatively very low cost. The technology offers interesting possibilities in construction of (1) large arrays of identical optical systems, (2) very small (microscopic) mirros and (3) lobster-eye type optics. Advantages and drawbacks of replica techology are discussed.

Optimal temperature ladders in replica exchange simulations

NASA Astrophysics Data System (ADS)

Denschlag, Robert; Lingenheil, Martin; Tavan, Paul

2009-04-01

In replica exchange simulations, a temperature ladder with N rungs spans a given temperature interval. Considering systems with heat capacities independent of the temperature, here we address the question of how large N should be chosen for an optimally fast diffusion of the replicas through the temperature space. Using a simple example we show that choosing average acceptance probabilities of about 45% and computing N accordingly maximizes the round trip rates r across the given temperature range. This result differs from previous analyses which suggested smaller average acceptance probabilities of about 23%. We show that the latter choice maximizes the ratio r/N instead of r.

Evaluation of a Small-Crack Monitoring System

NASA Technical Reports Server (NTRS)

Newman, John A.; Johnston, William M.

2010-01-01

A new system has been developed to obtain fatigue crack growth rate data from a series of images acquired during fatigue testing of specimens containing small surface cracks that initiate at highly-polished notches. The primary benefit associated with replica-based crack growth rate data methods is preserving a record of the crack configuration during the life of the specimen. Additionally, this system has the benefits of both reducing time and labor, and not requiring introduction of surface replica media into the crack. Fatigue crack growth rate data obtained using this new system are found to be in good agreement with similar results obtained from surface replicas.

Passive acoustic source localization using sources of opportunity.

PubMed

Verlinden, Christopher M A; Sarkar, J; Hodgkiss, W S; Kuperman, W A; Sabra, K G

2015-07-01

The feasibility of using data derived replicas from ships of opportunity for implementing matched field processing is demonstrated. The Automatic Identification System (AIS) is used to provide the library coordinates for the replica library and a correlation based processing procedure is used to overcome the impediment that the replica library is constructed from sources with different spectra and will further be used to locate another source with its own unique spectral structure. The method is illustrated with simulation and then verified using acoustic data from a 2009 experiment for which AIS information was retrieved from the United States Coast Guard Navigation Center Nationwide AIS database.

Materials Chemistry and Performance of Silicone-Based Replicating Compounds.

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

Brumbach, Michael T.; Mirabal, Alex James; Kalan, Michael

Replicating compounds are used to cast reproductions of surface features on a variety of materials. Replicas allow for quantitative measurements and recordkeeping on parts that may otherwise be difficult to measure or maintain. In this study, the chemistry and replicating capability of several replicating compounds was investigated. Additionally, the residue remaining on material surfaces upon removal of replicas was quantified. Cleaning practices were tested for several different replicating compounds. For all replicating compounds investigated, a thin silicone residue was left by the replica. For some compounds, additional inorganic species could be identified in the residue. Simple solvent cleaning could removemore » some residue.« less

Influence of collision on the flow through in-vitro rigid models of the vocal folds

NASA Astrophysics Data System (ADS)

Deverge, M.; Pelorson, X.; Vilain, C.; Lagrée, P.-Y.; Chentouf, F.; Willems, J.; Hirschberg, A.

2003-12-01

Measurements of pressure in oscillating rigid replicas of vocal folds are presented. The pressure upstream of the replica is used as input to various theoretical approximations to predict the pressure within the glottis. As the vocal folds collide the classical quasisteady boundary layer theory fails. It appears however that for physiologically reasonable shapes of the replicas, viscous effects are more important than the influence of the flow unsteadiness due to the wall movement. A simple model based on a quasisteady Bernoulli equation corrected for viscous effect, combined with a simple boundary layer separation model does globally predict the observed pressure behavior.

Systematic expansion in the order parameter for replica theory of the dynamical glass transition.

PubMed

Jacquin, Hugo; Zamponi, Francesco

2013-03-28

It has been shown recently that predictions from mode-coupling theory for the glass transition of hard-spheres become increasingly bad when dimensionality increases, whereas replica theory predicts a correct scaling. Nevertheless if one focuses on the regime around the dynamical transition in three dimensions, mode-coupling results are far more convincing than replica theory predictions. It seems thus necessary to reconcile the two theoretic approaches in order to obtain a theory that interpolates between low-dimensional, mode-coupling results, and "mean-field" results from replica theory. Even though quantitative results for the dynamical transition issued from replica theory are not accurate in low dimensions, two different approximation schemes--small cage expansion and replicated hyper-netted-chain (RHNC)--provide the correct qualitative picture for the transition, namely, a discontinuous jump of a static order parameter from zero to a finite value. The purpose of this work is to develop a systematic expansion around the RHNC result in powers of the static order parameter, and to calculate the first correction in this expansion. Interestingly, this correction involves the static three-body correlations of the liquid. More importantly, we separately demonstrate that higher order terms in the expansion are quantitatively relevant at the transition, and that the usual mode-coupling kernel, involving two-body direct correlation functions of the liquid, cannot be recovered from static computations.

Producing samples for the organization of proficiency tests. Study of the homogeneity of replicas produced from two atmosphere generation systems.

PubMed

Freville, Laurence; Moulut, Jean-Claude; Grzebyk, Michel; Kauffer, Edmond

2010-08-01

This article describes two atmosphere generation systems used for the production of replicas. The first, the Sputnic system, is based on the Sputnic air sampler developed by the National Institute of Occupational Health in Oslo (Norway). It is used to generate asbestos fibres or silica particles and allows the simultaneous production, by means of sampling on filters, of up to 114 replicas. The second is a multipurpose system that allows dust sampling on foams used with the CIP 10-R device. Twenty samples can be taken simultaneously. In total, 120 series of samples allowed characterization of the variability of the two generation systems used for the production of replicas loaded with asbestos fibres or silica dust. The coefficients of variation characterizing the dispersion of the filter loading in the Sputnic system are <10% for high densities asbestos fibre or silica dust samples. The coefficient of dispersion is on average higher when the asbestos fibre density is lower. The differences observed between the measurements taken on the different crowns of the Sputnic system are low and <2%. The results obtained with the multipurpose system show that replica dispersion is on average equal to 4%, which will allow proposal in the near future of a proficiency test dedicated to the quantitative analysis of crystalline silica on foams sampled with the CIP 10-R device.

Multiscale implementation of infinite-swap replica exchange molecular dynamics.

PubMed

Yu, Tang-Qing; Lu, Jianfeng; Abrams, Cameron F; Vanden-Eijnden, Eric

2016-10-18

Replica exchange molecular dynamics (REMD) is a popular method to accelerate conformational sampling of complex molecular systems. The idea is to run several replicas of the system in parallel at different temperatures that are swapped periodically. These swaps are typically attempted every few MD steps and accepted or rejected according to a Metropolis-Hastings criterion. This guarantees that the joint distribution of the composite system of replicas is the normalized sum of the symmetrized product of the canonical distributions of these replicas at the different temperatures. Here we propose a different implementation of REMD in which (i) the swaps obey a continuous-time Markov jump process implemented via Gillespie's stochastic simulation algorithm (SSA), which also samples exactly the aforementioned joint distribution and has the advantage of being rejection free, and (ii) this REMD-SSA is combined with the heterogeneous multiscale method to accelerate the rate of the swaps and reach the so-called infinite-swap limit that is known to optimize sampling efficiency. The method is easy to implement and can be trivially parallelized. Here we illustrate its accuracy and efficiency on the examples of alanine dipeptide in vacuum and C-terminal β-hairpin of protein G in explicit solvent. In this latter example, our results indicate that the landscape of the protein is a triple funnel with two folded structures and one misfolded structure that are stabilized by H-bonds.

77 FR 12240 - Application(s) for Duty-Free Entry of Scientific Instruments

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-29

... Institute, 5353 Parkside Dr MC 19-RE, Jupiter, FL 33458. Instrument: Freeze Fracture/Freeze Etch device... localization of membrane proteins using freeze fracture replica immuno- gold labeling, including all kinds of receptors and channels. Because freeze-fracture replica immuno-gold labeling has a high sensitivity for the...

Replica of the Presidential Medal of Freedom Award

NASA Image and Video Library

1970-04-18

S70-35562 (April 1970) --- A photographic replica of the Presidential Medal of Freedom Award which President Richard M. Nixon presented to the Apollo 13 Missions Operations Team (MOT). The presentation was made by the Chief Executive during a visit to the Manned Spacecraft Center (MSC) in April 1970.

Inexpensive Eddy-Current Standard

NASA Technical Reports Server (NTRS)

Berry, Robert F., Jr.

1985-01-01

Radial crack replicas serve as evaluation standards. Technique entails intimately joining two pieces of appropriate aluminum alloy stock and centering drilled hole through and along interface. Bore surface of hole presents two vertical stock interface lines 180 degrees apart. These lines serve as radial crack defect replicas during eddy-current technique setup and verification.

Replication Strategy for Spatiotemporal Data Based on Distributed Caching System

PubMed Central

Xiong, Lian; Tao, Yang; Xu, Juan; Zhao, Lun

2018-01-01

The replica strategy in distributed cache can effectively reduce user access delay and improve system performance. However, developing a replica strategy suitable for varied application scenarios is still quite challenging, owing to differences in user access behavior and preferences. In this paper, a replication strategy for spatiotemporal data (RSSD) based on a distributed caching system is proposed. By taking advantage of the spatiotemporal locality and correlation of user access, RSSD mines high popularity and associated files from historical user access information, and then generates replicas and selects appropriate cache node for placement. Experimental results show that the RSSD algorithm is simple and efficient, and succeeds in significantly reducing user access delay. PMID:29342897

NASA STS-132 Air and Space Museum

NASA Image and Video Library

2010-07-26

A replica of the Nobel Prize that is in the museum's collection and was flown aboard STS-132 Atlantis is seen, Tuesday, July 27, 2010, at the Smithsonian National Air and Space Museum in Washington. STS-132 astronaut Piers Sellers returned the replica during a ceremony at the museum. Photo Credit: (NASA/Paul E. Alers)

Transition in coupled replicas may not imply a finite-temperature ideal glass transition in glass-forming systems.

PubMed

Garrahan, Juan P

2014-03-01

A key open question in the glass transition field is whether a finite temperature thermodynamic transition to the glass state exists or not. Recent simulations of coupled replicas in atomistic models have found signatures of a static transition as a function of replica coupling. This can be viewed as evidence of an associated thermodynamic glass transition in the uncoupled system. We demonstrate here that a different interpretation is possible. We consider the triangular plaquette model, an interacting spin system which displays (East model-like) glassy dynamics in the absence of any static transition. We show that when two replicas are coupled, there is a curve of equilibrium phase transitions, between phases of small and large overlap, in the temperature-coupling plane (located on the self-dual line of an exact temperature-coupling duality of the system) which ends at a critical point. Crucially, in the limit of vanishing coupling the finite temperature transition disappears, and the uncoupled system is in the disordered phase at all temperatures. We discuss an interpretation of atomistic simulations in light of this result.

Skin microrelief profiles as a cutaneous aging index.

PubMed

Kim, Dai Hyun; Rhyu, Yeon Seung; Ahn, Hyo Hyun; Hwang, Eenjun; Uhm, Chang Sub

2016-10-01

An objective measurement of cutaneous topographical information is important for quantifying the degree of skin aging. Our aim was to improve methods for measuring microrelief patterns using a three-dimensional analysis based on silicone replicas and scanning electron microscope (SEM). Another objective was to compare the results with those obtained using a two-dimensional analysis method based on dermoscopy. Silicone replicas were obtained from forearms, dorsum of the hands and fingers of 51 volunteers. Cutaneous profiles obtained by SEM with silicone replicas showed more consistent correlations with age than data obtained by dermoscopy. This indicates the advantage of three-dimensional topography analysis using silicone replicas and SEM over the widely used dermoscopic assessment. The cutaneous age was calculated using stepwise linear regression, and the result was 57.40-9.47 × (number of furrows on dorsum of the hand) × (width of furrows on dorsum of the hand). © The Author 2016. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

How hot? Systematic convergence of the replica exchange method using multiple reservoirs.

PubMed

Ruscio, Jory Z; Fawzi, Nicolas L; Head-Gordon, Teresa

2010-02-01

We have devised a systematic approach to converge a replica exchange molecular dynamics simulation by dividing the full temperature range into a series of higher temperature reservoirs and a finite number of lower temperature subreplicas. A defined highest temperature reservoir of equilibrium conformations is used to help converge a lower but still hot temperature subreplica, which in turn serves as the high-temperature reservoir for the next set of lower temperature subreplicas. The process is continued until an optimal temperature reservoir is reached to converge the simulation at the target temperature. This gradual convergence of subreplicas allows for better and faster convergence at the temperature of interest and all intermediate temperatures for thermodynamic analysis, as well as optimizing the use of multiple processors. We illustrate the overall effectiveness of our multiple reservoir replica exchange strategy by comparing sampling and computational efficiency with respect to replica exchange, as well as comparing methods when converging the structural ensemble of the disordered Abeta(21-30) peptide simulated with explicit water by comparing calculated Rotating Overhauser Effect Spectroscopy intensities to experimentally measured values. Copyright 2009 Wiley Periodicals, Inc.

General Formalism of Mass Scaling Approach for Replica-Exchange Molecular Dynamics and its Application

NASA Astrophysics Data System (ADS)

Nagai, Tetsuro

2017-01-01

Replica-exchange molecular dynamics (REMD) has demonstrated its efficiency by combining trajectories of a wide range of temperatures. As an extension of the method, the author formalizes the mass-manipulating replica-exchange molecular dynamics (MMREMD) method that allows for arbitrary mass scaling with respect to temperature and individual particles. The formalism enables the versatile application of mass-scaling approaches to the REMD method. The key change introduced in the novel formalism is the generalized rules for the velocity and momentum scaling after accepted replica-exchange attempts. As an application of this general formalism, the refinement of the viscosity-REMD (V-REMD) method [P. H. Nguyen, J. Chem. Phys. 132, 144109 (2010)] is presented. Numerical results are provided using a pilot system, demonstrating easier and more optimized applicability of the new version of V-REMD as well as the importance of adherence to the generalized velocity scaling rules. With the new formalism, more sound and efficient simulations will be performed.

Multidimensional generalized-ensemble algorithms for complex systems.

PubMed

Mitsutake, Ayori; Okamoto, Yuko

2009-06-07

We give general formulations of the multidimensional multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential energy function E(0) by adding any physical quantity V of interest as a new energy term. These multidimensional generalized-ensemble algorithms then perform a random walk not only in E(0) space but also in V space. Among the three algorithms, the replica-exchange method is the easiest to perform because the weight factor is just a product of regular Boltzmann-like factors, while the weight factors for the multicanonical algorithm and simulated tempering are not a priori known. We give a simple procedure for obtaining the weight factors for these two latter algorithms, which uses a short replica-exchange simulation and the multiple-histogram reweighting techniques. As an example of applications of these algorithms, we have performed a two-dimensional replica-exchange simulation and a two-dimensional simulated-tempering simulation using an alpha-helical peptide system. From these simulations, we study the helix-coil transitions of the peptide in gas phase and in aqueous solution.

Sealant retention is better assessed through colour photographs than through the replica and the visual examination methods.

PubMed

Hu, Xuan; Fan, Mingwan; Rong, Wensheng; Lo, Edward C M; Bronkhorst, Ewald; Frencken, Jo E

2014-08-01

The aim of this study was to test the hypothesis that the colour photograph method has a higher level of validity for assessing sealant retention than the visual clinical examination and replica methods. Sealed molars were assessed by two evaluators. The scores for the three methods were compared against consensus scores derived through assessing retention from scanning electron microscopy images (reference standard). The presence/absence (survival) of retained sealants on occlusal surfaces was determined according to the traditional and modified categorizations of retention. Sensitivity, specificity, and Youden-index scores were calculated. Sealant retention assessment scores for visual clinical examinations and for colour photographs were compared with those of the reference standard on 95 surfaces, and sealant retention assessment scores for replicas were compared with those of the reference standard on 33 surfaces. The highest mean Youden-index score for the presence/absence of sealant material was observed for the colour photograph method, followed by that for the replica method; the visual clinical examination method scored lowest. The mean Youden-index score for the survival of retained sealants was highest for the colour photograph method for both the traditional (0.882) and the modified (0.768) categories of sealant retention, whilst the visual clinical examination method had the lowest Youden-index score for these categories (0.745 and 0.063, respectively). The colour photograph method had a higher validity than the replica and the visual examination methods for assessing sealant retention. © 2014 Eur J Oral Sci.

The decoupling of the glass transitions in the two-component p-spin spherical model

NASA Astrophysics Data System (ADS)

Ikeda, Harukuni; Ikeda, Atsushi

2016-07-01

Binary mixtures of large and small particles with a disparate size ratio exhibit a rich phenomenology at their glass transition points. In order to gain insights on such systems, we introduce and study a two-component version of the p-spin spherical spin glass model. We employ the replica method to calculate the free energy and the phase diagram. We show that when the strengths of the interactions of each component are not widely separated, the model has only one glass phase characterized by the conventional one-step replica symmetry breaking. However when the strengths of the interactions are well separated, the model has three glass phases depending on the temperature and component ratio. One is the ‘single’ glass phase in which only the spins of one component are frozen while the spins of the other component remain mobile. This phase is characterized by the one-step replica symmetry breaking. The second is the ‘double’ glass phase obtained by cooling the single glass phase further, in which the spins of the remaining mobile component are also frozen. This phase is characterized by the two-step replica symmetry breaking. The third is also the ‘double’ glass phase, which, however, is formed by the simultaneous freezing of the spins of both components at the same temperatures and is characterized by the one-step replica symmetry breaking. We discuss the implications of these results for the glass transitions of binary mixtures.

Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods.

PubMed

Roe, Daniel R; Bergonzo, Christina; Cheatham, Thomas E

2014-04-03

Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency.

Physical mapping of complex genomes

DOEpatents

Evans, Glen A.

1993-01-01

Method for simultaneous identification of overlapping cosmid clones among multiple cosmid clones and the use of the method for mapping complex genomes are provided. A library of cosmid clones that contains the DNA to be mapped is constructed and arranged in a manner such that individual clones can be identified and replicas of the arranged clones prepared. In preferred embodiments, the clones are arranged in a two dimensional matrix. In such embodiments, the cosmid clones in a row are pooled, mixed probes complementary to the ends of the DNA inserts int he pooled clones are synthesized, hybridized to a first replica of the library. Hybridizing clones, which include the pooled row, are identified. A second portion of clones is prepared by pooling cosmid clones that correspond to a column in the matrix. The second pool thereby includes one clone from the first portion pooled clones. This common clone is located on the replica at the intersection of the column and row. Mixed probes complementary to the ends of the DNA inserts in the second pooled portion of clones are prepared and hybridized to a second replica of the library. The hybridization pattern on the first and second replicas of the library are compared and cross-hybridizing clones, other than the clones in the pooled column and row, that hybridize to identical clones in the first and second replicas are identified. These clones necessarily include DNA inserts that overlap with the DNA insert int he common clone located at the intersection of the pooled row and pooled column. The DNA in the entire library may be mapped by pooling the clones in each of the rows and columns of the matrix, preparing mixed end-specific probes and hybridizing the probes from each row or column to a replica of the library. Since all clones in the library are located at the intersection of a column and a row, the overlapping clones for all clones in the library may be identified and a physical map constructed. In other preferred embodiments, the cosmid clones are arranged in a three dimensional matrix, pooled and compared in threes according to intersecting planes of the three dimensional matrix. Arrangements corresponding to geometries of higher dimensions may also be prepared and used to simultaneously identify overlapping clones in highly complex libraries with relatively few hybridization reactions.

Three-Dimensional Interpretation of Sculptural Heritage with Digital and Tangible 3D Printed Replicas

ERIC Educational Resources Information Center

Saorin, José Luis; Carbonell-Carrera, Carlos; Cantero, Jorge de la Torre; Meier, Cecile; Aleman, Drago Diaz

2017-01-01

Spatial interpretation features as a skill to acquire in the educational curricula. The visualization and interpretation of three-dimensional objects in tactile devices and the possibility of digital manufacturing with 3D printers, offers an opportunity to include replicas of sculptures in teaching and, thus, facilitate the 3D interpretation of…

Sparks and Shocks: Replicas of Historical Instruments in Museum Education

ERIC Educational Resources Information Center

Rhees, David J.

2015-01-01

This paper discusses the variety of ways in which The Bakken Museum has made use of replicas or simulations of historical instruments and experiments and demonstrations in education programs and exhibits for school children, families with children, and other museum audiences. Early efforts were stimulated in the mid-1980s by a collaboration with…

A Recovery-Oriented Approach to Dependable Services: Repairing Past Errors with System-Wide Undo

DTIC Science & Technology

2003-12-01

54 4.5.3 Handling propagating paradoxes: the squash interface . . . . . . . . . . . . . . . . . . . 54 4.6 Discussion...84 6.3.3 Compensating for paradoxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 6.3.4 Squashing propagating...the service and comparing the behavior of the replicas to detect and squash misbehaving replicas. While on paper Byzantine fault tolerance may seem to

Pressure induced increase of the exciton phonon interaction in ZnO/(ZnMg)O quantum wells

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

Jarosz, D.; Suchocki, A.; Kozanecki, A.

2016-03-15

It is a well-established experimental fact that exciton-phonon coupling is very efficient in ZnO. The intensities of the phonon-replicas in ZnO/(ZnMg)O quantum structures strongly depend on the internal electric field. We performed high-pressure measurements on the single ZnO/(ZnMg)O quantum well. We observed a strong increase of the intensity of the phonon-replicas relative to the zero phonon line. In our opinion this effect is related to pressure induced increase of the strain in quantum structure. As a consequence, an increase of the piezoelectric component of the electric field is observed which leads to an increase of the intensity of the phonon-replicas.

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.

PubMed

Gil-Ley, Alejandro; Bussi, Giovanni

2015-03-10

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.

Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics.

PubMed

Jiang, Ping; Yaşar, Fatih; Hansmann, Ulrich H E

2013-08-13

We compare the efficiency of multicanonical and replica exchange molecular dynamics for the sampling of folding/unfolding events in simulations of proteins with end-to-end β -sheet. In Go-model simulations of the 75-residue MNK6, we observe improvement factors of 30 in the number of folding/unfolding events of multicanonical molecular dynamics over replica exchange molecular dynamics. As an application, we use this enhanced sampling to study the folding landscape of the 36-residue DS119 with an all-atom physical force field and implicit solvent. Here, we find that the rate-limiting step is the formation of the central helix that then provides a scaffold for the parallel β -sheet formed by the two chain ends.

Replica Exchange Molecular Dynamics in the Age of Heterogeneous Architectures

NASA Astrophysics Data System (ADS)

Roitberg, Adrian

2014-03-01

The rise of GPU-based codes has allowed MD to reach timescales only dreamed of only 5 years ago. Even within this new paradigm there is still need for advanced sampling techniques. Modern supercomputers (e.g. Blue Waters, Titan, Keeneland) have made available to users a significant number of GPUS and CPUS, which in turn translate into amazing opportunities for dream calculations. Replica-exchange based methods can optimally use tis combination of codes and architectures to explore conformational variabilities in large systems. I will show our recent work in porting the program Amber to GPUS, and the support for replica exchange methods, where the replicated dimension could be Temperature, pH, Hamiltonian, Umbrella windows and combinations of those schemes.

Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems.

PubMed

Mori, Takaharu; Jung, Jaewoon; Sugita, Yuji

2013-12-10

Conformational sampling is fundamentally important for simulating complex biomolecular systems. The generalized-ensemble algorithm, especially the temperature replica-exchange molecular dynamics method (T-REMD), is one of the most powerful methods to explore structures of biomolecules such as proteins, nucleic acids, carbohydrates, and also of lipid membranes. T-REMD simulations have focused on soluble proteins rather than membrane proteins or lipid bilayers, because explicit membranes do not keep their structural integrity at high temperature. Here, we propose a new generalized-ensemble algorithm for membrane systems, which we call the surface-tension REMD method. Each replica is simulated in the NPγT ensemble, and surface tensions in a pair of replicas are exchanged at certain intervals to enhance conformational sampling of the target membrane system. We test the method on two biological membrane systems: a fully hydrated DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine) lipid bilayer and a WALP23-POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane system. During these simulations, a random walk in surface tension space is realized. Large-scale lateral deformation (shrinking and stretching) of the membranes takes place in all of the replicas without collapse of the lipid bilayer structure. There is accelerated lateral diffusion of DPPC lipid molecules compared with conventional MD simulation, and a much wider range of tilt angle of the WALP23 peptide is sampled due to large deformation of the POPC lipid bilayer and through peptide-lipid interactions. Our method could be applicable to a wide variety of biological membrane systems.

Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

PubMed Central

2015-01-01

Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency. PMID:24625009

Multi-Scale Porous Ultra High Temperature Ceramics

DTIC Science & Technology

2015-01-08

different techniques: replica, particle stabilized foams, ice templating (freeze casting) and partial sintering. The pore morphology (closed-bubble...the porosity, pore size, shape and morphology . X-Ray Tomography was used to study their 3D microstructure. The 3D microstructures captured with...four different techniques: replica, particle stabilized foams, ice templating (freeze casting) and partial sintering. The pore morphology (closed-bubble

PIN - APOLLO 11

NASA Image and Video Library

1969-08-05

S69-40941 (July 1969) --- This picture is of the gold replica of an olive branch, the traditional symbol of peace, which was left on the moon's surface by Apollo 11 crewmembers. Astronaut Neil A. Armstrong, commander, was in charge of placing the small replica (less than half a foot in length) on the moon. The gesture represents a fresh wish for peace for all mankind.

Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.

PubMed

Huang, Yu-Ming M; McCammon, J Andrew; Miao, Yinglong

2018-04-10

Through adding a harmonic boost potential to smooth the system potential energy surface, Gaussian accelerated molecular dynamics (GaMD) provides enhanced sampling and free energy calculation of biomolecules without the need of predefined reaction coordinates. This work continues to improve the acceleration power and energy reweighting of the GaMD by combining the GaMD with replica exchange algorithms. Two versions of replica exchange GaMD (rex-GaMD) are presented: force constant rex-GaMD and threshold energy rex-GaMD. During simulations of force constant rex-GaMD, the boost potential can be exchanged between replicas of different harmonic force constants with fixed threshold energy. However, the algorithm of threshold energy rex-GaMD tends to switch the threshold energy between lower and upper bounds for generating different levels of boost potential. Testing simulations on three model systems, including the alanine dipeptide, chignolin, and HIV protease, demonstrate that through continuous exchanges of the boost potential, the rex-GaMD simulations not only enhance the conformational transitions of the systems but also narrow down the distribution width of the applied boost potential for accurate energetic reweighting to recover biomolecular free energy profiles.

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.

PubMed

Czaplewski, Cezary; Kalinowski, Sebastian; Liwo, Adam; Scheraga, Harold A

2009-03-10

The replica exchange (RE) method is increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. Recently, we implemented the united-residue UNRES force field for mesoscopic MD. Initial results from UNRES MD simulations show that we are able to simulate folding events that take place in a microsecond or even a millisecond time scale. To speed up the search further, we applied the multiplexing replica exchange molecular dynamics (MREMD) method. The multiplexed variant (MREMD) of the RE method, developed by Rhee and Pande, differs from the original RE method in that several trajectories are run at a given temperature. Each set of trajectories run at a different temperature constitutes a layer. Exchanges are attempted not only within a single layer but also between layers. The code has been parallelized and scales up to 4000 processors. We present a comparison of canonical MD, REMD, and MREMD simulations of protein folding with the UNRES force-field. We demonstrate that the multiplexed procedure increases the power of replica exchange MD considerably and convergence of the thermodynamic quantities is achieved much faster.

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins

PubMed Central

Czaplewski, Cezary; Kalinowski, Sebastian; Liwo, Adam; Scheraga, Harold A.

2009-01-01

The replica exchange (RE) method is increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. Recently, we implemented the united-residue UNRES force field for mesoscopic MD. Initial results from UNRES MD simulations show that we are able to simulate folding events that take place in a microsecond or even a millisecond time scale. To speed up the search further, we applied the multiplexing replica exchange molecular dynamics (MREMD) method. The multiplexed variant (MREMD) of the RE method, developed by Rhee and Pande, differs from the original RE method in that several trajectories are run at a given temperature. Each set of trajectories run at a different temperature constitutes a layer. Exchanges are attempted not only within a single layer but also between layers. The code has been parallelized and scales up to 4000 processors. We present a comparison of canonical MD, REMD, and MREMD simulations of protein folding with the UNRES force-field. We demonstrate that the multiplexed procedure increases the power of replica exchange MD considerably and convergence of the thermodynamic quantities is achieved much faster. PMID:20161452

A new Strategy to Improve Drug Delivery to the Maxillary Sinuses: The Frequency Sweep Acoustic Airflow.

PubMed

El Merhie, Amira; Navarro, Laurent; Delavenne, Xavier; Leclerc, Lara; Pourchez, Jérémie

2016-05-01

Enhancement of intranasal sinus deposition involves nebulization of a drug superimposed by an acoustic airflow. We investigated the impact of fixed frequency versus frequency sweep acoustic airflow on the improvement of aerosolized drug penetration into maxillary sinuses. Fixed frequency and frequency sweep acoustic airflow were generated using a nebulizing system of variable frequency. The effect of sweep cycle and intensity variation was studied on the intranasal sinus deposition. We used a nasal replica created from CT scans using 3D printing. Sodium fluoride and gentamicin were chosen as markers. Studies performed using fixed frequency acoustic airflow showed that each of maxillary sinuses of the nasal replica required specific frequency for the optimal aerosol deposition. Intranasal sinus drug deposition experiments under the effect of the frequency sweep acoustic airflow showed an optimal aerosol deposition into both maxillary sinus of the nasal replica. Studies on the effect of the duration of the sweep cycle showed that the shorter the cycle the better the deposition. We demonstrate the benefit of frequency sweep acoustic airflow on drug deposition into maxillary sinuses. However further in vivo studies have to be conducted since delivery rates cannot be obviously determined from a nasal replica.

(Bio)Chemical Tailoring of Biogenic 3-D Nanopatterned Templates with Energy-Relevant Functionalities

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

Sandhage, Kenneth H; Kroger, Nils

2014-09-08

The overall aim of this research has been to obtain fundamental understanding of (bio)chemical methodologies that will enable utilization of the unique 3-D nanopatterned architectures naturally produced by diatoms for the syntheses of advanced functional materials attractive for applications in energy harvesting/conversion and storage. This research has been conducted in three thrusts: Thrust 1 (In vivo immobilization of proteins in diatom biosilica) is directed towards elucidating the fundamental mechanism(s) underlying the cellular processes of in vivo immobilization of proteins in diatom silica. Thrust 2 (Shape-preserving reactive conversion of diatom biosilica into porous, high-surface area inorganic replicas) is aimed at understandingmore » the fundamental mechanisms of shape preservation and nanostructural evolution associated with the reactive conversion and/or coating-based conversion of diatom biosilica templates into porous inorganic replicas. Thrust 3 (Immobilization of energy-relevant enzymes in diatom biosilica and onto diatom biosilica-derived inorganic replicas) involves use of the results from both Thrust 1 and 2 to develop strategies for in vivo and in vitro immobilization of enzymes in/on diatom biosilica and diatom biosilica-derived inorganic replicas, respectively. This Final Report describes progress achieved in all 3 of these thrusts.« less

Electron Phonon Coupling versus Photoelectron Energy Loss at the Origin of Replica Bands in Photoemission of FeSe on SrTiO3

NASA Astrophysics Data System (ADS)

Li, Fengmiao; Sawatzky, George A.

2018-06-01

The recent observation of replica bands in single-layer FeSe /SrTiO3 by angle-resolved photoemission spectroscopy (ARPES) has triggered intense discussions concerning the potential influence of the FeSe electrons coupling with substrate phonons on the superconducting transition temperature. Here we provide strong evidence that the replica bands observed in the single-layer FeSe /SrTiO3 system and several other cases are largely due to the energy loss processes of the escaping photoelectron, resulted from the well-known strong coupling of external propagating electrons to Fuchs-Kliewer surface phonons in ionic materials in general. The photoelectron energy loss in ARPES on single-layer FeSe /SrTiO3 is calculated using the demonstrated successful semiclassical dielectric theory in describing low energy electron energy loss spectroscopy of ionic insulators. Our result shows that the observed replica bands are mostly a result of extrinsic photoelectron energy loss and not a result of the electron phonon interaction of the Fe d electrons with the substrate phonons. The strong enhancement of the superconducting transition temperature in these monolayers remains an open question.

Neutron and gamma-ray dose-rates from the Little Boy replica

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

Plassmann, E.A.; Pederson, R.A.

1984-01-01

We report dose-rate information obtained at many locations in the near vicinity of, and at distances out to 0.64 km from, the Little Boy replica while it was operated as a critical assembly. The measurements were made with modified conventional dosimetry instruments that used an Anderson-Braun detector for neutrons and a Geiger-Mueller tube for gamma rays with suitable electronic modules to count particle-induced pulses. Thermoluminescent dosimetry methods provide corroborative data. Our analysis gives estimates of both neutron and gamma-ray relaxation lengths in air for comparison with earlier calculations. We also show the neutron-to-gamma-ray dose ratio as a function of distancemore » from the replica. Current experiments and further data analysis will refine these results. 7 references, 8 figures.« less

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

PubMed Central

2015-01-01

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide. PMID:25838811

An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations

NASA Astrophysics Data System (ADS)

Capelli, Riccardo; Tiana, Guido; Camilloni, Carlo

2018-05-01

Inferential methods can be used to integrate experimental informations and molecular simulations. The maximum entropy principle provides a framework for using equilibrium experimental data, and it has been shown that replica-averaged simulations, restrained using a static potential, are a practical and powerful implementation of such a principle. Here we show that replica-averaged simulations restrained using a time-dependent potential are equivalent to the principle of maximum caliber, the dynamic version of the principle of maximum entropy, and thus may allow us to integrate time-resolved data in molecular dynamics simulations. We provide an analytical proof of the equivalence as well as a computational validation making use of simple models and synthetic data. Some limitations and possible solutions are also discussed.

Proactive replica checking to assure reliability of data in cloud storage with minimum replication

NASA Astrophysics Data System (ADS)

Murarka, Damini; Maheswari, G. Uma

2017-11-01

The two major issues for cloud storage systems are data reliability and storage costs. For data reliability protection, multi-replica replication strategy which is used mostly in current clouds acquires huge storage consumption, leading to a large storage cost for applications within the loud specifically. This paper presents a cost-efficient data reliability mechanism named PRCR to cut back the cloud storage consumption. PRCR ensures data reliability of large cloud information with the replication that might conjointly function as a price effective benchmark for replication. The duplication shows that when resembled to the standard three-replica approach, PRCR will scale back to consume only a simple fraction of the cloud storage from one-third of the storage, thence considerably minimizing the cloud storage price.

An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations.

PubMed

Capelli, Riccardo; Tiana, Guido; Camilloni, Carlo

2018-05-14

Inferential methods can be used to integrate experimental informations and molecular simulations. The maximum entropy principle provides a framework for using equilibrium experimental data, and it has been shown that replica-averaged simulations, restrained using a static potential, are a practical and powerful implementation of such a principle. Here we show that replica-averaged simulations restrained using a time-dependent potential are equivalent to the principle of maximum caliber, the dynamic version of the principle of maximum entropy, and thus may allow us to integrate time-resolved data in molecular dynamics simulations. We provide an analytical proof of the equivalence as well as a computational validation making use of simple models and synthetic data. Some limitations and possible solutions are also discussed.

Vascular corrosion casting technique steps.

PubMed

Verli, Flaviana Dornela; Rossi-Schneider, Tissiana Raquel; Schneider, Felipe Luís; Yurgel, Liliane Soares; de Souza, Maria Antonieta Lopes

2007-01-01

The vascular corrosion casting technique produces a replica of vascular beds of normal or pathological tissues. Once associated with scanning electron microscopy (SEM), this technique provides details of the three-dimensional anatomic arrangement of the vascular replica, which is the main advantage of this method. The present study is intended to describe the steps of the vascular corrosion casting technique and the different ways to perform them. them.

Rooftop Energy Potential of Low Income Communities in America REPLICA

DOE Data Explorer

Mooney, Meghan (ORCID:0000000309406958); Sigrin, Ben

1970-01-01

The Rooftop Energy Potential of Low Income Communities in America REPLICA data set provides estimates of residential rooftop solar technical potential at the tract-level with emphasis on estimates for Low and Moderate Income LMI populations. In addition to technical potential REPLICA is comprised of 10 additional datasets at the tract-level to provide socio-demographic and market context. The model year vintage of REPLICA is 2015. The LMI solar potential estimates are made at the tract level grouped by Area Median Income AMI income tenure and building type. These estimates are based off of LiDAR data of 128 metropolitan areas statistical modeling and ACS 2011-2015 demographic data. The remaining datasets are supplemental datasets that can be used in conjunction with the technical potential data for general LMI solar analysis planning and policy making. The core dataset is a wide-format CSV file seeds_ii_replica.csv that can be tagged to a tract geometry using the GEOID or GISJOIN fields. In addition users can download geographic shapefiles for the main or supplemental datasets. This dataset was generated as part of the larger NREL-led SEEDSII Solar Energy Evolution and Diffusion Studies project and specifically for the NREL technical report titled Rooftop Solar Technical Potential for Low-to-Moderate Income Households in the United States by Sigrin and Mooney 2018. This dataset is intended to give researchers planners advocates and policy-makers access to credible data to analyze low-income solar issues and potentially perform cost-benefit analysis for program design. To explore the data in an interactive web mapping environment use the NREL SolarForAll app.

New approach to accuracy verification of 3D surface models: An analysis of point cloud coordinates.

PubMed

Lee, Wan-Sun; Park, Jong-Kyoung; Kim, Ji-Hwan; Kim, Hae-Young; Kim, Woong-Chul; Yu, Chin-Ho

2016-04-01

The precision of two types of surface digitization devices, i.e., a contact probe scanner and an optical scanner, and the trueness of two types of stone replicas, i.e., one without an imaging powder (SR/NP) and one with an imaging powder (SR/P), were evaluated using a computer-aided analysis. A master die was fabricated from stainless steel. Ten impressions were taken, and ten stone replicas were prepared from Type IV stone (Fujirock EP, GC, Leuven, Belgium). The precision of two types of scanners was analyzed using the root mean square (RMS), measurement error (ME), and limits of agreement (LoA) at each coordinate. The trueness of the stone replicas was evaluated using the total deviation. A Student's t-test was applied to compare the discrepancies between the CAD-reference-models of the master die (m-CRM) and point clouds for the two types of stone replicas (α=.05). The RMS values for the precision were 1.58, 1.28, and 0.98μm along the x-, y-, and z-axes in the contact probe scanner and 1.97, 1.32, and 1.33μm along the x-, y-, and z-axes in the optical scanner, respectively. A comparison with m-CRM revealed a trueness of 7.10μm for SR/NP and 8.65μm for SR/P. The precision at each coordinate (x-, y-, and z-axes) was revealed to be higher than the one assessed in the previous method (overall offset differences). A comparison between the m-CRM and 3D surface models of the stone replicas revealed a greater dimensional change in SR/P than in SR/NP. Copyright © 2015 Japan Prosthodontic Society. Published by Elsevier Ltd. All rights reserved.

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

PubMed

Jiang, Wei; Roux, Benoît

2010-07-01

Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters "lambda" can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor lambda in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the inter-conversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter lambda and the boosting potential, in an extended dual array of coupled lambda- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of T4 lysozyme was calculated. The tests demonstrate that the dual lambda-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

Fault Injection Campaign for a Fault Tolerant Duplex Framework

NASA Technical Reports Server (NTRS)

Sacco, Gian Franco; Ferraro, Robert D.; von llmen, Paul; Rennels, Dave A.

2007-01-01

Fault tolerance is an efficient approach adopted to avoid or reduce the damage of a system failure. In this work we present the results of a fault injection campaign we conducted on the Duplex Framework (DF). The DF is a software developed by the UCLA group [1, 2] that uses a fault tolerant approach and allows to run two replicas of the same process on two different nodes of a commercial off-the-shelf (COTS) computer cluster. A third process running on a different node, constantly monitors the results computed by the two replicas, and eventually restarts the two replica processes if an inconsistency in their computation is detected. This approach is very cost efficient and can be adopted to control processes on spacecrafts where the fault rate produced by cosmic rays is not very high.

Self-calibrating threshold detector

NASA Technical Reports Server (NTRS)

Barnes, J. R.; Huang, M. Y. (Inventor)

1980-01-01

A self calibrating threshold detector comprises a single demodulating channel which includes a mixer having one input receiving the incoming signal and another input receiving a local replica code. During a short time interval, an incorrect local code is applied to the mixer to incorrectly demodulate the incoming signal and to provide a reference level that calibrates the noise propagating through the channel. A sample and hold circuit is coupled to the channel for storing a sample of the reference level. During a relatively long time interval, the correct replica code provides an output level which ranges between the reference level and a maximum level that represents incoming signal presence and synchronism with the replica code. A summer substracts the stored sample reference from the output level to provide a resultant difference signal indicative of the acquisition of the expected signal.

Belief Propagation Algorithm for Portfolio Optimization Problems

PubMed Central

2015-01-01

The typical behavior of optimal solutions to portfolio optimization problems with absolute deviation and expected shortfall models using replica analysis was pioneeringly estimated by S. Ciliberti et al. [Eur. Phys. B. 57, 175 (2007)]; however, they have not yet developed an approximate derivation method for finding the optimal portfolio with respect to a given return set. In this study, an approximation algorithm based on belief propagation for the portfolio optimization problem is presented using the Bethe free energy formalism, and the consistency of the numerical experimental results of the proposed algorithm with those of replica analysis is confirmed. Furthermore, the conjecture of H. Konno and H. Yamazaki, that the optimal solutions with the absolute deviation model and with the mean-variance model have the same typical behavior, is verified using replica analysis and the belief propagation algorithm. PMID:26305462

Belief Propagation Algorithm for Portfolio Optimization Problems.

PubMed

Shinzato, Takashi; Yasuda, Muneki

2015-01-01

The typical behavior of optimal solutions to portfolio optimization problems with absolute deviation and expected shortfall models using replica analysis was pioneeringly estimated by S. Ciliberti et al. [Eur. Phys. B. 57, 175 (2007)]; however, they have not yet developed an approximate derivation method for finding the optimal portfolio with respect to a given return set. In this study, an approximation algorithm based on belief propagation for the portfolio optimization problem is presented using the Bethe free energy formalism, and the consistency of the numerical experimental results of the proposed algorithm with those of replica analysis is confirmed. Furthermore, the conjecture of H. Konno and H. Yamazaki, that the optimal solutions with the absolute deviation model and with the mean-variance model have the same typical behavior, is verified using replica analysis and the belief propagation algorithm.

Evaluation of generalized degrees of freedom for sparse estimation by replica method

NASA Astrophysics Data System (ADS)

Sakata, A.

2016-12-01

We develop a method to evaluate the generalized degrees of freedom (GDF) for linear regression with sparse regularization. The GDF is a key factor in model selection, and thus its evaluation is useful in many modelling applications. An analytical expression for the GDF is derived using the replica method in the large-system-size limit with random Gaussian predictors. The resulting formula has a universal form that is independent of the type of regularization, providing us with a simple interpretation. Within the framework of replica symmetric (RS) analysis, GDF has a physical meaning as the effective fraction of non-zero components. The validity of our method in the RS phase is supported by the consistency of our results with previous mathematical results. The analytical results in the RS phase are calculated numerically using the belief propagation algorithm.

Free-Energy Fluctuations and Chaos in the Sherrington-Kirkpatrick Model

NASA Astrophysics Data System (ADS)

Aspelmeier, T.

2008-03-01

The sample-to-sample fluctuations ΔFN of the free-energy in the Sherrington-Kirkpatrick model are shown rigorously to be related to bond chaos. Via this connection, the fluctuations become analytically accessible by replica methods. The replica calculation for bond chaos shows that the exponent μ governing the growth of the fluctuations with system size N, ΔFN˜Nμ, is bounded by μ≤(1)/(4).

Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method

DTIC Science & Technology

2011-12-01

REMD while reproducing the energy landscape of explicit solvent simulations . ’ INTRODUCTION Molecular dynamics (MD) simulations of proteins can pro...Mongan, J.; McCammon, J. A. Accelerated molecular dynamics : a promising and efficient simulation method for biomolecules. J. Chem. Phys. 2004, 120 (24...Chemical Theory and Computation ARTICLE (8) Abraham,M. J.; Gready, J. E. Ensuringmixing efficiency of replica- exchange molecular dynamics simulations . J

DIRAC File Replica and Metadata Catalog

NASA Astrophysics Data System (ADS)

Tsaregorodtsev, A.; Poss, S.

2012-12-01

File replica and metadata catalogs are essential parts of any distributed data management system, which are largely determining its functionality and performance. A new File Catalog (DFC) was developed in the framework of the DIRAC Project that combines both replica and metadata catalog functionality. The DFC design is based on the practical experience with the data management system of the LHCb Collaboration. It is optimized for the most common patterns of the catalog usage in order to achieve maximum performance from the user perspective. The DFC supports bulk operations for replica queries and allows quick analysis of the storage usage globally and for each Storage Element separately. It supports flexible ACL rules with plug-ins for various policies that can be adopted by a particular community. The DFC catalog allows to store various types of metadata associated with files and directories and to perform efficient queries for the data based on complex metadata combinations. Definition of file ancestor-descendent relation chains is also possible. The DFC catalog is implemented in the general DIRAC distributed computing framework following the standard grid security architecture. In this paper we describe the design of the DFC and its implementation details. The performance measurements are compared with other grid file catalog implementations. The experience of the DFC Catalog usage in the CLIC detector project are discussed.

Two-dimensional replica exchange approach for peptide-peptide interactions

NASA Astrophysics Data System (ADS)

Gee, Jason; Shell, M. Scott

2011-02-01

The replica exchange molecular dynamics (REMD) method has emerged as a standard approach for simulating proteins and peptides with rugged underlying free energy landscapes. We describe an extension to the original methodology—here termed umbrella-sampling REMD (UREMD)—that offers specific advantages in simulating peptide-peptide interactions. This method is based on the use of two dimensions in the replica cascade, one in temperature as in conventional REMD, and one in an umbrella sampling coordinate between the center of mass of the two peptides that aids explicit exploration of the complete association-dissociation reaction coordinate. To mitigate the increased number of replicas required, we pursue an approach in which the temperature and umbrella dimensions are linked at only fully associated and dissociated states. Coupled with the reweighting equations, the UREMD method aids accurate calculations of normalized free energy profiles and structural or energetic measures as a function of interpeptide separation distance. We test the approach on two families of peptides: a series of designed tetrapeptides that serve as minimal models for amyloid fibril formation, and a fragment of a classic leucine zipper peptide and its mutant. The results for these systems are compared to those from conventional REMD simulations, and demonstrate good convergence properties, low statistical errors, and, for the leucine zippers, an ability to sample near-native structures.

Zebrafish response to a robotic replica in three dimensions

PubMed Central

Ruberto, Tommaso; Mwaffo, Violet; Singh, Sukhgewanpreet; Neri, Daniele

2016-01-01

As zebrafish emerge as a species of choice for the investigation of biological processes, a number of experimental protocols are being developed to study their social behaviour. While live stimuli may elicit varying response in focal subjects owing to idiosyncrasies, tiredness and circadian rhythms, video stimuli suffer from the absence of physical input and rely only on two-dimensional projections. Robotics has been recently proposed as an alternative approach to generate physical, customizable, effective and consistent stimuli for behavioural phenotyping. Here, we contribute to this field of investigation through a novel four-degree-of-freedom robotics-based platform to manoeuvre a biologically inspired three-dimensionally printed replica. The platform enables three-dimensional motions as well as body oscillations to mimic zebrafish locomotion. In a series of experiments, we demonstrate the differential role of the visual stimuli associated with the biologically inspired replica and its three-dimensional motion. Three-dimensional tracking and information-theoretic tools are complemented to quantify the interaction between zebrafish and the robotic stimulus. Live subjects displayed a robust attraction towards the moving replica, and such attraction was lost when controlling for its visual appearance or motion. This effort is expected to aid zebrafish behavioural phenotyping, by offering a novel approach to generate physical stimuli moving in three dimensions. PMID:27853566

Random forest regression for magnetic resonance image synthesis.

PubMed

Jog, Amod; Carass, Aaron; Roy, Snehashis; Pham, Dzung L; Prince, Jerry L

2017-01-01

By choosing different pulse sequences and their parameters, magnetic resonance imaging (MRI) can generate a large variety of tissue contrasts. This very flexibility, however, can yield inconsistencies with MRI acquisitions across datasets or scanning sessions that can in turn cause inconsistent automated image analysis. Although image synthesis of MR images has been shown to be helpful in addressing this problem, an inability to synthesize both T 2 -weighted brain images that include the skull and FLuid Attenuated Inversion Recovery (FLAIR) images has been reported. The method described herein, called REPLICA, addresses these limitations. REPLICA is a supervised random forest image synthesis approach that learns a nonlinear regression to predict intensities of alternate tissue contrasts given specific input tissue contrasts. Experimental results include direct image comparisons between synthetic and real images, results from image analysis tasks on both synthetic and real images, and comparison against other state-of-the-art image synthesis methods. REPLICA is computationally fast, and is shown to be comparable to other methods on tasks they are able to perform. Additionally REPLICA has the capability to synthesize both T 2 -weighted images of the full head and FLAIR images, and perform intensity standardization between different imaging datasets. Copyright © 2016 Elsevier B.V. All rights reserved.

A rational repeating template method for synthesis of 2D hexagonally ordered mesoporous precious metals.

PubMed

Takai, Azusa; Doi, Yoji; Yamauchi, Yusuke; Kuroda, Kazuyuki

2011-03-01

A repeating template method is presented for the synthesis of mesoporous metals with 2D hexagonal mesostructures. First, a silica replica (i.e., silica nanorods arranged periodically) is prepared by using 2D hexagonally ordered mesoporous carbon as the template. After that, the obtained silica replica is used as the second template for the preparation of mesoporous ruthenium. After the ruthenium species are introduced into the silica replica, the ruthenium species are then reduced by a vapor-infiltration method by using the reducing agent dimethylamine borane. After the ruthenium deposition, the silica is chemically removed. Analysis by transmission and scanning electron microscopies, a nitrogen-adsorption-desorption isotherm, and small-angle X-ray scattering revealed that the mesoporous ruthenium had a 2D hexagonal mesostructure, although the mesostructural ordering is decreased compared to that of the original mesoporous carbon template. This method is widely applicable to other metal systems. By changing the metal species introduced into the silica replica, several mesoporous metals (palladium and platinum) can be synthesized. Ordered mesoporous ruthenium and palladium, which are not easily attainable by the soft-templating methods, can be prepared. This study has overcome the composition variation limitations of the soft-templating method. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Titanium Damage Tolerant Design Data for Propulsion Systems

DTIC Science & Technology

1977-08-01

for the threshold and 30 Hz tests were measured using cellulose acetate tape replicas with an accuracy of 0.001 in. (0.0025 mm) for changes in crack...monitored with the traveling telescope and verified with cellulose acetate tape replicas. Testing was performed in load control on servo-hydraulic...34 Contract F33615-75-C-5064, First Semiannual Report, AFML, December 1975. 2. Erdogan F. and M. Ratwani, "Fatigue and Fracture of Cylindrical Shells

Multicast Parametric Synchronous Sampling

DTIC Science & Technology

2011-09-01

enhancement in a parametric mixer device. Fig. 4 shows the principle of generating uniform, high quality replicas extending over previously un-attainable...critical part of the MPASS architecture and is responsible for the direct and continuous acquisition of data across all of the multicast signal copies...ii) ability to copy THz signals with impunity to tens of replicas ; (iii) all-optical delays > 1.9 us; (iv) 10’s of THz-fast all-optical sampling of

Broken Replica Symmetry Bounds in the Mean Field Spin Glass Model

NASA Astrophysics Data System (ADS)

Guerra, Francesco

By using a simple interpolation argument, in previous work we have proven the existence of the thermodynamic limit, for mean field disordered models, including the Sherrington-Kirkpatrick model, and the Derrida p-spin model. Here we extend this argument in order to compare the limiting free energy with the expression given by the Parisi Ansatz, and including full spontaneous replica symmetry breaking. Our main result is that the quenched average of the free energy is bounded from below by the value given in the Parisi Ansatz, uniformly in the size of the system. Moreover, the difference between the two expressions is given in the form of a sum rule, extending our previous work on the comparison between the true free energy and its replica symmetric Sherrington-Kirkpatrick approximation. We give also a variational bound for the infinite volume limit of the ground state energy per site.

Method for producing highly reflective metal surfaces

DOEpatents

Arnold, J.B.; Steger, P.J.; Wright, R.R.

1982-03-04

The invention is a novel method for producing mirror surfaces which are extremely smooth and which have high optical reflectivity. The method includes depositing, by electrolysis, an amorphous layer of nickel on an article and then diamond-machining the resulting nickel surface to increase its smoothness and reflectivity. The machined nickel surface then is passivated with respect to the formation of bonds with electrodeposited nickel. Nickel then is electrodeposited on the passivated surface to form a layer of electroplated nickel whose inside surface is a replica of the passivated surface. The mandrel then may be-re-passivated and provided with a layer of electrodeposited nickel, which is then recovered from the mandrel providing a second replica. The mandrel can be so re-used to provide many such replicas. As compared with producing each mirror-finished article by plating and diamond-machining, the new method is faster and less expensive.

Neutron and gamma dose and spectra measurements on the Little Boy replica

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

Hoots, S.; Wadsworth, D.

1984-06-01

The radiation-measurement team of the Weapons Engineering Division at Lawrence Livermore National Laboratory (LLNL) measured neutron and gamma dose and spectra on the Little Boy replica at Los Alamos National Laboratory (LANL) in April 1983. This assembly is a replica of the gun-type atomic bomb exploded over Hiroshima in 1945. These measurements support the National Academy of Sciences Program to reassess the radiation doses due to atomic bomb explosions in Japan. Specifically, the following types of information were important: neutron spectra as a function of geometry, gamma to neutron dose ratios out to 1.5 km, and neutron attenuation in themore » atmosphere. We measured neutron and gamma dose/fission from close-in to a kilometer out, and neutron and gamma spectra at 90 and 30/sup 0/ close-in. This paper describes these measurements and the results. 12 references, 13 figures, 5 tables.« less

Platinum replica electron microscopy: Imaging the cytoskeleton globally and locally.

PubMed

Svitkina, Tatyana M

2017-05-01

Structural studies reveal how smaller components of a system work together as a whole. However, combining high resolution of details with full coverage of the whole is challenging. In cell biology, light microscopy can image many cells in their entirety, but at a lower resolution, whereas electron microscopy affords very high resolution, but usually at the expense of the sample size and coverage. Structural analyses of the cytoskeleton are especially demanding, because cytoskeletal networks are unresolvable by light microscopy due to their density and intricacy, whereas their proper preservation is a challenge for electron microscopy. Platinum replica electron microscopy can uniquely bridge the gap between the "comfort zones" of light and electron microscopy by allowing high resolution imaging of the cytoskeleton throughout the entire cell and in many cells in the population. This review describes the principles and applications of platinum replica electron microscopy for studies of the cytoskeleton. Copyright © 2017 Elsevier Ltd. All rights reserved.

Platinum Replica Electron Microscopy: Imaging the Cytoskeleton Globally and Locally

PubMed Central

SVITKINA, Tatyana M.

2017-01-01

Structural studies reveal how smaller components of a system work together as a whole. However, combining high resolution of details with full coverage of the whole is challenging. In cell biology, light microscopy can image many cells in their entirety, but at a lower resolution, whereas electron microscopy affords very high resolution, but usually at the expense of the sample size and coverage. Structural analyses of the cytoskeleton are especially demanding, because cytoskeletal networks are unresolvable by light microscopy due to their density and intricacy, whereas their proper preservation is a challenge for electron microscopy. Platinum replica electron microscopy can uniquely bridge the gap between the “comfort zones” of light and electron microscopy by allowing high resolution imaging of the cytoskeleton throughout the entire cell and in many cells in the population. This review describes the principles and applications of platinum replica electron microscopy for studies of the cytoskeleton. PMID:28323208

Entanglement, replicas, and Thetas

NASA Astrophysics Data System (ADS)

Mukhi, Sunil; Murthy, Sameer; Wu, Jie-Qiang

2018-01-01

We compute the single-interval Rényi entropy (replica partition function) for free fermions in 1+1d at finite temperature and finite spatial size by two methods: (i) using the higher-genus partition function on the replica Riemann surface, and (ii) using twist operators on the torus. We compare the two answers for a restricted set of spin structures, leading to a non-trivial proposed equivalence between higher-genus Siegel Θ-functions and Jacobi θ-functions. We exhibit this proposal and provide substantial evidence for it. The resulting expressions can be elegantly written in terms of Jacobi forms. Thereafter we argue that the correct Rényi entropy for modular-invariant free-fermion theories, such as the Ising model and the Dirac CFT, is given by the higher-genus computation summed over all spin structures. The result satisfies the physical checks of modular covariance, the thermal entropy relation, and Bose-Fermi equivalence.

Kinetics from Replica Exchange Molecular Dynamics Simulations.

PubMed

Stelzl, Lukas S; Hummer, Gerhard

2017-08-08

Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

Method for producing highly reflective metal surfaces

DOEpatents

Arnold, Jones B.; Steger, Philip J.; Wright, Ralph R.

1983-01-01

The invention is a novel method for producing mirror surfaces which are extremely smooth and which have high optical reflectivity. The method includes electrolessly depositing an amorphous layer of nickel on an article and then diamond-machining the resulting nickel surface to increase its smoothness and reflectivity. The machined nickel surface then is passivated with respect to the formation of bonds with electrodeposited nickel. Nickel then is electrodeposited on the passivated surface to form a layer of electroplated nickel whose inside surface is a replica of the passivated surface. The electroplated nickel layer then is separated from the passivated surface. The mandrel then may be re-passivated and provided with a layer of electrodeposited nickel, which is then recovered from the mandrel providing a second replica. The mandrel can be so re-used to provide many such replicas. As compared with producing each mirror-finished article by plating and diamond-machining, the new method is faster and less expensive.

Histopathology of human superficial herpes simplex keratitis.

PubMed Central

Maudgal, P. C.; Missotten, L.

1978-01-01

In vivo corneal replicas were made in 20 cases of patients with superficial dendritic ulcers of the cornea. Histopathological study of the replicas and superficial epithelial cells showed that the dendrites are composed of rounded epithelial cells and variable sized syncytia containing bizarre shaped nuclei. Pseudopodia-like processes containing DNA and some RNA extend from the syncytia into the surrounding epithelial cells, which on coming into contact with these processes become rounded and liquefied to give rise to another syncytium. The epithelial cells adjacent to the dendrite and elongated and usually orientated parallel to the long axis of the lesion. Surrounding the terminal bulbs, they are disposed in an arcuate fashion. These cells show C-mitotic lesions, intranuclear and cytoplasmic inclusion bodies, and polykaryocyte formation. Microscopic examination of the corneal replicas shows the intranuclear lesions and rounding of cells up to about 2 mm away from the dendritic ulcers. These areas appear normal on clinical examination. Images PMID:629910

Probing exciton density of states through phonon-assisted emission in GaN epilayers: A and B exciton contributions

NASA Astrophysics Data System (ADS)

Cavigli, Lucia; Gabrieli, Riccardo; Gurioli, Massimo; Bogani, Franco; Feltin, Eric; Carlin, Jean-François; Butté, Raphaël; Grandjean, Nicolas; Vinattieri, Anna

2010-09-01

A detailed experimental investigation of the phonon-assisted emission in a high-quality c -plane GaN epilayer is presented up to 200 K. By performing photoluminescence and reflectivity measurements, we find important etaloning effects in the phonon-replica spectra, which have to be corrected before addressing the lineshape analysis. Direct experimental evidence for free exciton thermalization is found for the whole temperature range investigated. A close comparison with existing models for phonon replicas originating from a thermalized free exciton distribution shows that the simplified and commonly adopted description of the exciton-phonon interaction with a single excitonic band leads to a large discrepancy with experimental data. Only the consideration of the complex nature of the excitonic band in GaN, including A and B exciton contributions, allows accounting for the temperature dependence of the peak energy, intensity, and lineshape of the phonon replicas.

Measurements of π ^± differential yields from the surface of the T2K replica target for incoming 31 GeV/ c protons with the NA61/SHINE spectrometer at the CERN SPS

NASA Astrophysics Data System (ADS)

Abgrall, N.; Aduszkiewicz, A.; Ajaz, M.; Ali, Y.; Andronov, E.; Antićić, T.; Antoniou, N.; Baatar, B.; Bay, F.; Blondel, A.; Blümer, J.; Bogomilov, M.; Brandin, A.; Bravar, A.; Brzychczyk, J.; Bunyatov, S. A.; Busygina, O.; Christakoglou, P.; Ćirković, M.; Czopowicz, T.; Davis, N.; Debieux, S.; Dembinski, H.; Deveaux, M.; Diakonos, F.; Di Luise, S.; Dominik, W.; Dumarchez, J.; Dynowski, K.; Engel, R.; Ereditato, A.; Feofilov, G. A.; Fodor, Z.; Garibov, A.; Gaździcki, M.; Golubeva, M.; Grebieszkow, K.; Grzeszczuk, A.; Guber, F.; Haesler, A.; Hasegawa, T.; Hervé, A. E.; Hierholzer, M.; Igolkin, S.; Ivashkin, A.; Johnson, S. R.; Kadija, K.; Kapoyannis, A.; Kaptur, E.; Kisiel, J.; Kobayashi, T.; Kolesnikov, V. I.; Kolev, D.; Kondratiev, V. P.; Korzenev, A.; Kowalik, K.; Kowalski, S.; Koziel, M.; Krasnoperov, A.; Kuich, M.; Kurepin, A.; Larsen, D.; László, A.; Lewicki, M.; Lyubushkin, V. V.; Maćkowiak-Pawłowska, M.; Maksiak, B.; Malakhov, A. I.; Manić, D.; Marcinek, A.; Marino, A. D.; Marton, K.; Mathes, H.-J.; Matulewicz, T.; Matveev, V.; Melkumov, G. L.; Messerly, B.; Mills, G. B.; Morozov, S.; Mrówczyński, S.; Nagai, Y.; Nakadaira, T.; Naskręt, M.; Nirkko, M.; Nishikawa, K.; Panagiotou, A. D.; Paolone, V.; Pavin, M.; Petukhov, O.; Pistillo, C.; Płaneta, R.; Popov, B. A.; Posiadała-Zezula, M.; Puławski, S.; Puzović, J.; Rauch, W.; Ravonel, M.; Redij, A.; Renfordt, R.; Richter-Wąs, E.; Robert, A.; Röhrich, D.; Rondio, E.; Roth, M.; Rubbia, A.; Rumberger, B. T.; Rustamov, A.; Rybczynski, M.; Sadovsky, A.; Sakashita, K.; Sarnecki, R.; Schmidt, K.; Sekiguchi, T.; Selyuzhenkov, I.; Seryakov, A.; Seyboth, P.; Sgalaberna, D.; Shibata, M.; Słodkowski, M.; Staszel, P.; Stefanek, G.; Stepaniak, J.; Ströbele, H.; Šuša, T.; Szuba, M.; Tada, M.; Taranenko, A.; Tefelska, A.; Tefelski, D.; Tereshchenko, V.; Tsenov, R.; Turko, L.; Ulrich, R.; Unger, M.; Vassiliou, M.; Veberič, D.; Vechernin, V. V.; Vesztergombi, G.; Vinogradov, L.; Wilczek, A.; Włodarczyk, Z.; Wojtaszek-Szwarc, A.; Wyszyński, O.; Yarritu, K.; Zambelli, L.; Zimmerman, E. D.; Friend, M.; Galymov, V.; Hartz, M.; Hiraki, T.; Ichikawa, A.; Kubo, H.; Matsuoka, K.; Murakami, A.; Nakaya, T.; Suzuki, K.; Tzanov, M.; Yu, M.

2016-11-01

Measurements of particle emission from a replica of the T2K 90 cm-long carbon target were performed in the NA61/SHINE experiment at CERN SPS, using data collected during a high-statistics run in 2009. An efficient use of the long-target measurements for neutrino flux predictions in T2K requires dedicated reconstruction and analysis techniques. Fully-corrected differential yields of π ^± -mesons from the surface of the T2K replica target for incoming 31 GeV/ c protons are presented. A possible strategy to implement these results into the T2K neutrino beam predictions is discussed and the propagation of the uncertainties of these results to the final neutrino flux is performed.

Survey of Cyber Moving Target Techniques

DTIC Science & Technology

2013-09-25

Description: Details: The authors propose a very simple form of multivariant execution with two replicas where one replica runs with the stack growing ...upwards and the other runs with the stack growing down. Normally any single architecture only supports the stack growing in one direction, but the...April 2012. 8. “The NX Bit and ASLR,” Tom’s Hardware, 25 March 2009. 9. “Pwn2Own day 2: iPhone, BlackBerry beaten; Chrome, Firefox no-shows,” Ars

Lunar Tire Close-up

NASA Image and Video Library

2017-02-23

This is a close-up of an exact replica of the Apollo-era Lunar Roving Vehicle Wheel, of which twelve originals still rest on the surface of the Moon. The tire was designed to flex under load, without air, and was formed from a mesh of plated piano wire. Metal straps were hand riveted onto the mesh to reduce sinking into loose lunar soils. These replica wheels were tested in NASA Glenn's SLOPE Lab to establish a baseline for future improvements.

KENNEDY SPACE CENTER, FLA. - The Rocket Garden at the KSC Visitor Complex features eight authentic rockets from the past, including a Mercury-Atlas rocket. The garden also features a climb-in Mercury, Gemino and Apollo capsule replicas, seating pods and informative graphic elements.

NASA Image and Video Library

2003-07-22

KENNEDY SPACE CENTER, FLA. - The Rocket Garden at the KSC Visitor Complex features eight authentic rockets from the past, including a Mercury-Atlas rocket. The garden also features a climb-in Mercury, Gemino and Apollo capsule replicas, seating pods and informative graphic elements.

Faster protein folding using enhanced conformational sampling of molecular dynamics simulation.

PubMed

Kamberaj, Hiqmet

2018-05-01

In this study, we applied swarm particle-like molecular dynamics (SPMD) approach to enhance conformational sampling of replica exchange simulations. In particular, the approach showed significant improvement in sampling efficiency of conformational phase space when combined with replica exchange method (REM) in computer simulation of peptide/protein folding. First we introduce the augmented dynamical system of equations, and demonstrate the stability of the algorithm. Then, we illustrate the approach by using different fully atomistic and coarse-grained model systems, comparing them with the standard replica exchange method. In addition, we applied SPMD simulation to calculate the time correlation functions of the transitions in a two dimensional surface to demonstrate the enhancement of transition path sampling. Our results showed that folded structure can be obtained in a shorter simulation time using the new method when compared with non-augmented dynamical system. Typically, in less than 0.5 ns using replica exchange runs assuming that native folded structure is known and within simulation time scale of 40 ns in the case of blind structure prediction. Furthermore, the root mean square deviations from the reference structures were less than 2Å. To demonstrate the performance of new method, we also implemented three simulation protocols using CHARMM software. Comparisons are also performed with standard targeted molecular dynamics simulation method. Copyright © 2018 Elsevier Inc. All rights reserved.

3D printed replicas for endodontic education.

PubMed

Reymus, M; Fotiadou, C; Kessler, A; Heck, K; Hickel, R; Diegritz, C

2018-06-14

To assess the feasibility of producing artificial teeth for endodontic training using 3D printing technology, to analyse the accuracy of the printing process, and to evaluate the teeth by students when used during training. Sound extracted human teeth were selected, digitalized by cone beam computed tomography (CBCT) and appropriate software and finally reproduced by a stereolithographic printer. The printed teeth were scanned and compared with the original ones (trueness) and to one another (precision). Undergraduate dental students in the third and fourth years performed root canal treatment on printed molars and were subsequently asked to evaluate their experience with these compared to real teeth. The workflow was feasible for manufacturing 3D printed tooth replicas. The absolute deviation after printing (trueness) ranged from 50.9μm to 104.3μm. The values for precision ranged from 43.5μm to 68.2μm. Students reported great benefits in the use of the replicated teeth for training purposes. The presented workflow is feasible for any dental educational institution who has access to a CBCT unit and a stereolithographic printer. The accuracy of the printing process is suitable for the production of tooth replicas for endodontic training. Undergraduate students favoured the availability of these replicas and the fairness they ensured in training due to standardization. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

A polymeric master replication technology for mass fabrication of poly(dimethylsiloxane) microfluidic devices.

PubMed

Li, Hai-Fang; Lin, Jin-Ming; Su, Rong-Guo; Cai, Zong Wei; Uchiyama, Katsumi

2005-05-01

A protocol of producing multiple polymeric masters from an original glass master mold has been developed, which enables the production of multiple poly(dimethylsiloxane) (PDMS)-based microfluidic devices in a low-cost and efficient manner. Standard wet-etching techniques were used to fabricate an original glass master with negative features, from which more than 50 polymethylmethacrylate (PMMA) positive replica masters were rapidly created using the thermal printing technique. The time to replicate each PMMA master was as short as 20 min. The PMMA replica masters have excellent structural features and could be used to cast PDMS devices for many times. An integration geometry designed for laser-induced fluorescence (LIF) detection, which contains normal deep microfluidic channels and a much deeper optical fiber channel, was successfully transferred into PDMS devices. The positive relief on seven PMMA replica masters is replicated with regard to the negative original glass master, with a depth average variation of 0.89% for 26-microm deep microfluidic channels and 1.16% for the 90 mum deep fiber channel. The imprinted positive relief in PMMA from master-to-master is reproducible with relative standard deviations (RSDs) of 1.06% for the maximum width and 0.46% for depth in terms of the separation channel. The PDMS devices fabricated from the PMMA replica masters were characterized and applied to the separation of a fluorescein isothiocyanate (FITC)-labeled epinephrine sample.

Verification of a computer-aided replica technique for evaluating prosthesis adaptation using statistical agreement analysis.

PubMed

Mai, Hang-Nga; Lee, Kyeong Eun; Lee, Kyu-Bok; Jeong, Seung-Mi; Lee, Seok-Jae; Lee, Cheong-Hee; An, Seo-Young; Lee, Du-Hyeong

2017-10-01

The purpose of this study was to evaluate the reliability of computer-aided replica technique (CART) by calculating its agreement with the replica technique (RT), using statistical agreement analysis. A prepared metal die and a metal crown were fabricated. The gap between the restoration and abutment was replicated using silicone indicator paste (n = 25). Gap measurements differed in the control (RT) and experimental (CART) groups. In the RT group, the silicone replica was manually sectioned, and the marginal and occlusal gaps were measured using a microscope. In the CART group, the gap was digitized using optical scanning and image superimposition, and the gaps were measured using a software program. The agreement between the measurement techniques was evaluated by using the 95% Bland-Altman limits of agreement and concordance correlation coefficients (CCC). The least acceptable CCC was 0.90. The RT and CART groups showed linear association, with a strong positive correlation in gap measurements, but without significant differences. The 95% limits of agreement between the paired gap measurements were 3.84% and 7.08% of the mean. The lower 95% confidence limits of CCC were 0.9676 and 0.9188 for the marginal and occlusal gap measurements, respectively, and the values were greater than the allowed limit. The CART is a reliable digital approach for evaluating the fit accuracy of fixed dental prostheses.

Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method.

PubMed

Lu, Qing; Kim, Jaegil; Straub, John E

2013-03-14

The generalized Replica Exchange Method (gREM) is extended into the isobaric-isothermal ensemble, and applied to simulate a vapor-liquid phase transition in Lennard-Jones fluids. Merging an optimally designed generalized ensemble sampling with replica exchange, gREM is particularly well suited for the effective simulation of first-order phase transitions characterized by "backbending" in the statistical temperature. While the metastable and unstable states in the vicinity of the first-order phase transition are masked by the enthalpy gap in temperature replica exchange method simulations, they are transformed into stable states through the parameterized effective sampling weights in gREM simulations, and join vapor and liquid phases with a succession of unimodal enthalpy distributions. The enhanced sampling across metastable and unstable states is achieved without the need to identify a "good" order parameter for biased sampling. We performed gREM simulations at various pressures below and near the critical pressure to examine the change in behavior of the vapor-liquid phase transition at different pressures. We observed a crossover from the first-order phase transition at low pressure, characterized by the backbending in the statistical temperature and the "kink" in the Gibbs free energy, to a continuous second-order phase transition near the critical pressure. The controlling mechanisms of nucleation and continuous phase transition are evident and the coexistence properties and phase diagram are found in agreement with literature results.

Classical mutual information in mean-field spin glass models

NASA Astrophysics Data System (ADS)

Alba, Vincenzo; Inglis, Stephen; Pollet, Lode

2016-03-01

We investigate the classical Rényi entropy Sn and the associated mutual information In in the Sherrington-Kirkpatrick (S-K) model, which is the paradigm model of mean-field spin glasses. Using classical Monte Carlo simulations and analytical tools we investigate the S-K model in the n -sheet booklet. This is achieved by gluing together n independent copies of the model, and it is the main ingredient for constructing the Rényi entanglement-related quantities. We find a glassy phase at low temperatures, whereas at high temperatures the model exhibits paramagnetic behavior, consistent with the regular S-K model. The temperature of the paramagnetic-glassy transition depends nontrivially on the geometry of the booklet. At high temperatures we provide the exact solution of the model by exploiting the replica symmetry. This is the permutation symmetry among the fictitious replicas that are used to perform disorder averages (via the replica trick). In the glassy phase the replica symmetry has to be broken. Using a generalization of the Parisi solution, we provide analytical results for Sn and In and for standard thermodynamic quantities. Both Sn and In exhibit a volume law in the whole phase diagram. We characterize the behavior of the corresponding densities, Sn/N and In/N , in the thermodynamic limit. Interestingly, at the critical point the mutual information does not exhibit any crossing for different system sizes, in contrast with local spin models.

Replicas of Snoopy and Charlie Brown decorate top of console in MCC

NASA Technical Reports Server (NTRS)

1969-01-01

Replicas of Snoopy and Charlie Brown, the two characters from Charles Schulz's syndicated comic strip 'Peanuts', decorate the top of a console in the Mission Operations Control Room in the Mission Control Center, bldg 30, on the first day of the Apollo 10 lunar orbit mission. During the Apollo 10 lunar orbit operations the Lunar Module will be called Snoopy when it is separated from the Command/Service Modules. The code words for the Command Module will be Charlie Brown.

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

Kato, Go

We consider the situation where s replicas of a qubit with an unknown state and its orthogonal k replicas are given as an input, and we try to make c clones of the qubit with the unknown state. As a function of s, k, and c, we obtain the optimal fidelity between the qubit with an unknown state and the clone by explicitly giving a completely positive trace-preserving (CPTP) map that represents a cloning machine. We discuss dependency of the fidelity on the values of the parameters s, k, and c.

Manual of Military Decorations and Awards: DoD Service Awards - Campaign, Expeditionary, and Service Medals. Volume 2

DTIC Science & Technology

2010-11-23

Disaster Relief? Consider Creation of Campaign Medal National Security Threat? Advocate for Activation of National Defense Service Medal Consider...2) Arrowhead Device: The arrowhead device is a bronze replica of an Indian arrowhead 1/4 inch high. It is a Department of the Army device that...device is a bronze replica of an Indian arrowhead 1/4 inch high. It is a Department of the Army device that is authorized for wear on the AFEM. (3

Neutron dosimetry of the Little Boy device

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

Pederson, R.A.; Plassmann, E.A.

1984-01-01

Neutron dose rates at several angular locations and at distances out to 0.5 mile have been measured during critical operation of the Little Boy replica. We used modified remmetes and thermoluminescent dosimetry techniques for the measurements. The present status of our analysis is presented including estimates of the neutron-dose-relaxation length in air and the variation of the neutron-to-gamma-ray dose ratio with distance from the replica. These results are preliminary and are subject to detector calibration measurements.

Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein.

PubMed

Lazim, Raudah; Mei, Ye; Zhang, Dawei

2012-03-01

Replica exchange molecular dynamics (REMD) simulation provides an efficient conformational sampling tool for the study of protein folding. In this study, we explore the mechanism directing the structure variation from α/4β-fold protein to 3α-fold protein after mutation by conducting REMD simulation on 42 replicas with temperatures ranging from 270 K to 710 K. The simulation began from a protein possessing the primary structure of GA88 but the tertiary structure of GB88, two G proteins with "high sequence identity." Albeit the large Cα-root mean square deviation (RMSD) of the folded protein (4.34 Å at 270 K and 4.75 Å at 304 K), a variation in tertiary structure was observed. Together with the analysis of secondary structure assignment, cluster analysis and principal component, it provides insights to the folding and unfolding pathway of 3α-fold protein and α/4β-fold protein respectively paving the way toward the understanding of the ongoings during conformational variation.

The effects of the one-step replica symmetry breaking on the Sherrington-Kirkpatrick spin glass model in the presence of random field with a joint Gaussian probability density function for the exchange interactions and random fields

NASA Astrophysics Data System (ADS)

Hadjiagapiou, Ioannis A.; Velonakis, Ioannis N.

2018-07-01

The Sherrington-Kirkpatrick Ising spin glass model, in the presence of a random magnetic field, is investigated within the framework of the one-step replica symmetry breaking. The two random variables (exchange integral interaction Jij and random magnetic field hi) are drawn from a joint Gaussian probability density function characterized by a correlation coefficient ρ, assuming positive and negative values. The thermodynamic properties, the three different phase diagrams and system's parameters are computed with respect to the natural parameters of the joint Gaussian probability density function at non-zero and zero temperatures. The low temperature negative entropy controversy, a result of the replica symmetry approach, has been partly remedied in the current study, leading to a less negative result. In addition, the present system possesses two successive spin glass phase transitions with characteristic temperatures.

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.

PubMed

Karczyńska, Agnieszka S; Czaplewski, Cezary; Krupa, Paweł; Mozolewska, Magdalena A; Joo, Keehyoung; Lee, Jooyoung; Liwo, Adam

2017-12-05

Molecular simulations restrained to single or multiple templates are commonly used in protein-structure modeling. However, the restraints introduce additional barriers, thus impairing the ergodicity of simulations, which can affect the quality of the resulting models. In this work, the effect of restraint types and simulation schemes on ergodicity and model quality was investigated by performing template-restrained canonical molecular dynamics (MD), multiplexed replica-exchange molecular dynamics, and Hamiltonian replica exchange molecular dynamics (HREMD) simulations with the coarse-grained UNRES force field on nine selected proteins, with pseudo-harmonic log-Gaussian (unbounded) or Lorentzian (bounded) restraint functions. The best ergodicity was exhibited by HREMD. It has been found that non-ergodicity does not affect model quality if good templates are used to generate restraints. However, when poor-quality restraints not covering the entire protein are used, the improved ergodicity of HREMD can lead to significantly improved protein models. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Controlled replication of butterfly wings for achieving tunable photonic properties.

PubMed

Huang, Jingyun; Wang, Xudong; Wang, Zhong Lin

2006-10-01

The fine structure of the wing scale of a Morpho Peleides butterfly was examined carefully, and the entire configuration was completely replicated by a uniform Al(2)O(3) coating through a low-temperature ALD process. An inverted structure was achieved by removing the butterfly wing template at high temperature, forming a polycrystalline Al(2)O(3) shell structure with precisely controlled thickness. Other than the copy of the morphology of the structure, the optical property, such as the existence of PBG, was also inherited by the alumina replica. Reflection peaks at the violet/blue range were detected on both original wings and their replica, while a simple alumina coating shifted the reflection peak to longer wavelength because of the change of periodicity and refraction index. The alumina replicas also exhibited similar functional structures as waveguide and beam splitter, which may be used as the building blocks for photonic ICs with high reproducibility and lower fabrication cost compared to traditional lithography techniques.

Synthetic fossilization of soft biological tissues and their shape-preserving transformation into silica or electron-conductive replicas

DOE PAGES

Townson, Jason L.; Lin, Yu-Shen; Chou, Stanley S.; ...

2014-12-08

Structural preservation of complex biological systems from the subcellular to whole organism level in robust forms, enabling dissection and imaging while preserving 3D context, represents an enduring grand challenge in biology. Here we report a simple immersion method for structurally preserving intact organisms via conformal stabilization within silica. This self-limiting process, which we refer to as silica bioreplication, occurs by condensation of water-soluble silicic acid proximally to biomolecular interfaces throughout the organism. Conformal nanoscopic silicification of all biomolecular features imparts structural rigidity enabling the preservation of shape and nano-to-macroscale dimensional features upon drying to form a biocomposite and further highmore » temperature oxidative calcination to form silica replicas or reductive pyrolysis to form electrically conductive carbon replicas of complete organisms. Ultimately, the simplicity and generalizability of this approach should facilitate efforts in biological preservation and analysis and could enable the development of new classes of biomimetic composite materials.« less

Speculation and replication in temperature accelerated dynamics

DOE PAGES

Zamora, Richard J.; Perez, Danny; Voter, Arthur F.

2018-02-12

Accelerated Molecular Dynamics (AMD) is a class of MD-based algorithms for the long-time scale simulation of atomistic systems that are characterized by rare-event transitions. Temperature-Accelerated Dynamics (TAD), a traditional AMD approach, hastens state-to-state transitions by performing MD at an elevated temperature. Recently, Speculatively-Parallel TAD (SpecTAD) was introduced, allowing the TAD procedure to exploit parallel computing systems by concurrently executing in a dynamically generated list of speculative future states. Although speculation can be very powerful, it is not always the most efficient use of parallel resources. In this paper, we compare the performance of speculative parallelism with a replica-based technique, similarmore » to the Parallel Replica Dynamics method. A hybrid SpecTAD approach is also presented, in which each speculation process is further accelerated by a local set of replicas. Finally and overall, this work motivates the use of hybrid parallelism whenever possible, as some combination of speculation and replication is typically most efficient.« less

Computational aspects of the smectization process in liquid crystals: An example study of a perfectly aligned two-dimensional hard-boomerang system

NASA Astrophysics Data System (ADS)

Chrzanowska, Agnieszka

2017-06-01

A replica method for calculation of smectic liquid crystal properties within the Onsager theory has been presented and applied to an exemplary case of two-dimensional perfectly aligned needlelike boomerangs. The method allows one to consider the complete influence of the interaction terms in contrast to the Fourier expansion method which uses mostly first or second order terms of expansion. The program based on the replica algorithm is able to calculate a single representative layer as an equivalent set of layers, depending on the size of the considered width of the sample integration interval. It predicts successfully smectic density distributions, energies, and layer thicknesses for different types of layer arrangement—of the antiferroelectric or of the smectic A order type. Specific features of the algorithm performance and influence of the numerical accuracy on the physical properties are presented. Future applications of the replica method to freely rotating molecules are discussed.

Computational aspects of the smectization process in liquid crystals: An example study of a perfectly aligned two-dimensional hard-boomerang system.

PubMed

Chrzanowska, Agnieszka

2017-06-01

A replica method for calculation of smectic liquid crystal properties within the Onsager theory has been presented and applied to an exemplary case of two-dimensional perfectly aligned needlelike boomerangs. The method allows one to consider the complete influence of the interaction terms in contrast to the Fourier expansion method which uses mostly first or second order terms of expansion. The program based on the replica algorithm is able to calculate a single representative layer as an equivalent set of layers, depending on the size of the considered width of the sample integration interval. It predicts successfully smectic density distributions, energies, and layer thicknesses for different types of layer arrangement-of the antiferroelectric or of the smectic A order type. Specific features of the algorithm performance and influence of the numerical accuracy on the physical properties are presented. Future applications of the replica method to freely rotating molecules are discussed.

Characteristics and self-cleaning effect of the transparent super-hydrophobic film having nanofibers array structures

NASA Astrophysics Data System (ADS)

Lee, Kyungjun; Lyu, Sungnam; Lee, Sangmin; Kim, Youn Sang; Hwang, Woonbong

2010-09-01

Transparent super-hydrophobic films were fabricated using the PDMS method and silane process, based on anodization in phosphoric acid. Contact angle tests were performed to determine the contact angle of each film according to the anodizing time. Transmittance tests also were performed to obtain the transparency of each TPT (trimethylolpropane propoxylate triacrylate) replica film according to the anodizing time. The contact angle was determined by studying the drop shape, and the transmittance was measured using a UV-spectrometer. The contact angle increases with increasing anodizing time, because increasing pillar length can trap more air between the TPT replica film and a drop of water. The transmittance falls with increasing anodizing time because the increasing pillar length causes a scattering effect. This study shows that the pillar length and transparency are inversely proportional. The TPT replica film having nanofibers array structures was better than other films in aspect of self-cleaning by doing quantitative experimentation.

Charting the Replica Symmetric Phase

NASA Astrophysics Data System (ADS)

Coja-Oghlan, Amin; Efthymiou, Charilaos; Jaafari, Nor; Kang, Mihyun; Kapetanopoulos, Tobias

2018-02-01

Diluted mean-field models are spin systems whose geometry of interactions is induced by a sparse random graph or hypergraph. Such models play an eminent role in the statistical mechanics of disordered systems as well as in combinatorics and computer science. In a path-breaking paper based on the non-rigorous `cavity method', physicists predicted not only the existence of a replica symmetry breaking phase transition in such models but also sketched a detailed picture of the evolution of the Gibbs measure within the replica symmetric phase and its impact on important problems in combinatorics, computer science and physics (Krzakala et al. in Proc Natl Acad Sci 104:10318-10323, 2007). In this paper we rigorise this picture completely for a broad class of models, encompassing the Potts antiferromagnet on the random graph, the k-XORSAT model and the diluted k-spin model for even k. We also prove a conjecture about the detection problem in the stochastic block model that has received considerable attention (Decelle et al. in Phys Rev E 84:066106, 2011).

Speculation and replication in temperature accelerated dynamics

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

Zamora, Richard J.; Perez, Danny; Voter, Arthur F.

Accelerated Molecular Dynamics (AMD) is a class of MD-based algorithms for the long-time scale simulation of atomistic systems that are characterized by rare-event transitions. Temperature-Accelerated Dynamics (TAD), a traditional AMD approach, hastens state-to-state transitions by performing MD at an elevated temperature. Recently, Speculatively-Parallel TAD (SpecTAD) was introduced, allowing the TAD procedure to exploit parallel computing systems by concurrently executing in a dynamically generated list of speculative future states. Although speculation can be very powerful, it is not always the most efficient use of parallel resources. In this paper, we compare the performance of speculative parallelism with a replica-based technique, similarmore » to the Parallel Replica Dynamics method. A hybrid SpecTAD approach is also presented, in which each speculation process is further accelerated by a local set of replicas. Finally and overall, this work motivates the use of hybrid parallelism whenever possible, as some combination of speculation and replication is typically most efficient.« less

Predicting folding-unfolding transitions in proteins without a priori knowledge of the folded state

NASA Astrophysics Data System (ADS)

Okan, Osman; Turgut, Deniz; Garcia, Angel; Ozisik, Rahmi

2013-03-01

The common computational method of studying folding transitions in proteins is to compare simulated conformations against the folded structure, but this method obviously requires the folded structure to be known beforehand. In the current study, we show that the use of bond orientational order parameter (BOOP) Ql [Steinhardt PJ, Nelson DR, Ronchetti M, Phys. Rev. B 1983, 28, 784] is a viable alternative to the commonly adopted root mean squared distance (RMSD) measure in probing conformational transitions. Replica exchange molecular dynamics simulations of the trp-cage protein (with 20 residues) in TIP-3P water were used to compare BOOP against RMSD. The results indicate that the correspondence between BOOP and RMSD time series become stronger with increasing l. We finally show that robust linear models that incorporate different Ql can be parameterized from a given replica run and can be used to study other replica trajectories. This work is partially supported by NSF DUE-1003574.

A distinct group of CpG islands shows differential DNA methylation between replicas of the same cell line in vitro

PubMed Central

2013-01-01

Background CpG dinucleotide-rich genomic DNA regions, known as CpG islands (CGIs), can be methylated at their cytosine residues as an epigenetic mark that is stably inherited during cell mitosis. Differentially methylated regions (DMRs) are genomic regions showing different degrees of DNA methylation in multiple samples. In this study, we focused our attention on CGIs showing different DNA methylation between two culture replicas of the same cell line. Results We used methylation data of 35 cell lines from the Encyclopedia of DNA Elements (ENCODE) consortium to identify CpG islands that were differentially methylated between replicas of the same cell line and denoted them Inter Replicas Differentially Methylated CpG islands (IRDM-CGIs). We identified a group of IRDM-CGIs that was consistently shared by different cell lines, and denoted it common IRDM-CGIs. X chromosome CGIs were overrepresented among common IRDM-CGIs. Autosomal IRDM-CGIs were preferentially located in gene bodies and intergenic regions had a lower G + C content, a smaller mean length, and a reduced CpG percentage. Functional analysis of the genes associated with autosomal IRDM-CGIs showed that many of them are involved in DNA binding and development. Conclusions Our results show that several specific functional and structural features characterize common IRDM-CGIs. They may represent a specific subset of CGIs that are more prone to being differentially methylated for their intrinsic characteristics. PMID:24106769

An Ingenious Super Light Trapping Surface Templated from Butterfly Wing Scales

NASA Astrophysics Data System (ADS)

Han, Zhiwu; Li, Bo; Mu, Zhengzhi; Yang, Meng; Niu, Shichao; Zhang, Junqiu; Ren, Luquan

2015-08-01

Based on the super light trapping property of butterfly Trogonoptera brookiana wings, the SiO2 replica of this bionic functional surface was successfully synthesized using a simple and highly effective synthesis method combining a sol-gel process and subsequent selective etching. Firstly, the reflectivity of butterfly wing scales was carefully examined. It was found that the whole reflectance spectroscopy of the butterfly wings showed a lower level (less than 10 %) in the visible spectrum. Thus, it was confirmed that the butterfly wings possessed a super light trapping effect. Afterwards, the morphologies and detailed architectures of the butterfly wing scales were carefully investigated using the ultra-depth three-dimensional (3D) microscope and field emission scanning electronic microscopy (FESEM). It was composed by the parallel ridges and quasi-honeycomb-like structure between them. Based on the biological properties and function above, an exact SiO2 negative replica was fabricated through a synthesis method combining a sol-gel process and subsequent selective etching. At last, the comparative analysis of morphology feature size and the reflectance spectroscopy between the SiO2 negative replica and the flat plate was conducted. It could be concluded that the SiO2 negative replica inherited not only the original super light trapping architectures, but also the super light trapping characteristics of bio-template. This work may open up an avenue for the design and fabrication of super light trapping materials and encourage people to look for more super light trapping architectures in nature.

Study of the injection molding of a polarizing beam splitter.

PubMed

Jose de Carvalho, Edson; Braga, Edmundo da Silva; Cescato, Lucila H

2006-01-01

We describe the replication of a relief grating that behaves like a polarizing beam splitter by injection molding. Measurements of the grating master, nickel shim, and replica, performed by atomic force microscopy, allow establishing a limit for the injection molding technique (currently used in CD fabrication) to aspect ratios of approximately 0.15. Although this limit strongly reduces the diffraction efficiency of the elements as well as their polarizing properties, extinction ratios of approximately 10:1 were measured for the replicas in a large range of wavelengths.

Fluid dynamic study in a femoral artery branch casting of man with upstream main lumen curvature for steady flow

NASA Technical Reports Server (NTRS)

Cho, Y. I.; Back, L. H.; Back, M. R.

1985-01-01

An in-vitro, steady flow investigation was conducted in a hollow, transparent vascular replica of the profunda femoris branch of man for a range of physiological flow conditions. The replica casting tested was obtained from a human cadaver and indicated some plague formation along the main lumen and branch. The flow visualization observations and measured pressure distributions indicated the highly three-dimensional flow characteristics with arterial curvature and branching, and the important role of centrifugal effects in fluid transport mechanisms.

Replicas of Snoopy and Charlie Brown decorate top of console in MCC

NASA Image and Video Library

1969-05-18

S69-34314 (18 May 1969) --- Replicas of Snoopy and Charlie Brown, the two characters from Charles Schulz's syndicated comic strip, "Peanuts," decorate the top of a console in the Mission Operations Control Room in the Mission Control Center, Building 30, on the first day of the Apollo 10 lunar orbit mission. During lunar orbit operations, the Lunar Module will be called ?Snoopy? when it is separated from the Command and Service Modules. The code words for the Command Module will be ?Charlie Brown?.

Isobaric molecular dynamics version of the generalized replica exchange method (gREM): Liquid–vapor equilibrium

DOE PAGES

Malolepsza, Edyta; Secor, Maxim; Keyes, Tom

2015-09-23

A prescription for sampling isobaric generalized ensembles with molecular dynamics is presented and applied to the generalized replica exchange method (gREM), which was designed for simulating first-order phase transitions. The properties of the isobaric gREM ensemble are discussed and a study is presented of the liquid-vapor equilibrium of the guest molecules given for gas hydrate formation with the mW water model. As a result, phase diagrams, critical parameters, and a law of corresponding states are obtained.

NASA STS-132 Air and Space Museum

NASA Image and Video Library

2010-07-26

STS-132 astronaut Piers Sellers, left, and Dr. John Mather are seen with a replica of Mather's Nobel Prize, Tuesday, July 27, 2010, at the Smithsonian National Air and Space Museum in Washington. Sellers returned the replica that is in the museum's collection and was flown aboard STS-132 Atlantis. The prize was won by Mather and University of California, Berkeley researcher George Smoot in 2006 for their work using the Cosmic Background Explorer Satellite to understand the big-bang theory of the universe. Photo Credit: (NASA/Paul E. Alers)

Wavefront reversal technique for self-referencing collimation testing

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

Hii, King Ung; Kwek, Kuan Hiang

2010-02-01

We present a wavefront reversal technique to produce a dual-field fringe pattern for self-referencing collimation testing in wedge-plate lateral-shear interferometry. The method requires only a suitably placed cubic beam splitter to produce two replicas of the fringe field formed by the wedge-plate lateral-shear interferometer. One of the replicas has a fringe pattern that is the reverse of the other. With these two fringe fields, the collimation testing has a built-in reference, and the detection sensitivity is twice that of a single-wedge-plate technique.

Progress in mask replication using jet and flash imprint lithography

NASA Astrophysics Data System (ADS)

Selinidis, Kosta S.; Brooks, Cynthia B.; Doyle, Gary F.; Brown, Laura; Jones, Chris; Imhof, Joseph; LaBrake, Dwayne L.; Resnick, Douglas J.; Sreenivasan, S. V.

2011-04-01

The Jet and Flash Imprint Lithography (J-FILTM) process uses drop dispensing of UV curable resists to assist high resolution patterning for subsequent dry etch pattern transfer. The technology is actively being used to develop solutions for memory markets including Flash memory and patterned media for hard disk drives. It is anticipated that the lifetime of a single template (for patterned media) or mask (for semiconductor) will be on the order of 104 - 105imprints. This suggests that tens of thousands of templates/masks will be required to satisfy the needs of a manufacturing environment. Electron-beam patterning is too slow to feasibly deliver these volumes, but instead can provide a high quality "master" mask which can be replicated many times with an imprint lithography tool. This strategy has the capability to produce the required supply of "working" templates/masks. In this paper, we review the development of the mask form factor, imprint replication tools and processes specifically for semiconductor applications. The requirements needed for semiconductors dictate the need for a well defined form factor for both master and replica masks which is also compatible with the existing mask infrastructure established for the 6025 semi standard, 6" x 6" x 0.25" photomasks. Complying with this standard provides the necessary tooling needed for mask fabrication processes, cleaning, metrology, and inspection. The replica form factor has additional features specific to imprinting such as a pre-patterned mesa. A PerfectaTM MR5000 mask replication tool has been developed specifically to pattern replica masks from an e-beam written master. The system specifications include a throughput of four replicas per hour with an added image placement component of 5nm, 3sigma and a critical dimension uniformity error of less than 1nm, 3sigma. A new process has been developed to fabricate replicas with high contrast alignment marks so that designs for imprint can fit within current device layouts and maximize the usable printed area on the wafer. Initial performance results of this marks are comparable to the baseline fused silica align marks.

Characterization of fracture aperture for groundwater flow and transport

NASA Astrophysics Data System (ADS)

Sawada, A.; Sato, H.; Tetsu, K.; Sakamoto, K.

2007-12-01

This paper presents experiments and numerical analyses of flow and transport carried out on natural fractures and transparent replica of fractures. The purpose of this study was to improve the understanding of the role of heterogeneous aperture patterns on channelization of groundwater flow and dispersion in solute transport. The research proceeded as follows: First, a precision plane grinder was applied perpendicular to the fracture plane to characterize the aperture distribution on a natural fracture with 1 mm of increment size. Although both time and labor were intensive, this approach provided a detailed, three dimensional picture of the pattern of fracture aperture. This information was analyzed to provide quantitative measures for the fracture aperture distribution, including JRC (Joint Roughness Coefficient) and fracture contact area ratio. These parameters were used to develop numerical models with corresponding synthetic aperture patterns. The transparent fracture replica and numerical models were then used to study how transport is affected by the aperture spatial pattern. In the transparent replica, transmitted light intensity measured by a CCD camera was used to image channeling and dispersion due to the fracture aperture spatial pattern. The CCD image data was analyzed to obtain the quantitative fracture aperture and tracer concentration data according to Lambert-Beer's law. The experimental results were analyzed using the numerical models. Comparison of the numerical models to the transparent replica provided information about the nature of channeling and dispersion due to aperture spatial patterns. These results support to develop a methodology for defining representative fracture aperture of a simplified parallel fracture model for flow and transport in heterogeneous fractures for contaminant transport analysis.

The effect of changes in surface wettability on two-phase saturated flow in horizontal replicas of single natural fractures.

PubMed

Bergslien, Elisa; Fountain, John

2006-12-15

By using translucent epoxy replicas of natural single fractures, it is possible to optically measure aperture distribution and directly observe NAPL flow. However, detailed characterization of epoxy reveals that it is not a sufficiently good analogue to natural rock for many two-phase flow studies. The surface properties of epoxy, which is hydrophobic, are quite unlike those of natural rock, which is generally assumed to be hydrophilic. Different surface wettabilities result in dramatically different two-phase flow behavior and residual distributions. In hydrophobic replicas, the NAPL flows in well-developed channels, displacing water and filling all of the pore space. In hydrophilic replicas, the invading NAPL is confined to the largest aperture pathways and flow frequently occurs in pulses, with no limited or no stable channel development, resulting in isolated blobs with limited accessible surface area. The pulsing and channel abandonment behaviors described are significantly different from the piston-flow frequently assumed in current modeling practice. In addition, NAPL never achieved total saturation in hydrophilic models, indicating that significantly more than a monolayer of water was bound to the model surface. Despite typically only 60-80% NAPL saturation, there was generally good agreement between theoretically calculated Young-Laplace aperture invasion boundaries and the observed minimum apertures invaded. The key to determining whether surface wettability is negligible, or not, lies in accurate characterization of the contaminant-geologic media system under study. As long as the triple-point contact angle of the system is low (<20 degrees), the assumption of perfect water wettability is not a bad one.

Effect of two in-office whitening agents on the enamel surface in vivo: a morphological and non-contact profilometric study.

PubMed

Cadenaro, Milena; Breschi, Lorenzo; Nucci, Cesare; Antoniolli, Francesca; Visintini, Erika; Prati, Carlo; Matis, Bruce A; Di Lenarda, Roberto

2008-01-01

This study evaluated the morphological effects produced in vivo by two in-office bleaching agents on enamel surface roughness using a noncontact profilometric analysis of epoxy replicas. The null hypothesis tested was that there would be no difference in the micromorphology of the enamel surface during or after bleaching with two different bleaching agents. Eighteen subjects were selected and randomly assigned to two treatment groups (n=9). The tooth whitening materials tested were 38% hydrogen peroxide (HP) (Opalescence Xtra Boost) and 35% carbamide peroxide (CP) (Rembrandt Quik Start). The bleaching agents were applied in accordance with manufacturer protocols. The treatments were repeated four times at one-week intervals. High precision impressions of the upper right incisor were taken at baseline as the control (CTRL) and after each bleaching treatment (T0: first application, T1: second application at one week, T2: third application at two weeks and T3: fourth application at three weeks). Epoxy resin replicas were poured from impressions, and the surface roughness was analyzed by means of a non-contact profilometer (Talysurf CLI 1000). Epoxy replicas were then observed using SEM. All data were statistically analyzed using ANOVA and differences were determined with a t-test. No significant differences in surface roughness were found on enamel replicas using either 38% hydrogen peroxide or 35% carbamide peroxide in vivo. This in vivo study supports the null hypothesis that two in-office bleaching agents, with either a high concentration of hydrogen or carbamide peroxide, do not alter enamel surface roughness, even after multiple applications.

Parallel replica dynamics with a heterogeneous distribution of barriers: Application to n-hexadecane pyrolysis

NASA Astrophysics Data System (ADS)

Kum, Oyeon; Dickson, Brad M.; Stuart, Steven J.; Uberuaga, Blas P.; Voter, Arthur F.

2004-11-01

Parallel replica dynamics simulation methods appropriate for the simulation of chemical reactions in molecular systems with many conformational degrees of freedom have been developed and applied to study the microsecond-scale pyrolysis of n-hexadecane in the temperature range of 2100-2500 K. The algorithm uses a transition detection scheme that is based on molecular topology, rather than energetic basins. This algorithm allows efficient parallelization of small systems even when using more processors than particles (in contrast to more traditional parallelization algorithms), and even when there are frequent conformational transitions (in contrast to previous implementations of the parallel replica algorithm). The parallel efficiency for pyrolysis initiation reactions was over 90% on 61 processors for this 50-atom system. The parallel replica dynamics technique results in reaction probabilities that are statistically indistinguishable from those obtained from direct molecular dynamics, under conditions where both are feasible, but allows simulations at temperatures as much as 1000 K lower than direct molecular dynamics simulations. The rate of initiation displayed Arrhenius behavior over the entire temperature range, with an activation energy and frequency factor of Ea=79.7 kcal/mol and log A/s-1=14.8, respectively, in reasonable agreement with experiment and empirical kinetic models. Several interesting unimolecular reaction mechanisms were observed in simulations of the chain propagation reactions above 2000 K, which are not included in most coarse-grained kinetic models. More studies are needed in order to determine whether these mechanisms are experimentally relevant, or specific to the potential energy surface used.

Acoustic sources of opportunity in the marine environment - Applied to source localization and ocean sensing

NASA Astrophysics Data System (ADS)

Verlinden, Christopher M.

Controlled acoustic sources have typically been used for imaging the ocean. These sources can either be used to locate objects or characterize the ocean environment. The processing involves signal extraction in the presence of ambient noise, with shipping being a major component of the latter. With the advent of the Automatic Identification System (AIS) which provides accurate locations of all large commercial vessels, these major noise sources can be converted from nuisance to beacons or sources of opportunity for the purpose of studying the ocean. The source localization method presented here is similar to traditional matched field processing, but differs in that libraries of data-derived measured replicas are used in place of modeled replicas. In order to account for differing source spectra between library and target vessels, cross-correlation functions are compared instead of comparing acoustic signals directly. The library of measured cross-correlation function replicas is extrapolated using waveguide invariant theory to fill gaps between ship tracks, fully populating the search grid with estimated replicas allowing for continuous tracking. In addition to source localization, two ocean sensing techniques are discussed in this dissertation. The feasibility of estimating ocean sound speed and temperature structure, using ship noise across a drifting volumetric array of hydrophones suspended beneath buoys, in a shallow water marine environment is investigated. Using the attenuation of acoustic energy along eigenray paths to invert for ocean properties such as temperature, salinity, and pH is also explored. In each of these cases, the theory is developed, tested using numerical simulations, and validated with data from acoustic field experiments.

Multiple Replica Repulsion Technique for Efficient Conformational Sampling of Biological Systems

PubMed Central

Malevanets, Anatoly; Wodak, Shoshana J.

2011-01-01

Here, we propose a technique for sampling complex molecular systems with many degrees of freedom. The technique, termed “multiple replica repulsion” (MRR), does not suffer from poor scaling with the number of degrees of freedom associated with common replica exchange procedures and does not require sampling at high temperatures. The algorithm involves creation of multiple copies (replicas) of the system, which interact with one another through a repulsive potential that can be applied to the system as a whole or to portions of it. The proposed scheme prevents oversampling of the most populated states and provides accurate descriptions of conformational perturbations typically associated with sampling ground-state energy wells. The performance of MRR is illustrated for three systems of increasing complexity. A two-dimensional toy potential surface is used to probe the sampling efficiency as a function of key parameters of the procedure. MRR simulations of the Met-enkephalin pentapeptide, and the 76-residue protein ubiquitin, performed in presence of explicit water molecules and totaling 32 ns each, investigate the ability of MRR to characterize the conformational landscape of the peptide, and the protein native basin, respectively. Results obtained for the enkephalin peptide reflect more closely the extensive conformational flexibility of this peptide than previously reported simulations. Those obtained for ubiquitin show that conformational ensembles sampled by MRR largely encompass structural fluctuations relevant to biological recognition, which occur on the microsecond timescale, or are observed in crystal structures of ubiquitin complexes with other proteins. MRR thus emerges as a very promising simple and versatile technique for modeling the structural plasticity of complex biological systems. PMID:21843487

Statistical mechanics of the vertex-cover problem

NASA Astrophysics Data System (ADS)

Hartmann, Alexander K.; Weigt, Martin

2003-10-01

We review recent progress in the study of the vertex-cover problem (VC). The VC belongs to the class of NP-complete graph theoretical problems, which plays a central role in theoretical computer science. On ensembles of random graphs, VC exhibits a coverable-uncoverable phase transition. Very close to this transition, depending on the solution algorithm, easy-hard transitions in the typical running time of the algorithms occur. We explain a statistical mechanics approach, which works by mapping the VC to a hard-core lattice gas, and then applying techniques such as the replica trick or the cavity approach. Using these methods, the phase diagram of the VC could be obtained exactly for connectivities c < e, where the VC is replica symmetric. Recently, this result could be confirmed using traditional mathematical techniques. For c > e, the solution of the VC exhibits full replica symmetry breaking. The statistical mechanics approach can also be used to study analytically the typical running time of simple complete and incomplete algorithms for the VC. Finally, we describe recent results for the VC when studied on other ensembles of finite- and infinite-dimensional graphs.

Solute transport along preferential flow paths in unsaturated fractures

USGS Publications Warehouse

Su, Grace W.; Geller, Jil T.; Pruess, Karsten; Hunt, James R.

2001-01-01

Laboratory experiments were conducted to study solute transport along preferential flow paths in unsaturated, inclined fractures. Qualitative aspects of solute transport were identified in a miscible dye tracer experiment conducted in a transparent replica of a natural granite fracture. Additional experiments were conducted to measure the breakthrough curves of a conservative tracer introduced into an established preferential flow path in two different fracture replicas and a rock‐replica combination. The influence of gravity was investigated by varying fracture inclination. The relationship between the travel times of the solute and the relative influence of gravity was substantially affected by two modes of intermittent flow that occurred: the snapping rivulet and the pulsating blob modes. The measured travel times of the solute were evaluated with three transfer function models: the axial dispersion, the reactors‐in‐series, and the lognormal models. The three models described the solute travel times nearly equally well. A mechanistic model was also formulated to describe transport when the pulsating blob mode occurred which assumed blobs of water containing solute mixed with residual pools of water along the flow path.

Ubiquitous strong electron–phonon coupling at the interface of FeSe/SrTiO3

PubMed Central

Zhang, Chaofan; Liu, Zhongkai; Chen, Zhuoyu; Xie, Yanwu; He, Ruihua; Tang, Shujie; He, Junfeng; Li, Wei; Jia, Tao; Rebec, Slavko N.; Ma, Eric Yue; Yan, Hao; Hashimoto, Makoto; Lu, Donghui; Mo, Sung-Kwan; Hikita, Yasuyuki; Moore, Robert G.; Hwang, Harold Y.; Lee, Dunghai; Shen, Zhixun

2017-01-01

The observation of replica bands in single-unit-cell FeSe on SrTiO3 (STO)(001) by angle-resolved photoemission spectroscopy (ARPES) has led to the conjecture that the coupling between FeSe electrons and the STO phonons are responsible for the enhancement of Tc over other FeSe-based superconductors. However the recent observation of a similar superconducting gap in single-unit-cell FeSe/STO(110) raised the question of whether a similar mechanism applies. Here we report the ARPES study of the electronic structure of FeSe/STO(110). Similar to the results in FeSe/STO(001), clear replica bands are observed. We also present a comparative study of STO(001) and STO(110) bare surfaces, and observe similar replica bands separated by approximately the same energy, indicating this coupling is a generic feature of the STO surfaces and interfaces. Our findings suggest that the large superconducting gaps observed in FeSe films grown on different STO surface terminations are likely enhanced by a common mechanism. PMID:28186084

Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent.

PubMed

Peter, Emanuel K; Shea, Joan-Emma; Pivkin, Igor V

2016-05-14

In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC). The new development significantly can reduce the amount of replicas and the computational cost needed to enhance sampling in protein simulations. We introduce 2 different methods which primarily differ in the exchange scheme between the parallel ensembles. We apply this approach on folding of 2 different β-stranded peptides: the C-terminal β-hairpin fragment of GB1 and TrpZip4. Additionally, we use the new simulation technique to study the folding of TrpCage, a small fast folding α-helical peptide. Subsequently, we apply the new methodology on conformation changes in signaling of the light-oxygen voltage (LOV) sensitive domain from Avena sativa (AsLOV2). Our results agree well with data reported in the literature. In simulations of dialanine, we compare the statistical sampling of the 2 techniques with conventional REMD and analyze their performance. The new techniques can reduce the computational cost of REMD significantly and can be used in enhanced sampling simulations of biomolecules.

Pathways through equilibrated states with coexisting phases for gas hydrate formation

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

Malolepsza, Edyta; Keyes, Tom

Under ambient conditions, water freezes to either hexagonal ice or a hexagonal/cubic composite ice. The presence of hydrophobic guest molecules introduces a competing pathway: gas hydrate formation, with the guests in clathrate cages. Here, the pathways of the phase transitions are sought as sequences of states with coexisting phases, using a generalized replica exchange algorithm designed to sample them in equilibrium, avoiding nonequilibrium processes. For a dilute solution of methane in water under 200 atm, initializing the simulation with the full set of replicas leads to methane trapped in hexagonal/cubic ice, while gradually adding replicas with decreasing enthalpy produces themore » initial steps of hydrate growth. Once a small amount of hydrate is formed, water rearranges to form empty cages, eventually transforming the remainder of the system to metastable β ice, a scaffolding for hydrates. It is suggested that configurations with empty cages are reaction intermediates in hydrate formation when more guest molecules are available. Furthermore, free energy profiles show that methane acts as a catalyst reducing the barrier for β ice versus hexagonal/cubic ice formation.« less

Pathways through equilibrated states with coexisting phases for gas hydrate formation

DOE PAGES

Malolepsza, Edyta; Keyes, Tom

2015-12-01

Under ambient conditions, water freezes to either hexagonal ice or a hexagonal/cubic composite ice. The presence of hydrophobic guest molecules introduces a competing pathway: gas hydrate formation, with the guests in clathrate cages. Here, the pathways of the phase transitions are sought as sequences of states with coexisting phases, using a generalized replica exchange algorithm designed to sample them in equilibrium, avoiding nonequilibrium processes. For a dilute solution of methane in water under 200 atm, initializing the simulation with the full set of replicas leads to methane trapped in hexagonal/cubic ice, while gradually adding replicas with decreasing enthalpy produces themore » initial steps of hydrate growth. Once a small amount of hydrate is formed, water rearranges to form empty cages, eventually transforming the remainder of the system to metastable β ice, a scaffolding for hydrates. It is suggested that configurations with empty cages are reaction intermediates in hydrate formation when more guest molecules are available. Furthermore, free energy profiles show that methane acts as a catalyst reducing the barrier for β ice versus hexagonal/cubic ice formation.« less

Ubiquitous strong electron–phonon coupling at the interface of FeSe/SrTiO 3

DOE PAGES

Zhang, Chaofan; Liu, Zhongkai; Chen, Zhuoyu; ...

2017-02-10

The observation of replica bands in single-unit-cell FeSe on SrTiO 3 (STO)(001) by angle-resolved photoemission spectroscopy (ARPES) has led to the conjecture that the coupling between FeSe electrons and the STO phonons are responsible for the enhancement of T c over other FeSe-based superconductors. However the recent observation of a similar superconducting gap in single-unit-cell FeSe/STO(110) raised the question of whether a similar mechanism applies. Here we report the ARPES study of the electronic structure of FeSe/STO(110). Similar to the results in FeSe/STO(001), clear replica bands are observed. We also present a comparative study of STO(001) and STO(110) bare surfaces,more » and observe similar replica bands separated by approximately the same energy, indicating this coupling is a generic feature of the STO surfaces and interfaces. Lastly, our findings suggest that the large superconducting gaps observed in FeSe films grown on different STO surface terminations are likely enhanced by a common mechanism.« less

A simple and effective approach towards biomimetic replication of photonic structures from butterfly wings.

PubMed

Zhu, Shenmin; Zhang, Di; Chen, Zhixin; Gu, Jiajun; Li, Wenfei; Jiang, Haibo; Zhou, Gang

2009-08-05

A general sonochemical process is reported for the replication of photonic structures from Morpho butterfly wings in several hours. By selecting appropriate precursors, we can achieve exact replications of photonic structures in a variety of transparent metal oxides, such as titania, tin oxide and silica. The exact replications at the micro- and nanoscales were characterized by a combination of FE-SEM, TEM, EDX and Raman measurements. The optical properties of the replicas were investigated by using reflectance spectroscopy, and it was found that the interesting chromaticity of the reflected light could be adjusted simply by tuning the replica materials. An ultrasensitive SnO(2)-based chemical sensor was prepared from the SnO(2) replica. The sensor has a sensitivity of 35.3-50 ppm ethanol at 300 degrees C, accompanied by a rapid response and recovery (around 8-15 s), owing to its large surface area and photonic structure. Thus, this process could be developed to produce photonic structural ceramics which could be used in many passive and active infrared devices, especially high performance optical components and sensors.

Materials Suitable for preparing Inorganic Nanocasts of butterflies and other insects

NASA Astrophysics Data System (ADS)

Silver, J.; Fern, G. R.; Ireland, T. G.

2015-06-01

Replication of 3D-structures, in particular those that have a periodic modulation of a dielectric material at optical wavelengths and below have proven very difficult to fabricate. The majority of such replication techniques are complex or use moisture sensitive precursors requiring the use of for example a glove box. Here we demonstrate how an air stable supersaturated europium-doped yttrium nitrate phosphor precursor solution has the ability to easily impregnate a structure or produce a cast yielding faithful replicas composed of Y2O:Eu3+ after a final short annealing step. New replicas of Lepidoptera (moth) wing scales using field emission scanning electron microscopy, structures down to 10 nm have been imaged. Moreover as these replicas are made of phosphors, their luminescence in some cases may be modulated by the internal periodic modulation built into their structures. In this work we will discuss more recent results on the use of the phosphors for making nanocasts of moth wing scales and show a range of beautiful pictures to show what the method can achieve.

Validation of the BUGJEFF311.BOLIB, BUGENDF70.BOLIB and BUGLE-B7 broad-group libraries on the PCA-Replica (H2O/Fe) neutron shielding benchmark experiment

NASA Astrophysics Data System (ADS)

Pescarini, Massimo; Orsi, Roberto; Frisoni, Manuela

2016-03-01

The PCA-Replica 12/13 (H2O/Fe) neutron shielding benchmark experiment was analysed using the TORT-3.2 3D SN code. PCA-Replica reproduces a PWR ex-core radial geometry with alternate layers of water and steel including a pressure vessel simulator. Three broad-group coupled neutron/photon working cross section libraries in FIDO-ANISN format with the same energy group structure (47 n + 20 γ) and based on different nuclear data were alternatively used: the ENEA BUGJEFF311.BOLIB (JEFF-3.1.1) and UGENDF70.BOLIB (ENDF/B-VII.0) libraries and the ORNL BUGLE-B7 (ENDF/B-VII.0) library. Dosimeter cross sections derived from the IAEA IRDF-2002 dosimetry file were employed. The calculated reaction rates for the Rh-103(n,n')Rh-103m, In-115(n,n')In-115m and S-32(n,p)P-32 threshold activation dosimeters and the calculated neutron spectra are compared with the corresponding experimental results.

Replica Approach for Minimal Investment Risk with Cost

NASA Astrophysics Data System (ADS)

Shinzato, Takashi

2018-06-01

In the present work, the optimal portfolio minimizing the investment risk with cost is discussed analytically, where an objective function is constructed in terms of two negative aspects of investment, the risk and cost. We note the mathematical similarity between the Hamiltonian in the mean-variance model and the Hamiltonians in the Hopfield model and the Sherrington-Kirkpatrick model, show that we can analyze this portfolio optimization problem by using replica analysis, and derive the minimal investment risk with cost and the investment concentration of the optimal portfolio. Furthermore, we validate our proposed method through numerical simulations.

Surface-initiated polymerization within mesoporous silica spheres for the modular design of charge-neutral polymer particles.

PubMed

Müllner, Markus; Cui, Jiwei; Noi, Ka Fung; Gunawan, Sylvia T; Caruso, Frank

2014-06-03

We report a templating approach for the preparation of functional polymer replica particles via surface-initiated polymerization in mesoporous silica templates. Subsequent removal of the template resulted in discrete polymer particles. Furthermore, redox-responsive replica particles could be engineered to disassemble in a reducing environment. Particles, made of poly(methacryloyloxyethyl phosphorylcholine) (PMPC) or poly[oligo(ethylene glycol) methyl ether methacrylate] (POEGMA), exhibited very low association to human cancer cells (below 5%), which renders the reported charge-neutral polymer particles a modular and versatile class of highly functional carriers with potential applications in drug delivery.

Rotating stall investigation of 0.72 hub-tip ratio single-stage compressor

NASA Technical Reports Server (NTRS)

Graham, Robert W; Prian, Vasily D

1954-01-01

The rotating stall characteristics of a 0.72 hub-tip ratio, single-stage compressor were investigated. The stage was a 14-inch-diameter replica of the fourth stage of an experimental multistage compressor. No similarity existed between the frequency and propagation rate of the stall patterns observed in the single-stage replica and those observed in the multistage compressor after the fourth stage. A fatigue failure of the rotor blades occurred during the testing which was attributed to a resonance between the stall frequency and the natural bending frequency of the blades.

Replica-exchange Wang Landau sampling: pushing the limits of Monte Carlo simulations in materials sciences

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

Perera, Meewanage Dilina N; Li, Ying Wai; Eisenbach, Markus

We describe the study of thermodynamics of materials using replica-exchange Wang Landau (REWL) sampling, a generic framework for massively parallel implementations of the Wang Landau Monte Carlo method. To evaluate the performance and scalability of the method, we investigate the magnetic phase transition in body-centered cubic (bcc) iron using the classical Heisenberg model parameterized with first principles calculations. We demonstrate that our framework leads to a significant speedup without compromising the accuracy and precision and facilitates the study of much larger systems than is possible with its serial counterpart.

Replica Analysis for Portfolio Optimization with Single-Factor Model

NASA Astrophysics Data System (ADS)

Shinzato, Takashi

2017-06-01

In this paper, we use replica analysis to investigate the influence of correlation among the return rates of assets on the solution of the portfolio optimization problem. We consider the behavior of an optimal solution for the case where the return rate is described with a single-factor model and compare the findings obtained from our proposed methods with correlated return rates with those obtained with independent return rates. We then analytically assess the increase in the investment risk when correlation is included. Furthermore, we also compare our approach with analytical procedures for minimizing the investment risk from operations research.

Non-invasive Florentine Renaissance Panel Painting Replica Structures Investigation by Using Terahertz Time-Domain Imaging (THz-TDI) Technique

NASA Astrophysics Data System (ADS)

Koch Dandolo, Corinna L.; Picollo, Marcello; Cucci, Costanza; Jepsen, Peter Uhd

2016-11-01

The potentials of the Terahertz Time-Domain Imaging (THz-TDI) technique for a non-invasive inspection of panel paintings have been considered in detail. The THz-TD data acquired on a replica of a panel painting made in imitation of Italian Renaissance panel paintings were processed in order to provide insights as to the limits and potentials of the technique in detecting different kinds of underdrawings and paint layers. Constituent layers, construction techniques, and anomalies were identified and localized by interpreting the extracted THz dielectric stratigraphy.

Polyurethane Foam-Filled Skull Replica of Craniosynostosis for Surgical Training.

PubMed

Jeong, Yeon Jin; Lee, Jun Yong

2016-05-01

Craniosynostosis has a relatively low incidence in the general population and its treatment requires cautious approaches. For these reasons, patients are usually referred to several specialists or a medical center. Therefore, most trainees and young surgeons do not have any chances to experience patients of craniosynostosis, but learn about it only from textbooks. And for a surgeon who tries to operate on a craniosynostosis patient, it is hard to make a proper preoperative plan.The authors suggest a polyurethane foam-filled skull replica of craniosynostosis for trainees that can also be used in planning a craniosynostosis operation.

Influence of various environmental parameters on sweat gland activity.

PubMed

McMullen, Roger L; Gillece, Tim; Lu, Guojin; Laura, Donna; Chen, Susan

2013-01-01

The choice of environmental conditions when conducting antiperspirant studies greatly affects the quantity of sweat output. Our initial goal in this work was to develop an in-house procedure to test the efficacy of antiperspirant products using replica techniques in combination with image analysis. To ameliorate the skin replica method, we conducted rheological studies using dynamic mechanical analysis of the replica formulation. In terms of sweat output quantification, our preliminary results revealed a considerable amount of variation using the replica technique, leading us to conduct more fundamental studies of the factors that influence sweating behavior and how to best design the experimental strategy. In accordance with the FDA's protocol for antiperspirant testing, we carried out gravimetric analyses of axillae sweating under a variety of environmental conditions including temperature and humidity control. Subjects were first acclimatized in an environmentally controlled room for 30 min, and then placed in a sauna for an additional 30 or 45 min, depending on which test we administered. In Test 1 (30 min total in the sauna), the first 10 min in the sauna was another equilibration period, followed by a 20 min sweat production stage. We monitored axillae sweating during the last 20 min in the sauna by gravimetric analysis. At time (t) = 30 min in the sauna, skin replicas were taken and later analyzed using imaging and image analysis techniques. Test 1 was carried out on over 25 subjects, both male and female, from various racial backgrounds. In Test 2, subjects spent 45 min in the sauna after the initial 30-min period in the environmental room. During the 45 min, we obtained gravimetric readings of absorbent pads placed in the axillae. We conducted studies at various temperature and relative humidity settings. We also studied the influence of several external parameters on sudoriferous activity. Test 2 was a range-finding experiment on two subjects to determine the optimized environmental conditions for the hot room procedure. In addition to the replica and gravimetric techniques, we also measured flux density to determine the onset of firing of sweat glands to ensure that our environmental preconditioning step (30 min in the environmental room) brought subjects to the point that their sweat glands were activated. Although flux density measurements are usually carried out to determine transepidermal water loss (TEWL), we found that they can be equally useful for monitoring the onset of sweat production. Thermal infrared imaging experiments were also carried out allowing us to generate full-body images of subjects containing anatomical thermal distribution data with high accuracy. Overall, we conclude that our in-house hot room procedure offers much potential as an effective and cost-efficient screening tool for narrowing copious antiperspirant formulations to a select few for expensive clinical evaluation.

3D profilometric characterization of the aged skin surface using a skin replica and alicona Mex software.

PubMed

Pirisinu, Marco; Mazzarello, Vittorio

2016-05-01

The skin's surface is characterized by a network of furrows and wrinkles showing different height and depth. Different studies showed that processes such as aging, photo aging and cancer may alter dermal ultrastructure surface. The quantitative analysis of skin topography is a key point for understanding health condition of the skin. Here, for the first time, the skin fine structure was studied via a new approach where replica method was combined with Mex Alicona software and scanning electron microscopy (SEM). The skin texture of cheek and forearm were studied in 120 healthy sardinian volunteers. Patients were divided into three different aged groups. The skin areas of interest were reproduced by the silicone replica method, each replica was explored by SEM and digital images were taken. By using Mex Alicona software were created 3D imagine and a list of 24 surface texture parameters were obtained, of these the most representative were chosen in order to assess eventual changes between groups. The skin's texture of forearm and cheek showed a gradually loss of its typical polyhedric mesh with increasing age group. In particular, the photoexposition increased loss of dermal texture. At today, Alicona mex technology was exclusively used on palaeontology studies, our results showed that a deep analyze of skin texture was performed and support Mex alicona software as a new promising tool on dermatological research. This new analytical approach provided an easy and fast process to appreciate skin texture and its changes, by using high quality 3D dimension images. SCANNING 38:213-220, 2016. © 2015 Wiley Periodicals, Inc. © Wiley Periodicals, Inc.

Impact of airborne particle size, acoustic airflow and breathing pattern on delivery of nebulized antibiotic into the maxillary sinuses using a realistic human nasal replica.

PubMed

Leclerc, Lara; Pourchez, Jérémie; Aubert, Gérald; Leguellec, Sandrine; Vecellio, Laurent; Cottier, Michèle; Durand, Marc

2014-09-01

Improvement of clinical outcome in patients with sinuses disorders involves targeting delivery of nebulized drug into the maxillary sinuses. We investigated the impact of nebulization conditions (with and without 100 Hz acoustic airflow), particle size (9.9 μm, 2.8 μm, 550 nm and 230 nm) and breathing pattern (nasal vs. no nasal breathing) on enhancement of aerosol delivery into the sinuses using a realistic nasal replica developed by our team. After segmentation of the airways by means of high-resolution computed tomography scans, a well-characterized nasal replica was created using a rapid prototyping technology. A total of 168 intrasinus aerosol depositions were performed with changes of aerosol particle size and breathing patterns under different nebulization conditions using gentamicin as a marker. The results demonstrate that the fraction of aerosol deposited in the maxillary sinuses is enhanced by use of submicrometric aerosols, e.g. 8.155 ± 1.476 mg/L of gentamicin in the left maxillary sinus for the 2.8 μm particles vs. 2.056 ± 0.0474 for the 550 nm particles. Utilization of 100-Hz acoustic airflow nebulization also produced a 2- to 3-fold increase in drug deposition in the maxillary sinuses (e.g. 8.155 ± 1.476 vs. 3.990 ± 1.690 for the 2.8 μm particles). Our study clearly shows that optimum deposition was achieved using submicrometric particles and 100-Hz acoustic airflow nebulization with no nasal breathing. It is hoped that our new respiratory nasal replica will greatly facilitate the development of more effective delivery systems in the future.

Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.

PubMed

Yang, Mingjun; Huang, Jing; MacKerell, Alexander D

2015-06-09

Replica exchange (REX) is a powerful computational tool for overcoming the quasi-ergodic sampling problem of complex molecular systems. Recently, several multidimensional extensions of this method have been developed to realize exchanges in both temperature and biasing potential space or the use of multiple biasing potentials to improve sampling efficiency. However, increased computational cost due to the multidimensionality of exchanges becomes challenging for use on complex systems under explicit solvent conditions. In this study, we develop a one-dimensional (1D) REX algorithm to concurrently combine the advantages of overall enhanced sampling from Hamiltonian solute scaling and the specific enhancement of collective variables using Hamiltonian biasing potentials. In the present Hamiltonian replica exchange method, termed HREST-BP, Hamiltonian solute scaling is applied to the solute subsystem, and its interactions with the environment to enhance overall conformational transitions and biasing potentials are added along selected collective variables associated with specific conformational transitions, thereby balancing the sampling of different hierarchical degrees of freedom. The two enhanced sampling approaches are implemented concurrently allowing for the use of a small number of replicas (e.g., 6 to 8) in 1D, thus greatly reducing the computational cost in complex system simulations. The present method is applied to conformational sampling of two nitrogen-linked glycans (N-glycans) found on the HIV gp120 envelope protein. Considering the general importance of the conformational sampling problem, HREST-BP represents an efficient procedure for the study of complex saccharides, and, more generally, the method is anticipated to be of general utility for the conformational sampling in a wide range of macromolecular systems.

Marginal and Internal Adaptation of Zirconia Crowns: A Comparative Study of Assessment Methods.

PubMed

Cunali, Rafael Schlögel; Saab, Rafaella Caramori; Correr, Gisele Maria; Cunha, Leonardo Fernandes da; Ornaghi, Bárbara Pick; Ritter, André V; Gonzaga, Carla Castiglia

2017-01-01

Marginal and internal adaptation is critical for the success of indirect restorations. New imaging systems make it possible to evaluate these parameters with precision and non-destructively. This study evaluated the marginal and internal adaptation of zirconia copings fabricated with two different systems using both silicone replica and microcomputed tomography (micro-CT) assessment methods. A metal master model, representing a preparation for an all-ceramic full crown, was digitally scanned and polycrystalline zirconia copings were fabricated with either Ceramill Zi (Amann-Girrbach) or inCoris Zi (Dentslpy-Sirona), n=10. For each coping, marginal and internal gaps were evaluated by silicone replica and micro-CT assessment methods. Four assessment points of each replica cross-section and micro-CT image were evaluated using imaging software: marginal gap (MG), axial wall (AW), axio-occlusal angle (AO) and mid-occlusal wall (MO). Data were statistically analyzed by factorial ANOVA and Tukey test (a=0.05). There was no statistically significant difference between the methods for MG and AW. For AO, there were significant differences between methods for Amann copings, while for Dentsply-Sirona copings similar values were observed. For MO, both methods presented statistically significant differences. A positive correlation was observed determined by the two assessment methods for MG values. In conclusion, the assessment method influenced the evaluation of marginal and internal adaptation of zirconia copings. Micro-CT showed lower marginal and internal gap values when compared to the silicone replica technique, although the difference was not always statistically significant. Marginal gap and axial wall assessment points showed the lower gap values, regardless of ceramic system and assessment method used.

Insights into the folding pathway of the Engrailed Homeodomain protein using replica exchange molecular dynamics simulations.

PubMed

Koulgi, Shruti; Sonavane, Uddhavesh; Joshi, Rajendra

2010-11-01

Protein folding studies were carried out by performing microsecond time scale simulations on the ultrafast/fast folding protein Engrailed Homeodomain (EnHD) from Drosophila melanogaster. It is a three-helix bundle protein consisting of 54 residues (PDB ID: 1ENH). The positions of the helices are 8-20 (Helix I), 26-36 (Helix II) and 40-53 (Helix III). The second and third helices together form a Helix-Turn-Helix (HTH) motif which belongs to the family of DNA binding proteins. The molecular dynamics (MD) simulations were performed using replica exchange molecular dynamics (REMD). REMD is a method that involves simulating a protein at different temperatures and performing exchanges at regular time intervals. These exchanges were accepted or rejected based on the Metropolis criterion. REMD was performed using the AMBER FF03 force field with the generalised Born solvation model for the temperature range 286-373 K involving 30 replicas. The extended conformation of the protein was used as the starting structure. A simulation of 600 ns per replica was performed resulting in an overall simulation time of 18 μs. The protein was seen to fold close to the native state with backbone root mean square deviation (RMSD) of 3.16 Å. In this low RMSD structure, the Helix I was partially formed with a backbone RMSD of 3.37 Å while HTH motif had an RMSD of 1.81 Å. Analysis suggests that EnHD folds to its native structure via an intermediate in which the HTH motif is formed. The secondary structure development occurs first followed by tertiary packing. The results were in good agreement with the experimental findings. Copyright © 2010 Elsevier Inc. All rights reserved.

KSC-2011-8198

NASA Image and Video Library

2011-12-07

CAPE CANAVERAL, Fla. – Space shuttle Discovery sports three replica shuttle main engines (RSMEs) in Orbiter Processing Facility-1 at NASA’s Kennedy Space Center in Florida. The RSMEs were installed on Discovery during Space Shuttle Program transition and retirement activities. The replicas are built in the Pratt & Whitney Rocketdyne engine shop at Kennedy to replace the shuttle engines which will be placed in storage to support NASA's Space Launch System, under development. Discovery is being prepared for display at the Smithsonian’s National Air and Space Museum Steven F. Udvar-Hazy Center in Chantilly, Va. For more information, visit http://www.nasa.gov/shuttle. Photo credit: NASA/Jim Grossmann

Soft Lithography

NASA Astrophysics Data System (ADS)

Xia, Younan; Whitesides, George M.

1998-08-01

Soft lithography represents a non-photolithographic strategy based on selfassembly and replica molding for carrying out micro- and nanofabrication. It provides a convenient, effective, and low-cost method for the formation and manufacturing of micro- and nanostructures. In soft lithography, an elastomeric stamp with patterned relief structures on its surface is used to generate patterns and structures with feature sizes ranging from 30 nm to 100 mum. Five techniques have been demonstrated: microcontact printing (muCP), replica molding (REM), microtransfer molding (muTM), micromolding in capillaries (MIMIC), and solvent-assisted micromolding (SAMIM). In this chapter we discuss the procedures for these techniques and their applications in micro- and nanofabrication, surface chemistry, materials science, optics, MEMS, and microelectronics.

Combining Ultrasound Pulse-Echo and Transmission Computed Tomography for Quantitative Imaging the Cortical Shell of Long Bone Replicas

NASA Astrophysics Data System (ADS)

Shortell, Matthew P.; Althomali, Marwan A. M.; Wille, Marie-Luise; Langton, Christian M.

2017-11-01

We demonstrate a simple technique for quantitative ultrasound imaging of the cortical shell of long bone replicas. Traditional ultrasound computed tomography instruments use the transmitted or reflected waves for separate reconstructions but suffer from strong refraction artefacts in highly heterogenous samples such as bones in soft tissue. The technique described here simplifies the long bone to a two-component composite and uses both the transmitted and reflected waves for reconstructions, allowing the speed of sound and thickness of the cortical shell to be calculated accurately. The technique is simple to implement, computationally inexpensive and sample positioning errors are minimal.

Computation of free energy profiles with parallel adaptive dynamics

NASA Astrophysics Data System (ADS)

Lelièvre, Tony; Rousset, Mathias; Stoltz, Gabriel

2007-04-01

We propose a formulation of an adaptive computation of free energy differences, in the adaptive biasing force or nonequilibrium metadynamics spirit, using conditional distributions of samples of configurations which evolve in time. This allows us to present a truly unifying framework for these methods, and to prove convergence results for certain classes of algorithms. From a numerical viewpoint, a parallel implementation of these methods is very natural, the replicas interacting through the reconstructed free energy. We demonstrate how to improve this parallel implementation by resorting to some selection mechanism on the replicas. This is illustrated by computations on a model system of conformational changes.

A pilot study on the use of geometrically accurate face models to replicate ex vivo N95 mask fit.

PubMed

Golshahi, Laleh; Telidetzki, Karla; King, Ben; Shaw, Diana; Finlay, Warren H

2013-01-01

To test the feasibility of replicating a face mask seal in vitro, we created 5 geometrically accurate reconstructions of the head and neck of an adult human subject using different materials. Three breathing patterns were simulated with each replica and an attached N95 mask. Quantitative fit testing on the subject and the replicas showed that none of the 5 isotropic materials used allowed duplication of the ex vivo mask seal for the specific mask-face combination studied. Copyright © 2013 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom

DOE PAGES

Lincoff, James; Sasmal, Sukanya; Head-Gordon, Teresa

2016-11-03

Here, we compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchangemore » (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium.« less

Measurements of the absolute neutron fluence spectrum emitted at 0/sup 0/ and 90/sup 0/ from the Little-Boy replica

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

Roberts, J.H.; Gold, R.; Preston, C.C.

Nuclear research emulsions (NRE) have been used to characterize the neutron spectrum emitted by the Little-Boy replica. NRE were irradiated at the Little-Boy surface as well as approximately 2m from the center of the Little-Boy replica using polar angles of 0/sup 0/, 30/sup 0/, 60/sup 0/ and 90/sup 0/. For the NRE exposed at 2m, neutron background was determined using shadow shields of borated polyethylene. Emulsion scanning to date has concentrated exclusively on the 2m, 0/sup 0/ and 2m, 90/sup 0/ locations. Approximately 5000 proton-recoil tracks have been measured in NRE irradiated at each of these locations. At the 2m,more » 90/sup 0/ location the NRE neutron spectrum extends from 0.37 up to 8.2 MeV, whereas the NRE neutron spectrum at the 2m, 0/sup 0/ location is much softer and extends only up to 2.7 MeV. NRE neutron spectrometry results at these two locations are compared with both liquid scintillator neutron spectrometry and Monte Carlo calculations. 7 refs., 3 figs.« less

Replica approach to mean-variance portfolio optimization

NASA Astrophysics Data System (ADS)

Varga-Haszonits, Istvan; Caccioli, Fabio; Kondor, Imre

2016-12-01

We consider the problem of mean-variance portfolio optimization for a generic covariance matrix subject to the budget constraint and the constraint for the expected return, with the application of the replica method borrowed from the statistical physics of disordered systems. We find that the replica symmetry of the solution does not need to be assumed, but emerges as the unique solution of the optimization problem. We also check the stability of this solution and find that the eigenvalues of the Hessian are positive for r  =  N/T  <  1, where N is the dimension of the portfolio and T the length of the time series used to estimate the covariance matrix. At the critical point r  =  1 a phase transition is taking place. The out of sample estimation error blows up at this point as 1/(1  -  r), independently of the covariance matrix or the expected return, displaying the universality not only of the critical exponent, but also the critical point. As a conspicuous illustration of the dangers of in-sample estimates, the optimal in-sample variance is found to vanish at the critical point inversely proportional to the divergent estimation error.

Evaluating the Use of Synthetic Replicas for SEM Identification of Bloodstains (with Emphasis on Archaeological and Ethnographic Artifacts).

PubMed

Hortolà, Policarp

2015-12-01

Some archaeological or ethnographic specimens are unavailable for direct examination using a scanning electron microscope (SEM) due to methodological obstacles or legal issues. In order to assess the feasibility of using SEM synthetic replicas for the identification of bloodstains (BSs) via morphology of red blood cells (RBCs), three fragments of different natural raw material (inorganic, stone; plant, wood; animal, shell) were smeared with peripheral human blood. Afterwards, molds and casts of the bloodstained areas were made using vinyl polysiloxane (VPS) silicone impression and polyurethane (PU) resin casting material, respectively. Then, the original samples and the resulting casts were coated with gold and examined in secondary-electron mode using a high-vacuum SEM. Results suggest that PU resin casts obtained from VPS silicone molds can preserve RBC morphology in BSs, and consequently that synthetic replicas are feasible for SEM identification of BSs on cultural heritage specimens made of natural raw materials. Although the focus of this study was on BSs, the method reported in this paper may be applicable to organic residues other than blood, as well as to the surface of other specimens when, for any reason, the original is unavailable for an SEM.

Marshall Team Recreates Goddard Rocket

NASA Technical Reports Server (NTRS)

2003-01-01

In honor of the Centernial of Flight celebration and commissioned by the American Institute of Aeronautics and Astronautics (AIAA), a team of engineers from Marshall Space Flight Center (MSFC) built a replica of the first liquid-fueled rocket. The original rocket, designed and built by rocket engineering pioneer Robert H. Goddard in 1926, opened the door to modern rocketry. Goddard's rocket reached an altitude of 41 feet while its flight lasted only 2.5 seconds. The Marshall design team's plan was to stay as close as possible to an authentic reconstruction of Goddard's rocket. The same propellants were used - liquid oxygen and gasoline - as available during Goddard's initial testing and firing. The team also tried to construct the replica using the original materials and design to the greatest extent possible. By purposely using less advanced techniques and materials than many that are available today, the team encountered numerous technical challenges in testing the functional hardware. There were no original blueprints or drawings, only photographs and notes. However, this faithful adherence to historical accuracy has also allowed the team to experience many of the same challenges Goddard faced 77 years ago, and more fully appreciate the genius of this extraordinary man. The replica will undergo ground tests at MSFC this summer.

Around Marshall

NASA Image and Video Library

2003-07-01

In honor of the Centernial of Flight celebration and commissioned by the American Institute of Aeronautics and Astronautics (AIAA), a team of engineers from Marshall Space Flight Center (MSFC) built a replica of the first liquid-fueled rocket. The original rocket, designed and built by rocket engineering pioneer Robert H. Goddard in 1926, opened the door to modern rocketry. Goddard's rocket reached an altitude of 41 feet while its flight lasted only 2.5 seconds. The Marshall design team's plan was to stay as close as possible to an authentic reconstruction of Goddard's rocket. The same propellants were used - liquid oxygen and gasoline - as available during Goddard's initial testing and firing. The team also tried to construct the replica using the original materials and design to the greatest extent possible. By purposely using less advanced techniques and materials than many that are available today, the team encountered numerous technical challenges in testing the functional hardware. There were no original blueprints or drawings, only photographs and notes. However, this faithful adherence to historical accuracy has also allowed the team to experience many of the same challenges Goddard faced 77 years ago, and more fully appreciate the genius of this extraordinary man. The replica will undergo ground tests at MSFC this summer.

Surgical positioning of orthodontic mini-implants with guides fabricated on models replicated with cone-beam computed tomography.

PubMed

Kim, Seong-Hun; Choi, Yong-Suk; Hwang, Eui-Hwan; Chung, Kyu-Rhim; Kook, Yoon-Ah; Nelson, Gerald

2007-04-01

This article illustrates a new surgical guide system that uses cone-beam computed tomography (CBCT) images to replicate dental models; surgical guides for the proper positioning of orthodontic mini-implants were fabricated on the replicas, and the guides were used for precise placement. The indications, efficacy, and possible complications of this method are discussed. Patients who were planning to have orthodontic mini-implant treatment were recruited for this study. A CBCT system (PSR 9000N, Asahi Roentgen, Kyoto, Japan) was used to acquire virtual slices of the posterior maxilla that were 0.1 to 0.15 mm thick. Color 3-dimensional rapid prototyping was used to differentiate teeth, alveolus, and maxillary sinus wall. A surgical guide for the mini-implant was fabricated on the replica model. Proper positioning for mini-implants on the posterior maxilla was determined by viewing the CBCT images. The surgical guide was placed on the clinical site, and it allowed precise pilot drilling and accurate placement of the mini-implant. CBCT imaging allows remarkably lower radiation doses and thinner acquisition slices compared with medical computed tomography. Virtually reproduced replica models enable precise planning for mini-implant positions in anatomically complex sites.

Population Control of Self-Replicating Systems: Option C

NASA Technical Reports Server (NTRS)

Mccord, R. L.

1983-01-01

From the conception and development of the theory of self-replicating automata by John von Neumann, others have expanded on his theories. In 1980, Georg von Tiesenhausen and Wesley A. Darbro developed a report which is a "first' in presenting the theories in a conceptualized engineering setting. In that report several options involving self-replicating systems are presented. One of the options allows each primary to generate n replicas, one in each sequential time frame after its own generation. Each replica is limited to a maximum of m ancestors. This study involves determining the state vector of the replicas in an efficient manner. The problem is cast in matrix notation, where F = fij is a non-diagonalizable matrix. Any element fij represents the number of elements of type j = (c,d) in time frame k+1 generated from type i = (a,b) in time frame k. It is then shown that the state vector is: bar F(k)=bar F (non-zero) X F sub K = bar F (non-zero) xmx J sub kx m sub-1 where J is a matrix in Jordan form having the same eigenvalues as F. M is a matrix composed of the eigenvectors and the generalized eigenvectors of F.

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom.

PubMed

Lincoff, James; Sasmal, Sukanya; Head-Gordon, Teresa

2016-11-07

We compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchange (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium (http://www.omnia.md/).

Effects of spatially displaced feedback on remote manipulation tasks

NASA Technical Reports Server (NTRS)

Manahan, Meera K.; Stuart, Mark A.; Bierschwale, John M.; Hwang, Ellen Y.; Legendre, A. J.

1992-01-01

Several studies have been performed to determine the effects on computer and direct manipulation task performance when viewing conditions are spatially displaced. Whether results from these studies can be directly applied to remote manipulation tasks is quenstionable. The objective of this evaluation was to determine the effects of reversed, inverted, and inverted/reversed views on remote manipulation task performance using two 3-Degree of Freedom (DOF) hand controllers and a replica position hand controller. Results showed that trials using the inverted viewing condition showed the worst performance, followed by the inverted/reversed view and the reversed view when using the 2x3 DOF. However, these differences were not significant. The inverted and inverted/reversed viewing conditions were significantly worse than the normal and reversed viewing conditions when using the Kraft Replica. A second evaluation was conducted in which additional trials were performed with each viewing condition to determine the long term effects of spatially displaced views on task performance for the hand controllers. Results of the second evaluation indicated that there was more of a difference in performance between the perturbed viewing conditions and the normal viewing condition with the Kraft Replica than with the 2x3 DOF.

[Use of bacteriphages against Salmonella Enteritidis: a prevention tool].

PubMed

García, Cristina; Marín, Clara; Catalá-Gregori, Pablo; Soriano, Jose Miguel

2015-06-01

Salmonellosis is a highly prevalent disease still searching for preventive tools to avoid contamination level priority public health. The in vitro effect of bacteriophages against Salmonella enteritidis was evaluated as a prevention tool. Two tests with three concentrations of bacteriophages were conducted against two strains of Salmonella Enteritidis inoculated in fresh faeces of laying hens. Each test had a positive control. Thus, four groups in each test were evaluated. Each experimental group included two replicates, and three plates were incubated per replicate. The concentrations tested were three: commercial solution (5 × 10(7) pfu/mL), and two dilutions (1/10 and 1/30). One of the strains tested was CECT 4300, a certified strain of Colección Española de Cultivo Tipo and the other a field isolated strain in a sacrificed hen farm. Both strains were inoculated at 1.3 × 10(5) cfu/g of faeces in each of the four groups. Isolation and identification of bacteria by ISO6579 was done at various times after inoculation: 1 minute, 24 hours and 7 days. In the first test, with certified strain, Salmonella was isolated in all groups at time 1 minute. After 24 hours, Salmonella was isolated in all groups except in one of the replicas treated with 1/10 dilution of bacteriophages, one of the other replica plate treated with 1/10 dilution, and two plates of the two replicas treated with the commercial solution. After 7 days, the bacteria were not isolated from any of the experimental groups. In the second test, with the field strain, Salmonella was isolated in all groups at time 1 minute. After 24 hours, Salmonella was isolated in all groups except in one of the replicas treated with 1/10 dilution of bacteriophages and the two replicas treated with the commercial solution. Salmonella was not isolated in any of the experimental groups at 7 days. The use of bacteriophages reduced Salmonella enteritidis isolates in faeces at 24 hours after the application, so it could be considered as a prevention tool. At 7 days after inoculation of bacteria, no one was isolated in any of the experimental groups. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

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

Chen, Haixia; Zhang, Jing

We propose a scheme for continuous-variable quantum cloning of coherent states with phase-conjugate input modes using linear optics. The quantum cloning machine yields M identical optimal clones from N replicas of a coherent state and N replicas of its phase conjugate. This scheme can be straightforwardly implemented with the setups accessible at present since its optical implementation only employs simple linear optical elements and homodyne detection. Compared with the original scheme for continuous-variable quantum cloning with phase-conjugate input modes proposed by Cerf and Iblisdir [Phys. Rev. Lett. 87, 247903 (2001)], which utilized a nondegenerate optical parametric amplifier, our scheme losesmore » the output of phase-conjugate clones and is regarded as irreversible quantum cloning.« less

Efficiency reduction and pseudo-convergence in replica exchange sampling of peptide folding unfolding equilibria

NASA Astrophysics Data System (ADS)

Denschlag, Robert; Lingenheil, Martin; Tavan, Paul

2008-06-01

Replica exchange (RE) molecular dynamics (MD) simulations are frequently applied to sample the folding-unfolding equilibria of β-hairpin peptides in solution, because efficiency gains are expected from this technique. Using a three-state Markov model featuring key aspects of β-hairpin folding we show that RE simulations can be less efficient than conventional techniques. Furthermore we demonstrate that one is easily seduced to erroneously assign convergence to the RE sampling, because RE ensembles can rapidly reach long-lived stationary states. We conclude that typical REMD simulations covering a few tens of nanoseconds are by far too short for sufficient sampling of β-hairpin folding-unfolding equilibria.

Replicas of the Santa Maria, Nina, Pinta sail by OV-105 on KSC LC Pad 39B

NASA Technical Reports Server (NTRS)

1992-01-01

Replicas of Christopher Columbus' sailing ships Santa Maria, Nina, and Pinta sail by Endeavour, Orbiter Vehicle (OV) 105, on Kennedy Space Center (KSC) Launch Complex (LC) Pad 39B awaiting liftoff on its maiden voyage, STS-49. This view was taken from the water showing the three ships in the foreground with OV-105 on mobile launcher platform profiled against fixed service structure (FSS) tower and rectracted rotating service structure (RSS) in the background. Next to the launch pad (at right) are the sound suppression water system tower and the liquid hydrogen (LH2) storage tank. View provided by KSC with alternate number KSC-92PC-967.

Extreme ultraviolet performance of a multilayer coated high density toroidal grating

NASA Technical Reports Server (NTRS)

Thomas, Roger J.; Keski-Kuha, Ritva A. M.; Neupert, Werner M.; Condor, Charles E.; Gum, Jeffrey S.

1991-01-01

The performance of a multilayer coated diffraction grating has been evaluated at EUV wavelengths both in terms of absolute efficiency and spectral resolution. The application of ten-layer Ir/Si multilayer coating to a 3600-lines/mm blazed toroidal replica grating produced a factor of 9 enhancement in peak efficiency near the design wavelength of about 30 nm in first order, without degrading its excellent quasistigmatic spectral resolution. The measured EUV efficiency peaked at 3.3 percent and was improved over the full spectral range between 25 and 35 nm compared with the premultilayer replica which had a standard gold coating. In addition, the grating's spectral resolution of greater than 5000 was maintained.

Photographic replica of the plaque Apollo 13 astronauts will leave on moon

NASA Image and Video Library

1970-04-13

S70-34685 (April 1970) --- A photographic replica of the plaque which the Apollo 13 astronauts will leave behind on the moon during their lunar landing mission. Astronauts James A. Lovell Jr., commander; and Fred W. Haise Jr., lunar module pilot, will descend to the lunar surface in the Lunar Module (LM) "Aquarius". Astronaut John L. Swigert Jr., command module pilot, will remain with the Command and Service Modules (CSM) in lunar orbit. The plaque will be attached to the ladder of the landing gear strut on the LM?s descent stage. Commemorative plaques were also left on the moon by the Apollo 11 and Apollo 12 astronauts.

Light and transmission electron microscopy of the intact interfaces between non-submerged titanium-coated epoxy resin implants and bone or gingiva.

PubMed

Listgarten, M A; Buser, D; Steinemann, S G; Donath, K; Lang, N P; Weber, H P

1992-02-01

This experiment was aimed at studying the intact tissue/implant interface of non-submerged dental implants with a titanium surface. Epoxy-resin replicas were fabricated from 3.05 x 8 mm cylindrical titanium implants with a plasma-sprayed apical portion and a smooth coronal collar. The replicas were coated with a 90-120-nm-thick layer of pure titanium and autoclaved. The coated replicas were inserted as non-submerged endosseous implants in the edentulous premolar region of dog mandibles and allowed to heal for three months. Jaw sections containing the implants were processed for light and electron microscopic study of the intact tissue/implant interface with and without prior demineralization. Gingival connective tissue fibers were closely adapted to the titanium layer, in an orientation more or less parallel to the implant surface. There was no evidence of any fiber insertions into the surface irregularities of the smooth or rough titanium surface. Undemineralized bone was intimately adapted to the titanium surface without any intervening space. In demineralized sections, the collagen fibers of the bone matrix tended to be somewhat thinner and occasionally less densely packed in the vicinity of the implant surface. However, they extended all the way to the titanium surface, without any intervening fibril-free layer.

The use of a 3D laser scanner using superimpositional software to assess the accuracy of impression techniques.

PubMed

Shah, Sinal; Sundaram, Geeta; Bartlett, David; Sherriff, Martyn

2004-11-01

Several studies have made comparisons in the dimensional accuracy of different elastomeric impression materials. Most have used two-dimensional measuring devices, which neglect to account for the dimensional changes that exist along a three-dimensional surface. The aim of this study was to compare the dimensional accuracy of an impression technique using a polyether material (Impregum) and a vinyl poly siloxane material (President) using a laser scanner with three-dimensional superimpositional software. Twenty impressions, 10 with a polyether and 10 with addition silicone, of a stone master model that resembled a dental arch containing three acrylic posterior teeth were cast in orthodontic stone. One plastic tooth was prepared for a metal crown. The master model and the casts were digitised with the non-contacting laser scanner to produce a 3D image. 3D surface viewer software superimposed the master model to the stone replica and the difference between the images analysed. The mean difference between the model and the stone replica made from Impregum was 0.072mm (SD 0.006) and that for the silicone 0.097mm (SD 0.005) and this difference was statistically significantly, p=0.001. Both impression materials provided an accurate replica of the prepared teeth supporting the view that these materials are highly accurate.

A compression algorithm for the combination of PDF sets.

PubMed

Carrazza, Stefano; Latorre, José I; Rojo, Juan; Watt, Graeme

The current PDF4LHC recommendation to estimate uncertainties due to parton distribution functions (PDFs) in theoretical predictions for LHC processes involves the combination of separate predictions computed using PDF sets from different groups, each of which comprises a relatively large number of either Hessian eigenvectors or Monte Carlo (MC) replicas. While many fixed-order and parton shower programs allow the evaluation of PDF uncertainties for a single PDF set at no additional CPU cost, this feature is not universal, and, moreover, the a posteriori combination of the predictions using at least three different PDF sets is still required. In this work, we present a strategy for the statistical combination of individual PDF sets, based on the MC representation of Hessian sets, followed by a compression algorithm for the reduction of the number of MC replicas. We illustrate our strategy with the combination and compression of the recent NNPDF3.0, CT14 and MMHT14 NNLO PDF sets. The resulting compressed Monte Carlo PDF sets are validated at the level of parton luminosities and LHC inclusive cross sections and differential distributions. We determine that around 100 replicas provide an adequate representation of the probability distribution for the original combined PDF set, suitable for general applications to LHC phenomenology.

Manufacture of patient-specific vascular replicas for endovascular simulation using fast, low-cost method

NASA Astrophysics Data System (ADS)

Kaneko, Naoki; Mashiko, Toshihiro; Ohnishi, Taihei; Ohta, Makoto; Namba, Katsunari; Watanabe, Eiju; Kawai, Kensuke

2016-12-01

Patient-specific vascular replicas are essential to the simulation of endovascular treatment or for vascular research. The inside of silicone replica is required to be smooth for manipulating interventional devices without resistance. In this report, we demonstrate the fabrication of patient-specific silicone vessels with a low-cost desktop 3D printer. We show that the surface of an acrylonitrile butadiene styrene (ABS) model printed by the 3D printer can be smoothed by a single dipping in ABS solvent in a time-dependent manner, where a short dip has less effect on the shape of the model. The vascular mold is coated with transparent silicone and then the ABS mold is dissolved after the silicone is cured. Interventional devices can pass through the inside of the smoothed silicone vessel with lower pushing force compared to the vessel without smoothing. The material cost and time required to fabricate the silicone vessel is about USD $2 and 24 h, which is much lower than the current fabrication methods. This fast and low-cost method offers the possibility of testing strategies before attempting particularly difficult cases, while improving the training of endovascular therapy, enabling the trialing of new devices, and broadening the scope of vascular research.

Hollow Microneedles for Intradermal Injection Fabricated by Sacrificial Micromolding and Selective Electrodeposition

PubMed Central

Norman, James J.; Choi, Seong-O; Tong, Nhien T.; Aiyar, Avishek R.; Patel, Samirkumar R.; Prausnitz, Mark R.; Allen, Mark G.

2012-01-01

Limitations with standard intradermal injections have created a clinical need for an alternative, low-cost injection device. In this study, we designed a hollow metal microneedle for reliable intradermal injection and developed a high-throughput micromolding process to produce metal microneedles with complex geometries. To fabricate the microneedles, we laser-ablated a 70 μm × 70 μm square cavity near the tip of poly(lactic acid-co-glyoclic acid) (PLGA) microneedles. The master structure was a template for multiple micromolded PLGA replicas. Each replica was sputtered with a gold seed layer with minimal gold deposited in the cavity due to masking effects. In this way, nickel was electrodeposited selectively outside of the cavity, after which the polymer replica was dissolved to produce a hollow metal microneedle. Force-displacement tests showed the microneedles, with 12 μm thick electrodeposition, could penetrate skin with an insertion force 9 times less than their axial failure force. We injected fluid with the microneedles into pig skin in vitro and hairless guinea pig skin in vivo. The injections targeted 90% of the material within the skin with minimal leakage onto the skin surface. We conclude that hollow microneedles made by this simple microfabrication method can achieve targeted intradermal injection. PMID:23053452

Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding.

PubMed

Lee, Michael S; Olson, Mark A

2011-06-28

Temperature-based replica exchange (T-ReX) enhances sampling of molecular dynamics simulations by autonomously heating and cooling simulation clients via a Metropolis exchange criterion. A pathological case for T-ReX can occur when a change in state (e.g., folding to unfolding of a protein) has a large energetic difference over a short temperature interval leading to insufficient exchanges amongst replica clients near the transition temperature. One solution is to allow the temperature set to dynamically adapt in the temperature space, thereby enriching the population of clients near the transition temperature. In this work, we evaluated two approaches for adapting the temperature set: a method that equalizes exchange rates over all neighbor temperature pairs and a method that attempts to induce clients to visit all temperatures (dubbed "current maximization") by positioning many clients at or near the transition temperature. As a test case, we simulated the 57-residue SH3 domain of alpha-spectrin. Exchange rate equalization yielded the same unfolding-folding transition temperature as fixed-temperature ReX with much smoother convergence of this value. Surprisingly, the current maximization method yielded a significantly lower transition temperature, in close agreement with experimental observation, likely due to more extensive sampling of the transition state.

Fundamental Bounds for Sequence Reconstruction from Nanopore Sequencers.

PubMed

Magner, Abram; Duda, Jarosław; Szpankowski, Wojciech; Grama, Ananth

2016-06-01

Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic analysis of the impact of insertion-deletion (indel) errors in nanopore sequencers. In particular, we consider the following problems: (i) for given indel error characteristics and rate, what is the probability of accurate reconstruction as a function of sequence length; (ii) using replicated extrusion (the process of passing a DNA strand through the nanopore), what is the number of replicas needed to accurately reconstruct the true sequence with high probability? Our results provide a number of important insights: (i) the probability of accurate reconstruction of a sequence from a single sample in the presence of indel errors tends quickly (i.e., exponentially) to zero as the length of the sequence increases; and (ii) replicated extrusion is an effective technique for accurate reconstruction. We show that for typical distributions of indel errors, the required number of replicas is a slow function (polylogarithmic) of sequence length - implying that through replicated extrusion, we can sequence large reads using nanopore sequencers. Moreover, we show that in certain cases, the required number of replicas can be related to information-theoretic parameters of the indel error distributions.

Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing.

PubMed

Chodera, John D; Shirts, Michael R

2011-11-21

The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in discovering new ways to enhance the phase space mixing of these protocols in order to improve sampling of uncorrelated configurations. Here, we demonstrate how both of these classes of algorithms can be considered as special cases of Gibbs sampling within a Markov chain Monte Carlo framework. Gibbs sampling is a well-studied scheme in the field of statistical inference in which different random variables are alternately updated from conditional distributions. While the update of the conformational degrees of freedom by Metropolis Monte Carlo or molecular dynamics unavoidably generates correlated samples, we show how judicious updating of the thermodynamic state indices--corresponding to thermodynamic parameters such as temperature or alchemical coupling variables--can substantially increase mixing while still sampling from the desired distributions. We show how state update methods in common use can lead to suboptimal mixing, and present some simple, inexpensive alternatives that can increase mixing of the overall Markov chain, reducing simulation times necessary to obtain estimates of the desired precision. These improved schemes are demonstrated for several common applications, including an alchemical expanded ensemble simulation, parallel tempering, and multidimensional replica exchange umbrella sampling.

Complex, multi-scale small intestinal topography replicated in cellular growth substrates fabricated via chemical vapor deposition of Parylene C.

PubMed

Koppes, Abigail N; Kamath, Megha; Pfluger, Courtney A; Burkey, Daniel D; Dokmeci, Mehmet; Wang, Lin; Carrier, Rebecca L

2016-08-22

Native small intestine possesses distinct multi-scale structures (e.g., crypts, villi) not included in traditional 2D intestinal culture models for drug delivery and regenerative medicine. The known impact of structure on cell function motivates exploration of the influence of intestinal topography on the phenotype of cultured epithelial cells, but the irregular, macro- to submicron-scale features of native intestine are challenging to precisely replicate in cellular growth substrates. Herein, we utilized chemical vapor deposition of Parylene C on decellularized porcine small intestine to create polymeric intestinal replicas containing biomimetic irregular, multi-scale structures. These replicas were used as molds for polydimethylsiloxane (PDMS) growth substrates with macro to submicron intestinal topographical features. Resultant PDMS replicas exhibit multiscale resolution including macro- to micro-scale folds, crypt and villus structures, and submicron-scale features of the underlying basement membrane. After 10 d of human epithelial colorectal cell culture on PDMS substrates, the inclusion of biomimetic topographical features enhanced alkaline phosphatase expression 2.3-fold compared to flat controls, suggesting biomimetic topography is important in induced epithelial differentiation. This work presents a facile, inexpensive method for precisely replicating complex hierarchal features of native tissue, towards a new model for regenerative medicine and drug delivery for intestinal disorders and diseases.

Batesian mimicry promotes pre- and postmating isolation in a snake mimicry complex.

PubMed

Pfennig, David W; Akcali, Christopher K; Kikuchi, David W

2015-04-01

We evaluated whether Batesian mimicry promotes early-stage reproductive isolation. Many Batesian mimics occur not only in sympatry with their model (as expected), but also in allopatry. As a consequence of local adaptation within both sympatry (where mimetic traits are favored) and allopatry (where nonmimetic traits are favored), divergent, predator-mediated natural selection should disfavor immigrants between these selective environments as well as any between-environment hybrids. This selection might form the basis for both pre- and postmating isolation, respectively. We tested for such selection in a snake mimicry complex by placing clay replicas of sympatric, allopatric, or hybrid phenotypes in both sympatry and allopatry and measuring predation attempts. As predicted, replicas with immigrant phenotypes were disfavored in both selective environments. Replicas with hybrid phenotypes were also disfavored, but only in a region of sympatry where previous studies have detected strong selection favoring precise mimicry. By fostering immigrant inviability and ecologically dependent selection against hybrids (at least in some habitats), Batesian mimicry might therefore promote reproductive isolation. Thus, although Batesian mimicry has long been viewed as a mechanism for convergent evolution, it might play an underappreciated role in fueling divergent evolution and possibly even the evolution of reproductive isolation and speciation. © 2015 The Author(s).

Quantifying Antimicrobial Resistance at Veal Calf Farms

PubMed Central

Bosman, Angela B.; Wagenaar, Jaap; Stegeman, Arjan; Vernooij, Hans; Mevius, Dik

2012-01-01

This study was performed to determine a sampling strategy to quantify the prevalence of antimicrobial resistance on veal calf farms, based on the variation in antimicrobial resistance within and between calves on five farms. Faecal samples from 50 healthy calves (10 calves/farm) were collected. From each individual sample and one pooled faecal sample per farm, 90 selected Escherichia coli isolates were tested for their resistance against 25 mg/L amoxicillin, 25 mg/L tetracycline, 0.5 mg/L cefotaxime, 0.125 mg/L ciprofloxacin and 8/152 mg/L trimethoprim/sulfamethoxazole (tmp/s) by replica plating. From each faecal sample another 10 selected E. coli isolates were tested for their resistance by broth microdilution as a reference. Logistic regression analysis was performed to compare the odds of testing an isolate resistant between both test methods (replica plating vs. broth microdilution) and to evaluate the effect of pooling faecal samples. Bootstrap analysis was used to investigate the precision of the estimated prevalence of resistance to each antimicrobial obtained by several simulated sampling strategies. Replica plating showed similar odds of E. coli isolates tested resistant compared to broth microdilution, except for ciprofloxacin (OR 0.29, p≤0.05). Pooled samples showed in general lower odds of an isolate being resistant compared to individual samples, although these differences were not significant. Bootstrap analysis showed that within each antimicrobial the various compositions of a pooled sample provided consistent estimates for the mean proportion of resistant isolates. Sampling strategies should be based on the variation in resistance among isolates within faecal samples and between faecal samples, which may vary by antimicrobial. In our study, the optimal sampling strategy from the perspective of precision of the estimated levels of resistance and practicality consists of a pooled faecal sample from 20 individual animals, of which 90 isolates are tested for their susceptibility by replica plating. PMID:22970313

A Dual-Channel Acquisition Method Based on Extended Replica Folding Algorithm for Long Pseudo-Noise Code in Inter-Satellite Links.

PubMed

Zhao, Hongbo; Chen, Yuying; Feng, Wenquan; Zhuang, Chen

2018-05-25

Inter-satellite links are an important component of the new generation of satellite navigation systems, characterized by low signal-to-noise ratio (SNR), complex electromagnetic interference and the short time slot of each satellite, which brings difficulties to the acquisition stage. The inter-satellite link in both Global Positioning System (GPS) and BeiDou Navigation Satellite System (BDS) adopt the long code spread spectrum system. However, long code acquisition is a difficult and time-consuming task due to the long code period. Traditional folding methods such as extended replica folding acquisition search technique (XFAST) and direct average are largely restricted because of code Doppler and additional SNR loss caused by replica folding. The dual folding method (DF-XFAST) and dual-channel method have been proposed to achieve long code acquisition in low SNR and high dynamic situations, respectively, but the former is easily affected by code Doppler and the latter is not fast enough. Considering the environment of inter-satellite links and the problems of existing algorithms, this paper proposes a new long code acquisition algorithm named dual-channel acquisition method based on the extended replica folding algorithm (DC-XFAST). This method employs dual channels for verification. Each channel contains an incoming signal block. Local code samples are folded and zero-padded to the length of the incoming signal block. After a circular FFT operation, the correlation results contain two peaks of the same magnitude and specified relative position. The detection process is eased through finding the two largest values. The verification takes all the full and partial peaks into account. Numerical results reveal that the DC-XFAST method can improve acquisition performance while acquisition speed is guaranteed. The method has a significantly higher acquisition probability than folding methods XFAST and DF-XFAST. Moreover, with the advantage of higher detection probability and lower false alarm probability, it has a lower mean acquisition time than traditional XFAST, DF-XFAST and zero-padding.

Paraxial light distribution in the focal region of a lens: a comparison of several analytical solutions and a numerical result.

PubMed

Wu, Yang; Kelly, Damien P

2014-12-12

The distribution of the complex field in the focal region of a lens is a classical optical diffraction problem. Today, it remains of significant theoretical importance for understanding the properties of imaging systems. In the paraxial regime, it is possible to find analytical solutions in the neighborhood of the focus, when a plane wave is incident on a focusing lens whose finite extent is limited by a circular aperture. For example, in Born and Wolf's treatment of this problem, two different, but mathematically equivalent analytical solutions, are presented that describe the 3D field distribution using infinite sums of [Formula: see text] and [Formula: see text] type Lommel functions. An alternative solution expresses the distribution in terms of Zernike polynomials, and was presented by Nijboer in 1947. More recently, Cao derived an alternative analytical solution by expanding the Fresnel kernel using a Taylor series expansion. In practical calculations, however, only a finite number of terms from these infinite series expansions is actually used to calculate the distribution in the focal region. In this manuscript, we compare and contrast each of these different solutions to a numerically calculated result, paying particular attention to how quickly each solution converges for a range of different spatial locations behind the focusing lens. We also examine the time taken to calculate each of the analytical solutions. The numerical solution is calculated in a polar coordinate system and is semi-analytic. The integration over the angle is solved analytically, while the radial coordinate is sampled with a sampling interval of [Formula: see text] and then numerically integrated. This produces an infinite set of replicas in the diffraction plane, that are located in circular rings centered at the optical axis and each with radii given by [Formula: see text], where [Formula: see text] is the replica order. These circular replicas are shown to be fundamentally different from the replicas that arise in a Cartesian coordinate system.

Paraxial light distribution in the focal region of a lens: a comparison of several analytical solutions and a numerical result

NASA Astrophysics Data System (ADS)

Wu, Yang; Kelly, Damien P.

2014-12-01

The distribution of the complex field in the focal region of a lens is a classical optical diffraction problem. Today, it remains of significant theoretical importance for understanding the properties of imaging systems. In the paraxial regime, it is possible to find analytical solutions in the neighborhood of the focus, when a plane wave is incident on a focusing lens whose finite extent is limited by a circular aperture. For example, in Born and Wolf's treatment of this problem, two different, but mathematically equivalent analytical solutions, are presented that describe the 3D field distribution using infinite sums of ? and ? type Lommel functions. An alternative solution expresses the distribution in terms of Zernike polynomials, and was presented by Nijboer in 1947. More recently, Cao derived an alternative analytical solution by expanding the Fresnel kernel using a Taylor series expansion. In practical calculations, however, only a finite number of terms from these infinite series expansions is actually used to calculate the distribution in the focal region. In this manuscript, we compare and contrast each of these different solutions to a numerically calculated result, paying particular attention to how quickly each solution converges for a range of different spatial locations behind the focusing lens. We also examine the time taken to calculate each of the analytical solutions. The numerical solution is calculated in a polar coordinate system and is semi-analytic. The integration over the angle is solved analytically, while the radial coordinate is sampled with a sampling interval of ? and then numerically integrated. This produces an infinite set of replicas in the diffraction plane, that are located in circular rings centered at the optical axis and each with radii given by ?, where ? is the replica order. These circular replicas are shown to be fundamentally different from the replicas that arise in a Cartesian coordinate system.

On the validity and robustness of the scale error phenomenon in early childhood.

PubMed

DeLoache, Judy S; LoBue, Vanessa; Vanderborght, Mieke; Chiong, Cynthia

2013-02-01

Scale errors is a term referring to very young children's serious efforts to perform actions on miniature replica objects that are impossible due to great differences in the size of the child's body and the size of the target objects. We report three studies providing further documentation of scale errors and investigating the validity and robustness of the phenomenon. In the first, we establish that 2-year-olds' behavior in response to prompts to "pretend" with miniature replica objects differs dramatically from scale errors. The second and third studies address the robustness of the phenomenon and its relative imperviousness to attempts to influence the rate of scale errors. Copyright © 2012 Elsevier Inc. All rights reserved.

Difference in dimer conformation between amyloid-β(1-42) and (1-43) proteins: Replica exchange molecular dynamics simulations in water

NASA Astrophysics Data System (ADS)

Yano, Atsushi; Okamoto, Akisumi; Nomura, Kazuya; Higai, Shin'ichi; Kurita, Noriyuki

2014-03-01

We searched stable conformations of amyloid-β (Aβ) dimers composed of Aβ(1-42) or Aβ(1-43) protein in water by replica-exchange molecular dynamics simulations and found that Thr43 of the C-terminal of Aβ(1-43) is hydrogen bonded to Arg5 of the same monomer in the Aβ(1-43) dimer, resulting in its ring-shaped conformation, while Aβ(1-42) has no such hydrogen-bond. This conformation is expected to aggregate more easily into a compact conformation of Aβ fibrils. We also investigated the binding affinity and the specific interactions between Aβ monomers by ab initio fragment molecular orbital calculations to elucidate which Aβ residues contribute to the dimerization.

[Cervical adaptation of complete cast crowns of various metal alloys, with and without die spacers].

PubMed

Stephano, C B; Roselino, R F; Roselino, R B; Campos, G M

1989-01-01

A metallic replica from a dental preparation for crown was used to make 8 class-IV stone dies. The wax patterns for the casting of the crowns were obtained in two conditions: a) from the stone die with no spacer; and b) from the stone die with an acrylic spacer. Thus, 64 metallic crowns were casted, using 4 different alloys: DURACAST (Cu-Al), NICROCAST (Ni-Cr) and DURABOND (Ni-Cr), and gold. The casted crowns were fitted in the metallic replica and measured as to the cervical discrepance of fitting. The results showed that the use of die spacers decreases the clinical discrepancies of fitting of the casted crowns (in a statistically significant level), no matter the metallic alloy employed.

Impact of Data Placement on Resilience in Large-Scale Object Storage Systems

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

Carns, Philip; Harms, Kevin; Jenkins, John

Distributed object storage architectures have become the de facto standard for high-performance storage in big data, cloud, and HPC computing. Object storage deployments using commodity hardware to reduce costs often employ object replication as a method to achieve data resilience. Repairing object replicas after failure is a daunting task for systems with thousands of servers and billions of objects, however, and it is increasingly difficult to evaluate such scenarios at scale on realworld systems. Resilience and availability are both compromised if objects are not repaired in a timely manner. In this work we leverage a high-fidelity discrete-event simulation model tomore » investigate replica reconstruction on large-scale object storage systems with thousands of servers, billions of objects, and petabytes of data. We evaluate the behavior of CRUSH, a well-known object placement algorithm, and identify configuration scenarios in which aggregate rebuild performance is constrained by object placement policies. After determining the root cause of this bottleneck, we then propose enhancements to CRUSH and the usage policies atop it to enable scalable replica reconstruction. We use these methods to demonstrate a simulated aggregate rebuild rate of 410 GiB/s (within 5% of projected ideal linear scaling) on a 1,024-node commodity storage system. We also uncover an unexpected phenomenon in rebuild performance based on the characteristics of the data stored on the system.« less

Nuclear research emulsion neutron spectrometry at the Little-Boy replica

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

Gold, R.; Roberts, J.H.; Preston, C.C.

Nuclear research emulsions (NRE) have been used to characterize the neutron spectrum emitted by the Little-Boy replica. NRE were irradiated at the Little-Boy surface as well as approximately 2 m from the center of the Little-Boy replica using polar angles of 0/sup 0/, 30/sup 0/, 60/sup 0/ and 90/sup 0/. For the NRE exposed at 2 m, neutron background was determined using shadow shields of borated polyethylene. Emulsion scanning to date has concentrated exclusively on the 2-m, 0/sup 0/ and 2-m, 90/sup 0/ locations. Approximately 5000 proton-recoil tracks have been measured in NRE irradiated at each of these locations. Neutronmore » spectra obtained from these NRE proton-recoil spectra are compared with both liquid scintillator neutron spectrometry and Monte Carlo calculations. NRE and liquid scintillator neutron spectra generally agree within experimental uncertainties at the 2-m, 90/sup 0/ location. However, at the 2-m, 0/sup 0/ location, the neutron spectra derived from these two independent experimental methods differ significantly. NRE spectra and Monte Carlo calculations exhibit general agreement with regard to both intensity as well as energy dependence. Better agreement is attained between theory and experiment at the 2-m, 90/sup 0/ location, where the neutron intensity is considerably higher. 14 refs., 18 figs., 11 tabs.« less

Imaging Cytoskeleton Components by Electron Microscopy.

PubMed

Svitkina, Tatyana

2016-01-01

The cytoskeleton is a complex of detergent-insoluble components of the cytoplasm playing critical roles in cell motility, shape generation, and mechanical properties of a cell. Fibrillar polymers-actin filaments, microtubules, and intermediate filaments-are major constituents of the cytoskeleton, which constantly change their organization during cellular activities. The actin cytoskeleton is especially polymorphic, as actin filaments can form multiple higher order assemblies performing different functions. Structural information about cytoskeleton organization is critical for understanding its functions and mechanisms underlying various forms of cellular activity. Because of the nanometer-scale thickness of cytoskeletal fibers, electron microscopy (EM) is a key tool to determine the structure of the cytoskeleton. This article describes application of rotary shadowing (or metal replica) EM for visualization of the cytoskeleton. The procedure is applicable to thin cultured cells growing on glass coverslips and consists of detergent extraction of cells to expose their cytoskeleton, chemical fixation to provide stability, ethanol dehydration and critical point drying to preserve three-dimensionality, rotary shadowing with platinum to create contrast, and carbon coating to stabilize replicas. This technique provides easily interpretable three-dimensional images, in which individual cytoskeletal fibers are clearly resolved, and individual proteins can be identified by immunogold labeling. More importantly, replica EM is easily compatible with live cell imaging, so that one can correlate the dynamics of a cell or its components, e.g., expressed fluorescent proteins, with high resolution structural organization of the cytoskeleton in the same cell.

Visualization of nasal airflow patterns in a patient affected with atrophic rhinitis using particle image velocimetry

NASA Astrophysics Data System (ADS)

Garcia, G. J. M.; Mitchell, G.; Bailie, N.; Thornhill, D.; Watterson, J.; Kimbell, J. S.

2007-10-01

The relationship between airflow patterns in the nasal cavity and nasal function is poorly understood. This paper reports an experimental study of the interplay between symptoms and airflow patterns in a patient affected with atrophic rhinitis. This pathology is characterized by mucosal dryness, fetor, progressive atrophy of anatomical structures, a spacious nasal cavity, and a paradoxical sensation of nasal congestion. A physical replica of the patient's nasal geometry was made and particle image velocimetry (PIV) was used to visualize and measure the flow field. The nasal replica was based on computed tomography (CT) scans of the patient and was built in three steps: three-dimensional reconstruction of the CT scans; rapid prototyping of a cast; and sacrificial use of the cast to form a model of the nasal passage in clear silicone. Flow patterns were measured by running a water-glycerol mixture through the replica and evaluating the displacement of particles dispersed in the liquid using PIV. The water-glycerol flow rate used corresponded to an air flow rate representative of a human breathing at rest. The trajectory of the flow observed in the left passage of the nose (more affected by atrophic rhinitis) differed markedly from what is considered normal, and was consistent with patterns of epithelial damage observed in cases of the condition. The data are also useful for validation of computational fluid dynamics predictions.

Marshall Team Fires Recreated Goddard Rocket

NASA Technical Reports Server (NTRS)

2003-01-01

In honor of the Centernial of Flight Celebration and commissioned by the American Institute of Aeronautics and Astronautics (AIAA), a team of engineers from Marshall Space Flight Center (MSFC) built a replica of the first liquid-fueled rocket. The original rocket, designed and built by rocket engineering pioneer Robert H. Goddard in 1926, opened the door to modern rocketry. Goddard's rocket reached an altitude of 41 feet while its flight lasted only 2.5 seconds. The Marshall design team's plan was to stay as close as possible to an authentic reconstruction of Goddard's rocket. The same propellants were used - liquid oxygen and gasoline - as available during Goddard's initial testing and firing. The team also tried to construct the replica using the original materials and design to the greatest extent possible. By purposely using less advanced techniques and materials than many that are available today, the team encountered numerous technical challenges in testing the functional hardware. There were no original blueprints or drawings, only photographs and notes. However, this faithful adherence to historical accuracy has allowed the team to experience many of the same challenges Goddard faced 77 years ago, and more fully appreciate the genius of this extraordinary man. In this photo, the replica is shown firing in the A-frame launch stand in near-flight configuration at MSFC's Test Area 116 during the American Institute of Aeronautics and Astronautics 39th Joint Propulsion Conference on July 23, 2003.

Around Marshall

NASA Image and Video Library

2003-07-23

In honor of the Centernial of Flight Celebration and commissioned by the American Institute of Aeronautics and Astronautics (AIAA), a team of engineers from Marshall Space Flight Center (MSFC) built a replica of the first liquid-fueled rocket. The original rocket, designed and built by rocket engineering pioneer Robert H. Goddard in 1926, opened the door to modern rocketry. Goddard's rocket reached an altitude of 41 feet while its flight lasted only 2.5 seconds. The Marshall design team's plan was to stay as close as possible to an authentic reconstruction of Goddard's rocket. The same propellants were used - liquid oxygen and gasoline - as available during Goddard's initial testing and firing. The team also tried to construct the replica using the original materials and design to the greatest extent possible. By purposely using less advanced techniques and materials than many that are available today, the team encountered numerous technical challenges in testing the functional hardware. There were no original blueprints or drawings, only photographs and notes. However, this faithful adherence to historical accuracy has allowed the team to experience many of the same challenges Goddard faced 77 years ago, and more fully appreciate the genius of this extraordinary man. In this photo, the replica is shown firing in the A-frame launch stand in near-flight configuration at MSFC's Test Area 116 during the American Institute of Aeronautics and Astronautics 39th Joint Propulsion Conference on July 23, 2003.

3D-glass molds for facile production of complex droplet microfluidic chips.

PubMed

Tovar, Miguel; Weber, Thomas; Hengoju, Sundar; Lovera, Andrea; Munser, Anne-Sophie; Shvydkiv, Oksana; Roth, Martin

2018-03-01

In order to leverage the immense potential of droplet microfluidics, it is necessary to simplify the process of chip design and fabrication. While polydimethylsiloxane (PDMS) replica molding has greatly revolutionized the chip-production process, its dependence on 2D-limited photolithography has restricted the design possibilities, as well as further dissemination of microfluidics to non-specialized labs. To break free from these restrictions while keeping fabrication straighforward, we introduce an approach to produce complex multi-height (3D) droplet microfluidic glass molds and subsequent chip production by PDMS replica molding. The glass molds are fabricated with sub-micrometric resolution using femtosecond laser machining technology, which allows directly realizing designs with multiple levels or even continuously changing heights. The presented technique significantly expands the experimental capabilities of the droplet microfluidic chip. It allows direct fabrication of multilevel structures such as droplet traps for prolonged observation and optical fiber integration for fluorescence detection. Furthermore, the fabrication of novel structures based on sloped channels (ramps) enables improved droplet reinjection and picoinjection or even a multi-parallelized drop generator based on gradients of confinement. The fabrication of these and other 3D-features is currently only available at such resolution by the presented strategy. Together with the simplicity of PDMS replica molding, this provides an accessible solution for both specialized and non-specialized labs to customize microfluidic experimentation and expand their possibilities.

Structure of Alzheimer's 10-35 β peptide from replica-exchange molecular dynamics simulations in explicit water

NASA Astrophysics Data System (ADS)

Baumketner, Andriy; Shea, Joan-Emma

2006-03-01

We report a replica-exchange molecular dynamics study of the 10-35 fragment of Alzheimer's disease amyloid β peptide, Aβ10-35, in aqueous solution. This fragment was previously seen [J. Str. Biol. 130 (2000) 130] to possess all the most important amyloidogenic properties characteristic of full-length Aβ peptides. Our simulations attempted to fold Aβ10-35 from first principles. The peptide was modeled using all-atom OPLS/AA force field in conjunction with the TIP3P explicit solvent model. A total of 72 replicas were considered and simulated over 40 ns of total time, including 5 ns of initial equilibration. We find that Aβ10-35 does not possess any unique folded state, a 3D structure of predominant population, under normal temperature and pressure. Rather, this peptide exists as a mixture of collapsed globular states that remain in rapid dynamic equilibrium with each other. This conformational ensemble is seen to be dominated by random coil and bend structures with insignificant presence of α-helical or β-sheet structure. We find that, overall, the 3D structure of Aβ10-35 is shaped by salt bridges formed between oppositely charged residues.Of all possible salt bridges, K28-D23 was seen to have the highest formation probability, totaling more than 60% of the time.

A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations

NASA Astrophysics Data System (ADS)

Jo, Sunhwan; Jiang, Wei

2015-12-01

Replica Exchange with Solute Tempering (REST2) is a powerful sampling enhancement algorithm of molecular dynamics (MD) in that it needs significantly smaller number of replicas but achieves higher sampling efficiency relative to standard temperature exchange algorithm. In this paper, we extend the applicability of REST2 for quantitative biophysical simulations through a robust and generic implementation in greatly scalable MD software NAMD. The rescaling procedure of force field parameters controlling REST2 "hot region" is implemented into NAMD at the source code level. A user can conveniently select hot region through VMD and write the selection information into a PDB file. The rescaling keyword/parameter is written in NAMD Tcl script interface that enables an on-the-fly simulation parameter change. Our implementation of REST2 is within communication-enabled Tcl script built on top of Charm++, thus communication overhead of an exchange attempt is vanishingly small. Such a generic implementation facilitates seamless cooperation between REST2 and other modules of NAMD to provide enhanced sampling for complex biomolecular simulations. Three challenging applications including native REST2 simulation for peptide folding-unfolding transition, free energy perturbation/REST2 for absolute binding affinity of protein-ligand complex and umbrella sampling/REST2 Hamiltonian exchange for free energy landscape calculation were carried out on IBM Blue Gene/Q supercomputer to demonstrate efficacy of REST2 based on the present implementation.

Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach.

PubMed

Curuksu, Jeremy; Zacharias, Martin

2009-03-14

Although molecular dynamics (MD) simulations have been applied frequently to study flexible molecules, the sampling of conformational states separated by barriers is limited due to currently possible simulation time scales. Replica-exchange (Rex)MD simulations that allow for exchanges between simulations performed at different temperatures (T-RexMD) can achieve improved conformational sampling. However, in the case of T-RexMD the computational demand grows rapidly with system size. A Hamiltonian RexMD method that specifically enhances coupled dihedral angle transitions has been developed. The method employs added biasing potentials as replica parameters that destabilize available dihedral substates and was applied to study coupled dihedral transitions in nucleic acid molecules. The biasing potentials can be either fixed at the beginning of the simulation or optimized during an equilibration phase. The method was extensively tested and compared to conventional MD simulations and T-RexMD simulations on an adenine dinucleotide system and on a DNA abasic site. The biasing potential RexMD method showed improved sampling of conformational substates compared to conventional MD simulations similar to T-RexMD simulations but at a fraction of the computational demand. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions including explicit solvent and ions and can be easily extended to other types of molecules.

Precision of Fit of Titanium and Cast Implant Frameworks Using a New Matching Formula

PubMed Central

Sierraalta, Marianella; Vivas, Jose L.; Razzoog, Michael E.; Wang, Rui-Feng

2012-01-01

Statement of the Problem. Fit of prosthodontic frameworks is linked to the lifetime survival of dental implants and maintenance of surrounding bone. Purpose. The purpose of this study was to evaluate and compare the precision of fit of milled one-piece Titanium fixed complete denture frameworks to that of conventional cast frameworks. Material and Methods. Fifteen casts fabricated from a single edentulous CAD/CAM surgical guide were separated in two groups and resin patterns simulating the framework for a fixed complete denture developed. Five casts were sent to dental laboratories to invest, cast in a Palladium-Gold alloy and fit the framework. Ten casts had the resin pattern scanned for fabrication of milled bars in Titanium. Using measuring software, positions of implant replicas in the definitive model were recorded. The three dimensional spatial orientation of each implant replica was matched to the implant replica. Results. Results demonstrated the mean vertical gap of the Cast framework was 0.021 (+0.004) mm and 0.012 (0.002) mm determined by fixed and unfixed best-fit matching coordinate system. For Titanium frameworks they were 0.0037 (+0.0028) mm and 0.0024 (+0.0005) mm, respectively. Conclusions. Milled one-piece Titanium fixed complete denture frameworks provided a more accurate precision of fit then traditional cast frameworks. PMID:22550486

Cloning

MedlinePlus

Cloning describes the processes used to create an exact genetic replica of another cell, tissue or organism. ... named Dolly. There are three different types of cloning: Gene cloning, which creates copies of genes or ...

Neutron and gamma-ray dose measurements at various distances from the Little Boy replica

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

Huntzinger, C.J.; Hankins, D.E.

We measured neutron and gamma-ray dose rates at various distances from the Little Boy-Comet Critical Assembly at Los Alamos National Laboratory (LANL) in April of 1983. The Little Boy-Comet Assembly is a replica of the atomic weapon detonated over Hiroshima, designed to be operated at various steady-state power levels. The selected distances for measurement ranged from 107 m to 567 m. Gamma-ray measurements were made with a Reuter-Stokes environmental ionization chamber which has a sensitivity of 1.0 ..mu..R/hour. Neutron measurements were made with a pulsed-source remmeter which has a sensitivity of 0.1 ..mu..rem/hour, designed and built at Lawrence Livermore Nationalmore » Laboratory (LLNL). 12 references, 7 figures, 6 tables.« less

Hot-embossing replication of self-centering optical fiber alignment structures prototyped by deep proton writing

NASA Astrophysics Data System (ADS)

Ebraert, Evert; Wissmann, Markus; Guttmann, Markus; Kolew, Alexander; Worgull, Matthias; Barié, Nicole; Schneider, Marc; Hofmann, Andreas; Beri, Stefano; Watté, Jan; Thienpont, Hugo; Van Erps, Jürgen

2016-07-01

This paper presents the hot-embossing replication of self-centering fiber alignment structures for high-precision, single-mode optical fiber connectors. To this end, a metal mold insert was fabricated by electroforming a polymer prototype patterned by means of deep proton writing (DPW). To achieve through-hole structures, we developed a postembossing process step to remove the residual layer inherently present in hot-embossed structures. The geometrical characteristics of the hot-embossed replicas are compared, before and after removal of the residual layer, with the DPW prototypes. Initial measurements on the optical performance of the replicas are performed. The successful replication of these components paves the way toward low-cost mass replication of DPW-fabricated prototypes in a variety of high-tech plastics.

SEM/EDX and vis spectrophotometry study of the stability of resin-bound mortars used for casting replicas and filling missing parts of historic stone fountains.

PubMed

Roig-Salom, José-Luis; Doménech-Carbó, María-Teresa; de la Cruz-Cañizares, Juana; Bolívar-Galiano, Fernando; Pelufo-Carbonell, María-José; Peraza-Zurita, Yaiza

2003-04-01

A study by SEM/EDX and spectrophotometry in the visible region attempting to assess the stability of new resin-bound mortars used for casting replicas of marble historic fountains is presented in this paper. Different accelerating tests such as thermal ageing, UV light ageing, ageing in an SO(2) pollutant chamber, freezing cycles ageing, salt crystallisation ageing, natural ageing and biological attack have been applied to a series of test specimens prepared with polyester-, epoxy- and gel-coat-bound mortars. Examination of morphology, measurement of chemical composition and chromatic coordinates before and after ageing treatments establish the higher stability and resistance properties of these resin-bound mortars by comparison to those from the natural marbles.

Maximizing and minimizing investment concentration with constraints of budget and investment risk

NASA Astrophysics Data System (ADS)

Shinzato, Takashi

2018-01-01

In this paper, as a first step in examining the properties of a feasible portfolio subset that is characterized by budget and risk constraints, we assess the maximum and minimum of the investment concentration using replica analysis. To do this, we apply an analytical approach of statistical mechanics. We note that the optimization problem considered in this paper is the dual problem of the portfolio optimization problem discussed in the literature, and we verify that these optimal solutions are also dual. We also present numerical experiments, in which we use the method of steepest descent that is based on Lagrange's method of undetermined multipliers, and we compare the numerical results to those obtained by replica analysis in order to assess the effectiveness of our proposed approach.

Stability of the Mézard-Parisi Solution for Random Manifolds

NASA Astrophysics Data System (ADS)

Carlucci, D. M.; de Dominicis, C.; Temesvari, T.

1996-08-01

The eigenvalues of the Hessian associated with random manifolds are constructed for the general case of R steps of replica symmetry breaking. For the Parisi limit Rrightarrow infty (continuum replica symmetry breaking) which is relevant for the manifold dimension D<2, they are shown to be non negative. Les valeurs propres de la hessienne, associée avec une variété aléatoire, sont construites dans le cas général de R étapes de brisure de la symétrie des répliques. Dans la limite de Parisi, Rrightarrow infty (brisure continue de la symétrie des répliques) qui est pertinente pour la dimension de la variété D<2, on montre qu'elles sont non négatives.

Acousto-optic replication of ultrashort laser pulses

NASA Astrophysics Data System (ADS)

Yushkov, Konstantin B.; Molchanov, Vladimir Ya.; Ovchinnikov, Andrey V.; Chefonov, Oleg V.

2017-10-01

Precisely controlled sequences of ultrashort laser pulses are required in various scientific and engineering applications. We developed a phase-only acousto-optic pulse shaping method for replication of ultrashort laser pulses in a TW laser system. A sequence of several Fourier-transform-limited pulses is generated from a single femtosecond laser pulse by means of applying a piecewise linear phase modulation over the whole emission spectrum. Analysis demonstrates that the main factor which limits maximum delay between the pulse replicas is spectral resolution of the acousto-optic dispersive delay line used for pulse shaping. In experiments with a Cr:forsterite laser system, we obtained delays from 0.3 to 3.5 ps between two replicas of 190 fs transform-limited pulses at the central wavelength of laser emission, 1230 nm.

Resonant and Inelastic Andreev Tunneling Observed on a Carbon Nanotube Quantum Dot.

PubMed

Gramich, J; Baumgartner, A; Schönenberger, C

2015-11-20

We report the observation of two fundamental subgap transport processes through a quantum dot (QD) with a superconducting contact. The device consists of a carbon nanotube contacted by a Nb superconducting and a normal metal contact. First, we find a single resonance with position, shape, and amplitude consistent with the theoretically predicted resonant Andreev tunneling (AT) through a single QD level. Second, we observe a series of discrete replicas of resonant AT at a separation of ~145 μeV, with a gate, bias, and temperature dependence characteristic for boson-assisted, inelastic AT, in which energy is exchanged between a bosonic bath and the electrons. The magnetic field dependence of the replica's amplitudes and energies suggest that two different bosons couple to the tunnel process.

A practical guide to replica-exchange Wang—Landau simulations

NASA Astrophysics Data System (ADS)

Vogel, Thomas; Li, Ying Wai; Landau, David P.

2018-04-01

This paper is based on a series of tutorial lectures about the replica-exchange Wang-Landau (REWL) method given at the IX Brazilian Meeting on Simulational Physics (BMSP 2017). It provides a practical guide for the implementation of the method. A complete example code for a model system is available online. In this paper, we discuss the main parallel features of this code after a brief introduction to the REWL algorithm. The tutorial section is mainly directed at users who have written a single-walker Wang–Landau program already but might have just taken their first steps in parallel programming using the Message Passing Interface (MPI). In the last section, we answer “frequently asked questions” from users about the implementation of REWL for different scientific problems.

A prospective study of anti-aging topical therapies using a quantitative method of assessment.

PubMed

Rubino, Corrado; Farace, Francesco; Dessy, Luca A; Sanna, Marco P G; Mazzarello, Vittorio

2005-04-01

In the treatment of photoaged skin, glycolic acid works by removing superficial portions of the epidermis and stimulating dermis regeneration. Vitamins A, C, and E should stimulate collagen production and antioxidants should prevent free radical damage and skin aging. However, the effectiveness of different therapies has often relied on subjective methods of assessment. Histologic analysis has seldom been used because of the drawback of permanent scarring. In the literature, the use of a quantitative method for the assessment of facial rejuvenation has been described: the silicone replica technique. The authors' aim was to promote and recommend the use of this technique and, in particular, to test the effect of glycolic acid and multivitamin- and antioxidant-based products on skin texture. The authors performed a prospective, randomized, double-blind, controlled study on 30 women treated topically in the outer canthal region (crow's-feet area). Patients were divided into three groups (groups A, B, and C); each group consisted of five patients between the ages of 31 and 40 years and five patients between the ages of 41 and 50 years. Group A was treated by glycolic acid application, initially at home for 2 weeks, followed by a higher concentration administered in the office weekly for six applications. Group B was treated by topical application at home of a multivitamin product daily for 3 months. Group C was treated with a cream base (placebo) for 3 months and represented the control group. Skin areas under treatment were photographed and reproduced by the silicone replica technique at baseline and at the end of treatment. This technique reproduces exactly the skin's texture. Digital images were obtained from skin replicas and analyzed by specific software for different parameters: roughness, microsulcus number, and width. Pretreatment and posttreatment values were compared using the Wilcoxon signed-rank test. In group A, microsulcus number and width were statistically decreased, but roughness was not. In groups B and C, parameters were not statistically modified. The silicone replica technique allowed a quantitative analysis of results obtained with different topical therapies. In particular, it confirmed the efficacy of glycolic acid in skin rejuvenation.

The Construction and Validation of All-Atom Bulk-Phase Models of Amorphous Polymers Using the TIGER2/TIGER3 Empirical Sampling Method

PubMed Central

Li, Xianfeng; Murthy, Sanjeeva; Latour, Robert A.

2011-01-01

A new empirical sampling method termed “temperature intervals with global exchange of replicas and reduced radii” (TIGER3) is presented and demonstrated to efficiently equilibrate entangled long-chain molecular systems such as amorphous polymers. The TIGER3 algorithm is a replica exchange method in which simulations are run in parallel over a range of temperature levels at and above a designated baseline temperature. The replicas sampled at temperature levels above the baseline are run through a series of cycles with each cycle containing four stages – heating, sampling, quenching, and temperature level reassignment. The method allows chain segments to pass through one another at elevated temperature levels during the sampling stage by reducing the van der Waals radii of the atoms, thus eliminating chain entanglement problems. Atomic radii are then returned to their regular values and re-equilibrated at elevated temperature prior to quenching to the baseline temperature. Following quenching, replicas are compared using a Metropolis Monte Carlo exchange process for the construction of an approximate Boltzmann-weighted ensemble of states and then reassigned to the elevated temperature levels for additional sampling. Further system equilibration is performed by periodic implementation of the previously developed TIGER2 algorithm between cycles of TIGER3, which applies thermal cycling without radii reduction. When coupled with a coarse-grained modeling approach, the combined TIGER2/TIGER3 algorithm yields fast equilibration of bulk-phase models of amorphous polymer, even for polymers with complex, highly branched structures. The developed method was tested by modeling the polyethylene melt. The calculated properties of chain conformation and chain segment packing agreed well with published data. The method was also applied to generate equilibrated structural models of three increasingly complex amorphous polymer systems: poly(methyl methacrylate), poly(butyl methacrylate), and DTB-succinate copolymer. Calculated glass transition temperature (Tg) and structural parameter profile (S(q)) for each resulting polymer model were found to be in close agreement with experimental Tg values and structural measurements obtained by x-ray diffraction, thus validating that the developed methods provide realistic models of amorphous polymer structure. PMID:21769156

Strategic planning toolset for reproduction of machinebuilding engines and equipment

NASA Astrophysics Data System (ADS)

Boyko, A. A.; Kukartsev, V. V.; Lobkov, K. Y.; Stupina, A. A.

2018-05-01

This article illustrates a replica of a dynamic model of machine-building equipment. The model was designed on the basis of a ‘system dynamics method’ including the Powersim Studio toolset. The given model provides the basis and delineates the reproduction process of equipment in its natural as well as appraisal forms. The presented model was employed as a tool to explore reproduction of a wide range of engines and equipment in machine-building industry. As a result of these experiments, a variety of reproducible options were revealed which include productive capacity and distribution of equipment among technology groups. The authors’ research concludes that the replica of the dynamic model designed by us has proved to be universal. This also opens the way for further research exploring a wide range of industrial equipment reproduction.

Finite temperature properties of clusters by replica exchange metadynamics: the water nonamer.

PubMed

Zhai, Yingteng; Laio, Alessandro; Tosatti, Erio; Gong, Xin-Gao

2011-03-02

We introduce an approach for the accurate calculation of thermal properties of classical nanoclusters. On the basis of a recently developed enhanced sampling technique, replica exchange metadynamics, the method yields the true free energy of each relevant cluster structure, directly sampling its basin and measuring its occupancy in full equilibrium. All entropy sources, whether vibrational, rotational anharmonic, or especially configurational, the latter often forgotten in many cluster studies, are automatically included. For the present demonstration, we choose the water nonamer (H(2)O)(9), an extremely simple cluster, which nonetheless displays a sufficient complexity and interesting physics in its relevant structure spectrum. Within a standard TIP4P potential description of water, we find that the nonamer second relevant structure possesses a higher configurational entropy than the first, so that the two free energies surprisingly cross for increasing temperature.

Finite Temperature Properties of Clusters by Replica Exchange Metadynamics: The Water Nonamer

NASA Astrophysics Data System (ADS)

Zhai, Yingteng; Laio, Alessandro; Tosatti, Erio; Gong, Xingao

2012-02-01

We introduce an approach for the accurate calculation of thermal properties of classical nanoclusters. Based on a recently developed enhanced sampling technique, replica exchange metadynamics, the method yields the true free energy of each relevant cluster structure, directly sampling its basin and measuring its occupancy in full equilibrium. All entropy sources, whether vibrational, rotational anharmonic and especially configurational -- the latter often forgotten in many cluster studies -- are automatically included. For the present demonstration we choose the water nonamer (H2O)9, an extremely simple cluster which nonetheless displays a sufficient complexity and interesting physics in its relevant structure spectrum. Within a standard TIP4P potential description of water, we find that the nonamer second relevant structure possesses a higher configurational entropy than the first, so that the two free energies surprisingly cross for increasing temperature.

Domestic dogs comprehend human communication with iconic signs.

PubMed

Kaminski, Juliane; Tempelmann, Sebastian; Call, Josep; Tomasello, Michael

2009-11-01

A key skill in early human development is the ability to comprehend communicative intentions as expressed in both nonlinguistic gestures and language. In the current studies, we confronted domestic dogs (some of whom knew many human 'words') with a task in which they had to infer the intended referent of a human's communicative act via iconic signs--specifically, replicas and photographs. Both trained and untrained dogs successfully used iconic replicas to fetch the desired item, with many doing so from the first trial. Dogs' ability to use photographs in this same situation was less consistent. Because simple matching to sample in experimental contexts typically takes hundreds of trials (and because similarity between iconic sign and target item did not predict success), we propose that dogs' skillful performance in the current task reflects important aspects of the comprehension of human communicative intentions.

An application of computer image-processing and filmy replica technique to the copper electroplating method of stress analysis

NASA Astrophysics Data System (ADS)

Sugiura, M.; Seika, M.

1994-02-01

In this study, a new technique to measure the density of slip-bands automatically is developed, namely, a TV image of the slip-bands observed through a microscope is directly processed by an image-processing system using a personal computer and an accurate value of the density of slip-bands is measured quickly. In the case of measuring the local stresses in machine parts of large size with the copper plating foil, the direct observation of slip-bands through an optical microscope is difficult. In this study, to facilitate a technique close to the direct microscopic observation of slip-bands in the foil attached to a large-sized specimen, the replica method using a platic film of acetyl cellulose is applied to replicate the slip-bands in the attached foil.

The Law of Self-Acting Machines and Irreversible Processes with Reversible Replicas

NASA Astrophysics Data System (ADS)

Valev, Pentcho

2002-11-01

Clausius and Kelvin saved Carnot theorem and developed the second law by assuming that Carnot machines can work in the absence of an operator and that all the irreversible processes have reversible replicas. The former assumption restored Carnot theorem as an experience of mankind whereas the latter generated "the law of ever increasing entropy". Both assumptions are wrong so it makes sense to return to Carnot theorem (or some equivalent) and test it experimentally. Two testable paradigms - the system performing two types of reversible work and the system in dynamical equilibrium - suggest that perpetuum mobile of the second kind in the presence of an operator is possible. The deviation from the second law prediction, expressed as difference between partial derivatives in a Maxwell relation, measures the degree of structural-functional evolution for the respective system.

Investigation of correlation between full-scale and fifth-scale wind tunnel tests of a Bell helicopter Textron Model 222

NASA Technical Reports Server (NTRS)

Squires, P. K.

1982-01-01

Reasons for lack of correlation between data from a fifth-scale wind tunnel test of the Bell Helicopter Textron Model 222 and a full-scale test of the model 222 prototype in the NASA Ames 40-by 80-foot tunnel were investigated. This investigation centered around a carefully designed fifth-scale wind tunnel test of an accurately contoured model of the Model 222 prototype mounted on a replica of the full-scale mounting system. The improvement in correlation for drag characteristics in pitch and yaw with the fifth-scale model mounted on the replica system is shown. Interference between the model and mounting system was identified as a significant effect and was concluded to be a primary cause of the lack of correlation in the earlier tests.

Multiband full-bandwidth anisotropic Eliashberg theory of interfacial electron-phonon coupling and high - Tc superconductivity in FeSe /SrTiO3

NASA Astrophysics Data System (ADS)

Aperis, Alex; Oppeneer, Peter M.

2018-02-01

We examine the impact of interfacial phonons on the superconducting state of FeSe /SrTiO3 developing a material's specific multiband, full bandwidth, and anisotropic Eliashberg theory for this system. Our self-consistent calculations highlight the importance of the interfacial electron-phonon interaction, which is hidden behind the seemingly weak-coupling constant λm=0.4 , in mediating the high Tc, and explain other puzzling experimental observations, such as the s -wave symmetry and replica bands. We discover that the formation of replica bands has a Tc decreasing effect that is nevertheless compensated by deep Fermi-sea Cooper pairing which has a Tc enhancing effect. We predict a strong-coupling dip-hump signature in the tunneling spectra due to the interfacial coupling.

L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib† †Electronic supplementary information (ESI) available: pKa shift for Cys797; geometries of TSs identified with QM/MM calculations; analysis of the minimum free-energy path for Cys797 alkylation; analysis of MD replicas; convergence for US simulations; replica of simulation of Cys797 alkylation; conformational FESs obtained from each MD replica. See DOI: 10.1039/c7sc04761d

PubMed Central

Callegari, D.; Ranaghan, K. E.; Woods, C. J.; Minari, R.; Tiseo, M.; Mor, M.; Mulholland, A. J.

2018-01-01

Osimertinib is a third-generation inhibitor approved for the treatment of non-small cell lung cancer. It overcomes resistance to first-generation inhibitors by incorporating an acrylamide group which alkylates Cys797 of EGFR T790M. The mutation of a residue in the P-loop (L718Q) was shown to cause resistance to osimertinib, but the molecular mechanism of this process is unknown. Here, we investigated the inhibitory process for EGFR T790M (susceptible to osimertinib) and EGFR T790M/L718Q (resistant to osimertinib), by modelling the chemical step (i.e., alkylation of Cys797) using QM/MM simulations and the recognition step by MD simulations coupled with free-energy calculations. The calculations indicate that L718Q has a negligible impact on both the activation energy for Cys797 alkylation and the free-energy of binding for the formation of the non-covalent complex. The results show that Gln718 affects the conformational space of the EGFR–osimertinib complex, stabilizing a conformation of acrylamide which prevents reaction with Cys797. PMID:29732058

Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation.

PubMed

Sidler, Dominik; Schwaninger, Arthur; Riniker, Sereina

2016-10-21

In molecular dynamics (MD) simulations, free-energy differences are often calculated using free energy perturbation or thermodynamic integration (TI) methods. However, both techniques are only suited to calculate free-energy differences between two end states. Enveloping distribution sampling (EDS) presents an attractive alternative that allows to calculate multiple free-energy differences in a single simulation. In EDS, a reference state is simulated which "envelopes" the end states. The challenge of this methodology is the determination of optimal reference-state parameters to ensure equal sampling of all end states. Currently, the automatic determination of the reference-state parameters for multiple end states is an unsolved issue that limits the application of the methodology. To resolve this, we have generalised the replica-exchange EDS (RE-EDS) approach, introduced by Lee et al. [J. Chem. Theory Comput. 10, 2738 (2014)] for constant-pH MD simulations. By exchanging configurations between replicas with different reference-state parameters, the complexity of the parameter-choice problem can be substantially reduced. A new robust scheme to estimate the reference-state parameters from a short initial RE-EDS simulation with default parameters was developed, which allowed the calculation of 36 free-energy differences between nine small-molecule inhibitors of phenylethanolamine N-methyltransferase from a single simulation. The resulting free-energy differences were in excellent agreement with values obtained previously by TI and two-state EDS simulations.

Unlearning of Mixed States in the Hopfield Model —Extensive Loading Case—

NASA Astrophysics Data System (ADS)

Hayashi, Kao; Hashimoto, Chinami; Kimoto, Tomoyuki; Uezu, Tatsuya

2018-05-01

We study the unlearning of mixed states in the Hopfield model for the extensive loading case. Firstly, we focus on case I, where several embedded patterns are correlated with each other, whereas the rest are uncorrelated. Secondly, we study case II, where patterns are divided into clusters in such a way that patterns in any cluster are correlated but those in two different clusters are not correlated. By using the replica method, we derive the saddle point equations for order parameters under the ansatz of replica symmetry. The same equations are also derived by self-consistent signal-to-noise analysis in case I. In both cases I and II, we find that when the correlation between patterns is large, the network loses its ability to retrieve the embedded patterns and, depending on the parameters, a confused memory, which is a mixed state and/or spin glass state, emerges. By unlearning the mixed state, the network acquires the ability to retrieve the embedded patterns again in some parameter regions. We find that to delete the mixed state and to retrieve the embedded patterns, the coefficient of unlearning should be chosen appropriately. We perform Markov chain Monte Carlo simulations and find that the simulation and theoretical results agree reasonably well, except for the spin glass solution in a parameter region due to the replica symmetry breaking. Furthermore, we find that the existence of many correlated clusters reduces the stabilities of both embedded patterns and mixed states.

Novel approach to the fabrication of an artificial small bone using a combination of sponge replica and electrospinning methods

NASA Astrophysics Data System (ADS)

Kim, Yang-Hee; Lee, Byong-Taek

2011-06-01

In this study, a novel artificial small bone consisting of ZrO2-biphasic calcium phosphate/polymethylmethacrylate-polycaprolactone-hydroxyapatite (ZrO2-BCP/PMMA-PCL-HAp) was fabricated using a combination of sponge replica and electrospinning methods. To mimic the cancellous bone, the ZrO2/BCP scaffold was composed of three layers, ZrO2, ZrO2/BCP and BCP, fabricated by the sponge replica method. The PMMA-PCL fibers loaded with HAp powder were wrapped around the ZrO2/BCP scaffold using the electrospinning process. To imitate the Haversian canal region of the bone, HAp-loaded PMMA-PCL fibers were wrapped around a steel wire of 0.3 mm diameter. As a result, the bundles of fiber wrapped around the wires imitated the osteon structure of the cortical bone. Finally, the ZrO2/BCP scaffold was surrounded by HAp-loaded PMMA-PCL composite bundles. After removal of the steel wires, the ZrO2/BCP scaffold and bundles of HAp-loaded PMMA-PCL formed an interconnected structure resembling the human bone. Its diameter, compressive strength and porosity were approximately 12 mm, 5 MPa and 70%, respectively, and the viability of MG-63 osteoblast-like cells was determined to be over 90% by the MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assay. This artificial bone shows excellent cytocompatibility and is a promising bone regeneration material.

Novel approach to the fabrication of an artificial small bone using a combination of sponge replica and electrospinning methods

PubMed Central

Kim, Yang-Hee; Lee, Byong-Taek

2011-01-01

In this study, a novel artificial small bone consisting of ZrO2-biphasic calcium phosphate/polymethylmethacrylate-polycaprolactone-hydroxyapatite (ZrO2-BCP/PMMA-PCL-HAp) was fabricated using a combination of sponge replica and electrospinning methods. To mimic the cancellous bone, the ZrO2/BCP scaffold was composed of three layers, ZrO2, ZrO2/BCP and BCP, fabricated by the sponge replica method. The PMMA-PCL fibers loaded with HAp powder were wrapped around the ZrO2/BCP scaffold using the electrospinning process. To imitate the Haversian canal region of the bone, HAp-loaded PMMA-PCL fibers were wrapped around a steel wire of 0.3 mm diameter. As a result, the bundles of fiber wrapped around the wires imitated the osteon structure of the cortical bone. Finally, the ZrO2/BCP scaffold was surrounded by HAp-loaded PMMA-PCL composite bundles. After removal of the steel wires, the ZrO2/BCP scaffold and bundles of HAp-loaded PMMA-PCL formed an interconnected structure resembling the human bone. Its diameter, compressive strength and porosity were approximately 12 mm, 5 MPa and 70%, respectively, and the viability of MG-63 osteoblast-like cells was determined to be over 90% by the MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assay. This artificial bone shows excellent cytocompatibility and is a promising bone regeneration material. PMID:27877406

Evaluation of the marginal and internal gaps of three different dental prostheses: comparison of the silicone replica technique and three-dimensional superimposition analysis

PubMed Central

2017-01-01

PURPOSE The purposes of this study were to evaluate the marginal and internal gaps, and the potential clinical applications of three different methods of dental prostheses fabrication, and to compare the prostheses prepared using the silicone replica technique (SRT) and those prepared using the three-dimensional superimposition analysis (3DSA). MATERIALS AND METHODS Five Pekkton, lithium disilicate, and zirconia crowns were each manufactured and tested using both the SRT and the two-dimensional section of the 3DSA. The data were analyzed with the nonparametric version of a two-way analysis of variance using rank-transformed values and the Tukey's post-hoc test (α = .05). RESULTS Significant differences were observed between the fabrication methods in the marginal gap (P < .010), deep chamfer (P < .001), axial wall (P < .001), and occlusal area (P < .001). A significant difference in the occlusal area was found between the two measurement methods (P < .030), whereas no significant differences were found in the marginal gap (P > .350), deep chamfer (P > .719), and axial wall (P > .150). As the 3DSA method is three-dimensional, it allows for the measurement of arbitrary points. CONCLUSION All of the three fabrication methods are valid for measuring clinical objectives because they produced prostheses within the clinically acceptable range. Furthermore, a three-dimensional superimposition analysis verification method such as the silicone replica technique is also applicable in clinical settings. PMID:28680546

Ferromagnetic transition in a simple variant of the Ising model on multiplex networks

NASA Astrophysics Data System (ADS)

Krawiecki, A.

2018-02-01

Multiplex networks consist of a fixed set of nodes connected by several sets of edges which are generated separately and correspond to different networks ("layers"). Here, a simple variant of the Ising model on multiplex networks with two layers is considered, with spins located in the nodes and edges corresponding to ferromagnetic interactions between them. Critical temperatures for the ferromagnetic transition are evaluated for the layers in the form of random Erdös-Rényi graphs or heterogeneous scale-free networks using the mean-field approximation and the replica method, from the replica symmetric solution. Both methods require the use of different "partial" magnetizations, associated with different layers of the multiplex network, and yield qualitatively similar results. If the layers are strongly heterogeneous the critical temperature differs noticeably from that for the Ising model on a network being a superposition of the two layers, evaluated in the mean-field approximation neglecting the effect of the underlying multiplex structure on the correlations between the degrees of nodes. The critical temperature evaluated from the replica symmetric solution depends sensitively on the correlations between the degrees of nodes in different layers and shows satisfactory quantitative agreement with that obtained from Monte Carlo simulations. The critical behavior of the magnetization for the model with strongly heterogeneous layers can depend on the distributions of the degrees of nodes and is then determined by the properties of the most heterogeneous layer.

Characterisation of oil and aluminium complex on replica and historical 19th c. Turkey red textiles by non-destructive diffuse reflectance FTIR spectroscopy.

PubMed

Wertz, Julie H; Tang, Pik Leung; Quye, Anita; France, David J

2018-06-11

This work investigates historical and replica Turkey red textiles with diffuse reflectance infrared (DRIFT) spectroscopy to study the coordination complex between cellulose, fatty acids, and the aluminium ions that form the basis of the colour lake. Turkey red was produced in Scotland for around 150 years, and is held in many museum and archive collections. The textile was renowned for its brilliant red hue, and for its fastness to light, washing, rubbing, and bleaching. This was attributed to its unusual preparatory process, the chemistry of which was never fully understood, that involved imbuing cotton with a solution of aqueous fatty acids and then aluminium in the following step. Here we show, for the first time, a characterisation of the Turkey red complex on replica and historical textiles. The development of techniques for non-destructive and in situ analysis of historical textiles is valuable for improving understanding of their chemistry, hopefully contributing to better conservation and display practices. The results show the fatty acids condense onto the cellulose polymer via hydrogen bonding between the CO and OH of the respective compounds, then the aluminium forms a bridging complex with the fatty acid carboxyl. This contributes to an improved understanding of Turkey red textiles, and shows the useful application of handheld diffuse FTIR instruments for heritage textile research. Copyright © 2018. Published by Elsevier B.V.

78 FR 22364 - Petition for Waiver of Compliance

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-15

... petition, is a replica of Union Pacific 119, which was constructed in 1979 from the same blueprints and... U.S. National Park Service at the Golden Spike National Historic Site in Promontory Summit, UT...

Space Shuttle Project

NASA Image and Video Library

1992-10-15

On the 500th arniversary of Christopher Columbus' discovery of the New World, replicas of his three ships sailed past the launch pad at the Kennedy Space Center (KSC) while the space shuttle Columbia sat poised for lift off.

75 FR 30300 - Restricting the Mailing of Replica or Inert Explosive Devices

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-01

... not dangerous but bear a realistic appearance to explosive devices, to Registered Mail\\TM\\ service... explosive devices such as simulated grenades, but that are not dangerous, are permitted in the mail when all...

75 FR 282 - Restricting the Mailing of Replica or Inert Explosive Devices

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-05

... commitments. We believe this revised proposed rule will minimize the chances of operational disruptions caused... occurrences. Comment: The proposal is in violation of the Second Amendment. We no longer propose to prohibit...

Growth on solid media.

PubMed

Elbing, Karen; Brent, Roger

2002-08-01

Detailed protocols are provided for titering and isolating bacterial colonies by serial dilutions, or alternatively by streaking or spreading a plate. Support protocols describe replica plating as well as methods for storing strains as agar stabs or frozen glycerol stocks.

Label free biosensor incorporating a replica-molded, vertically emitting distributed feedback laser

NASA Astrophysics Data System (ADS)

Lu, M.; Choi, S. S.; Wagner, C. J.; Eden, J. G.; Cunningham, B. T.

2008-06-01

A label free biosensor based upon a vertically emitting distributed feedback (DFB) laser has been demonstrated. The DFB laser comprises a replica-molded, one-dimensional dielectric grating coated with laser dye-doped polymer as the gain medium. Adsorption of biomolecules onto the laser surface alters the DFB laser emission wavelength, thereby permitting the kinetic adsorption of a protein polymer monolayer or the specific binding of small molecules to be quantified. A bulk sensitivity of 16.6nm per refractive index unit and the detection of a monolayer of the protein polymer poly(Lys, Phe) have been observed with this biosensor. The sensor represents a departure from conventional passive resonant optical sensors from the standpoint that the device actively generates its own narrowband high intensity output without stringent requirements on the coupling alignments, resulting in a simple, robust illumination and detection configuration.

Renormalization of entanglement entropy from topological terms

NASA Astrophysics Data System (ADS)

Anastasiou, Giorgos; Araya, Ignacio J.; Olea, Rodrigo

2018-05-01

We propose a renormalization scheme for entanglement entropy of three-dimensional CFTs with a four-dimensional asymptotically AdS gravity dual in the context of the gauge/gravity correspondence. The procedure consists in adding the Chern form as a boundary term to the area functional of the Ryu-Takayanagi minimal surface. We provide an explicit prescription for the renormalized entanglement entropy, which is derived via the replica trick. This is achieved by considering a Euclidean gravitational action renormalized by the addition of the Chern form at the spacetime boundary, evaluated in the conically-singular replica manifold. We show that the addition of this boundary term cancels the divergent part of the entanglement entropy, recovering the results obtained by Taylor and Woodhead. We comment on how this prescription for renormalizing the entanglement entropy is in line with the general program of topological renormalization in asymptotically AdS gravity.

The 2003 Goddard Rocket Replica Project: A Reconstruction of the World's First Functional Liquid Rocket System

NASA Technical Reports Server (NTRS)

Farr, R. A.; Elam, S. K.; Hicks, G. D.; Sanders, T. M.; London, J. R.; Mayne, A. W.; Christensen, D. L.

2003-01-01

As a part of NASA s 2003 Centennial of Flight celebration, engineers and technicians at Marshall Space Flight Center (MSFC), Huntsville, Alabama, in cooperation with the Alabama-Mississippi AIAA Section, have reconstructed historically accurate, functional replicas of Dr. Robert H. Goddard s 1926 first liquid- fuel rocket. The purposes of this project were to clearly understand, recreate, and document the mechanisms and workings of the 1926 rocket for exhibit and educational use, creating a vital resource for researchers studying the evolution of liquid rocketry for years to come. The MSFC team s reverse engineering activity has created detailed engineering-quality drawings and specifications describing the original rocket and how it was built, tested, and operated. Static hot-fire tests, as well as flight demonstrations, have further defined and quantified the actual performance and engineering actual performance and engineering challenges of this major segment in early aerospace history.

Magneto-optical far-infrared absorption spectroscopy of the hole states of indium phosphide

NASA Astrophysics Data System (ADS)

Lewis, R. A.; Wang, Y.-J.

2005-03-01

Far-infrared absorption spectroscopy in magnetic fields of up to 30 T of the zinc acceptor impurity in indium phosphide has revealed for the first time a series of free-hole transitions (Landau-related series) in addition to the familiar bound-hole transitions (Lyman series) as well as hitherto unobserved phonon replicas of both series. Analysis of these data permits the simultaneous direct experimental determination of (i) the hole effective mass, (ii) the species-specific binding energy of the acceptor impurity, (iii) the absolute energy levels of the acceptor excited states of both odd and even parity, (iv) more reliable, and in some cases the only, g factors for acceptor states, through relaxation of the selection rules for phonon replicas, and (v) the LO phonon energy. The method is applicable to other semiconductors and may lead to the reappraisal of their physical parameters.

Stability of the quantum Sherrington-Kirkpatrick spin glass model

NASA Astrophysics Data System (ADS)

Young, A. P.

2017-09-01

I study in detail the quantum Sherrington-Kirkpatrick (SK) model, i.e., the infinite-range Ising spin glass in a transverse field, by solving numerically the effective one-dimensional model that the quantum SK model can be mapped to in the thermodynamic limit. I find that the replica symmetric solution is unstable down to zero temperature, in contrast to some previous claims, and so there is not only a line of transitions in the (longitudinal) field-temperature plane (the de Almeida-Thouless, AT, line) where replica symmetry is broken, but also a quantum de Almeida-Thouless (QuAT) line in the transverse field-longitudinal field plane at T =0 . If the QuAT line also occurs in models with short-range interactions its presence might affect the performance of quantum annealers when solving spin glass-type problems with a bias (i.e., magnetic field).

Search for Length Dependent Stable Structures of Polyglutamaine Proteins with Replica Exchange Molecular Dynamic

NASA Astrophysics Data System (ADS)

Kluber, Alexander; Hayre, Robert; Cox, Daniel

2012-02-01

Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.

Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange.

PubMed

Khavrutskii, Ilja V; Wallqvist, Anders

2010-11-09

This paper introduces an efficient single-topology variant of Thermodynamic Integration (TI) for computing relative transformation free energies in a series of molecules with respect to a single reference state. The presented TI variant that we refer to as Single-Reference TI (SR-TI) combines well-established molecular simulation methodologies into a practical computational tool. Augmented with Hamiltonian Replica Exchange (HREX), the SR-TI variant can deliver enhanced sampling in select degrees of freedom. The utility of the SR-TI variant is demonstrated in calculations of relative solvation free energies for a series of benzene derivatives with increasing complexity. Noteworthy, the SR-TI variant with the HREX option provides converged results in a challenging case of an amide molecule with a high (13-15 kcal/mol) barrier for internal cis/trans interconversion using simulation times of only 1 to 4 ns.

Comparative characterization of short monomeric polyglutamine peptides by replica exchange molecular dynamics simulation.

PubMed

Nakano, Miki; Watanabe, Hirofumi; Rothstein, Stuart M; Tanaka, Shigenori

2010-05-27

Polyglutamine (polyQ) diseases are caused by an abnormal expansion of CAG repeats. While their detailed structure remains unclear, polyQ peptides assume beta-sheet structures when they aggregate. To investigate the conformational ensemble of short, monomeric polyQ peptides, which consist of 15 glutamine residues (Q(15)), we performed replica exchange molecular dynamics (REMD) simulations. We found that Q(15) can assume multiple configurations due to all of the residues affecting the formation of side-chain hydrogen bonds. Analysis of the free energy landscape reveals that Q(15) has a basin for random-coil structures and another for alpha-helix or beta-turn structures. To investigate properties of aggregated polyQ peptides, we performed multiple molecular dynamics (MMD) simulations for monomeric and oligomeric Q(15). MMD revealed that the formation of oligomers stabilizes the beta-turn structure by increasing the number of hydrogen bonds between the main chains.

The fabrication of subwavelength anti-reflective nanostructures using a bio-template

NASA Astrophysics Data System (ADS)

Xie, Guoyong; Zhang, Guoming; Lin, Feng; Zhang, Jin; Liu, Zhongfan; Mu, Shichen

2008-03-01

This paper describes a paradigm, a simple, low-cost and conventional approach to the fabrication of large-area subwavelength anti-reflective nanostructures on films directly with a bio-template. Specifically, the nano-nipple arrays on the surface of cicada wings have been precisely replicated to a PMMA (polymethyl methacrylate) film with high reproducibility by a technique of replica molding, which mainly involves two processes: one is that a negative Au mold is prepared directly from the bio-template of the cicada wing by thermal deposition; the other is that the Au mold is used to obtain the replica of the nanostructures on the original cicada wing by casting polymer. The reflectance spectra measurement shows that the replicated PMMA film can considerably reduce reflectivity at its surface over a large wavelength range from 250 to 800 nm, indicating that the anti-reflective property has also been inherited by the PMMA film.

Replica analysis for the duality of the portfolio optimization problem

NASA Astrophysics Data System (ADS)

Shinzato, Takashi

2016-11-01

In the present paper, the primal-dual problem consisting of the investment risk minimization problem and the expected return maximization problem in the mean-variance model is discussed using replica analysis. As a natural extension of the investment risk minimization problem under only a budget constraint that we analyzed in a previous study, we herein consider a primal-dual problem in which the investment risk minimization problem with budget and expected return constraints is regarded as the primal problem, and the expected return maximization problem with budget and investment risk constraints is regarded as the dual problem. With respect to these optimal problems, we analyze a quenched disordered system involving both of these optimization problems using the approach developed in statistical mechanical informatics and confirm that both optimal portfolios can possess the primal-dual structure. Finally, the results of numerical simulations are shown to validate the effectiveness of the proposed method.

Phase diagram of two-dimensional hard ellipses.

PubMed

Bautista-Carbajal, Gustavo; Odriozola, Gerardo

2014-05-28

We report the phase diagram of two-dimensional hard ellipses as obtained from replica exchange Monte Carlo simulations. The replica exchange is implemented by expanding the isobaric ensemble in pressure. The phase diagram shows four regions: isotropic, nematic, plastic, and solid (letting aside the hexatic phase at the isotropic-plastic two-step transition [E. P. Bernard and W. Krauth, Phys. Rev. Lett. 107, 155704 (2011)]). At low anisotropies, the isotropic fluid turns into a plastic phase which in turn yields a solid for increasing pressure (area fraction). Intermediate anisotropies lead to a single first order transition (isotropic-solid). Finally, large anisotropies yield an isotropic-nematic transition at low pressures and a high-pressure nematic-solid transition. We obtain continuous isotropic-nematic transitions. For the transitions involving quasi-long-range positional ordering, i.e., isotropic-plastic, isotropic-solid, and nematic-solid, we observe bimodal probability density functions. This supports first order transition scenarios.

C3PO - A Dynamic Data Placement Agent for ATLAS Distributed Data Management

NASA Astrophysics Data System (ADS)

Beermann, T.; Lassnig, M.; Barisits, M.; Serfon, C.; Garonne, V.; ATLAS Collaboration

2017-10-01

This paper introduces a new dynamic data placement agent for the ATLAS distributed data management system. This agent is designed to pre-place potentially popular data to make it more widely available. It therefore incorporates information from a variety of sources. Those include input datasets and sites workload information from the ATLAS workload management system, network metrics from different sources like FTS and PerfSonar, historical popularity data collected through a tracer mechanism and more. With this data it decides if, when and where to place new replicas that then can be used by the WMS to distribute the workload more evenly over available computing resources and then ultimately reduce job waiting times. This paper gives an overview of the architecture and the final implementation of this new agent. The paper also includes an evaluation of the placement algorithm by comparing the transfer times and the new replica usage.

Methods and apparatus for multi-resolution replication of files in a parallel computing system using semantic information

DOEpatents

Faibish, Sorin; Bent, John M.; Tzelnic, Percy; Grider, Gary; Torres, Aaron

2015-10-20

Techniques are provided for storing files in a parallel computing system using different resolutions. A method is provided for storing at least one file generated by a distributed application in a parallel computing system. The file comprises one or more of a complete file and a sub-file. The method comprises the steps of obtaining semantic information related to the file; generating a plurality of replicas of the file with different resolutions based on the semantic information; and storing the file and the plurality of replicas of the file in one or more storage nodes of the parallel computing system. The different resolutions comprise, for example, a variable number of bits and/or a different sub-set of data elements from the file. A plurality of the sub-files can be merged to reproduce the file.

Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta

PubMed Central

Zhang, Zhe; Schindler, Christina E. M.; Lange, Oliver F.; Zacharias, Martin

2015-01-01

The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC) based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamiltonian replica exchange and well-tempered ensemble approaches, have been combined with the MC method and were evaluated on 20 protein complexes using unbound partner structures. The well-tempered ensemble method combined with a 2-dimensional temperature and Hamiltonian replica exchange scheme (WTE-H-REMC) was identified as the most efficient search strategy. Comparison with prolonged MC searches indicates that the WTE-H-REMC approach requires approximately 5 times fewer MC steps to identify near native docking geometries compared to conventional MC searches. PMID:26053419

Replica analysis of the class of antibodies produced by single cells

PubMed Central

Ivanyi, J.; Dresser, D. W.

1970-01-01

Improvements have been made in a localized haemolysis in gel replica assay developed previously. The technique is designed to show if an individual antibody producing cell releases antibody of one or more classes. The techniques can also be used to indicate the specificity of antibodies produced by individual cells by using two different antigens in the test system. In experiments where both slides of a slide-pair are untreated or treated identically, and 100% coincidence of plaques is expected, the technique has been shown to detect about 95% coincidence. Pairs of slides treated differently to reveal plaques due to antibodies of different classes show a mean of about 3·5% coincident plaques. This `background' of coincidence which it is thought is not due to `double-producers', is one of the limiting factors of the technique. ImagesFig. 1Fig. 2Fig. 3Fig. 4 PMID:4920598

Entropy generation in Gaussian quantum transformations: applying the replica method to continuous-variable quantum information theory

NASA Astrophysics Data System (ADS)

Gagatsos, Christos N.; Karanikas, Alexandros I.; Kordas, Georgios; Cerf, Nicolas J.

2016-02-01

In spite of their simple description in terms of rotations or symplectic transformations in phase space, quadratic Hamiltonians such as those modelling the most common Gaussian operations on bosonic modes remain poorly understood in terms of entropy production. For instance, determining the quantum entropy generated by a Bogoliubov transformation is notably a hard problem, with generally no known analytical solution, while it is vital to the characterisation of quantum communication via bosonic channels. Here we overcome this difficulty by adapting the replica method, a tool borrowed from statistical physics and quantum field theory. We exhibit a first application of this method to continuous-variable quantum information theory, where it enables accessing entropies in an optical parametric amplifier. As an illustration, we determine the entropy generated by amplifying a binary superposition of the vacuum and a Fock state, which yields a surprisingly simple, yet unknown analytical expression.

Cellular complexity captured in durable silica biocomposites

PubMed Central

Kaehr, Bryan; Townson, Jason L.; Kalinich, Robin M.; Awad, Yasmine H.; Swartzentruber, B. S.; Dunphy, Darren R.; Brinker, C. Jeffrey

2012-01-01

Tissue-derived cultured cells exhibit a remarkable range of morphological features in vitro, depending on phenotypic expression and environmental interactions. Translation of these cellular architectures into inorganic materials would provide routes to generate hierarchical nanomaterials with stabilized structures and functions. Here, we describe the fabrication of cell/silica composites (CSCs) and their conversion to silica replicas using mammalian cells as scaffolds to direct complex structure formation. Under mildly acidic solution conditions, silica deposition is restricted to the molecularly crowded cellular template. Inter- and intracellular heterogeneity from the nano- to macroscale is captured and dimensionally preserved in CSCs following drying and subjection to extreme temperatures allowing, for instance, size and shape preserving pyrolysis of cellular architectures to form conductive carbon replicas. The structural and behavioral malleability of the starting material (cultured cells) provides opportunities to develop robust and economical biocomposites with programmed structures and functions. PMID:23045634

Nontrivial Critical Fixed Point for Replica-Symmetry-Breaking Transitions.

PubMed

Charbonneau, Patrick; Yaida, Sho

2017-05-26

The transformation of the free-energy landscape from smooth to hierarchical is one of the richest features of mean-field disordered systems. A well-studied example is the de Almeida-Thouless transition for spin glasses in a magnetic field, and a similar phenomenon-the Gardner transition-has recently been predicted for structural glasses. The existence of these replica-symmetry-breaking phase transitions has, however, long been questioned below their upper critical dimension, d_{u}=6. Here, we obtain evidence for the existence of these transitions in d

Replica analysis for the duality of the portfolio optimization problem.

PubMed

Shinzato, Takashi

2016-11-01

In the present paper, the primal-dual problem consisting of the investment risk minimization problem and the expected return maximization problem in the mean-variance model is discussed using replica analysis. As a natural extension of the investment risk minimization problem under only a budget constraint that we analyzed in a previous study, we herein consider a primal-dual problem in which the investment risk minimization problem with budget and expected return constraints is regarded as the primal problem, and the expected return maximization problem with budget and investment risk constraints is regarded as the dual problem. With respect to these optimal problems, we analyze a quenched disordered system involving both of these optimization problems using the approach developed in statistical mechanical informatics and confirm that both optimal portfolios can possess the primal-dual structure. Finally, the results of numerical simulations are shown to validate the effectiveness of the proposed method.

Ising Criticality of the Clock Model from Density of States Obtained by the Replica Exchange-Wang-Landau Method

NASA Astrophysics Data System (ADS)

Cadilhe, Antonio

2018-04-01

We performed extensive simulations, using the Replica Exchange-Wang-Landau method, of the clock model for orders 3 and 4 on a square lattice, where critical behaviors are expected to belong to the Ising universality class. Though order 2 represents the Ising model, thus, being exactly solvable in two-dimensions, we still provide such results for comparison to the other two orders. Results for various energy related quantities such as the mean energy per spin, specific heat, as well as logarithm scaling of the peak of the specific heat are presented and shown to follow Ising behavior. Additionally, we also present results related to magnetic quantities, such as the magnetization, magnetic susceptibility, and corresponding scaling behavior of the peak of the magnetic susceptibility. Again, our results show scaling in conformity to Ising critical behavior.

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

PubMed Central

Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

2013-01-01

We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems. PMID:23665897

Adaptively biased molecular dynamics for free energy calculations

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2008-04-01

We present an adaptively biased molecular dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using nonequilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential and is inspired by the metadynamics method. The ABMD method has several useful features, including a small number of control parameters and an O(t ) numerical cost with molecular dynamics time t. The ABMD method naturally allows for extensions based on multiple walkers and replica exchange, where different replicas can have different temperatures and/or collective variables. This is beneficial not only in terms of the speed and accuracy of a calculation, but also in terms of the amount of useful information that may be obtained from a given simulation. The workings of the ABMD method are illustrated via a study of the folding of the Ace-GGPGGG-Nme peptide in a gaseous and solvated environment.

Measurement and prediction of flow through a replica segment of a mildly atherosclerotic coronary artery of man

NASA Technical Reports Server (NTRS)

Back, L. H.; Radbill, J. R.; Cho, Y. I.; Crawford, D. W.

1986-01-01

Pressure distributions were measured along a hollow vascular axisymmetric replica of a segment of the left circumflex coronary artery of man with mildly atherosclerotic diffuse disease. A large range of physiological Reynolds numbers from about 60 to 500, including hyperemic response, was spanned in the flows investigation using a fluid simulating blood kinematic viscosity. Predicted pressure distributions from the numerical solution of the Navier-Stokes equations were similar in trend and magnitude to the measurements. Large variations in the predicted velocity profiles occurred along the lumen. The influence of the smaller scale multiple flow obstacles along the wall (lesion variations) led to sharp spikes in the predicted wall shear stresses. Reynolds number similarity was discussed, and estimates of what time averaged in vivo pressure drop and shear stress might be were given for a vessel segment.

LHCb experience with LFC replication

NASA Astrophysics Data System (ADS)

Bonifazi, F.; Carbone, A.; Perez, E. D.; D'Apice, A.; dell'Agnello, L.; Duellmann, D.; Girone, M.; Re, G. L.; Martelli, B.; Peco, G.; Ricci, P. P.; Sapunenko, V.; Vagnoni, V.; Vitlacil, D.

2008-07-01

Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. a database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informatics (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements.

Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories.

PubMed

Morishita, Tetsuya; Yonezawa, Yasushige; Ito, Atsushi M

2017-07-11

Efficient and reliable estimation of the mean force (MF), the derivatives of the free energy with respect to a set of collective variables (CVs), has been a challenging problem because free energy differences are often computed by integrating the MF. Among various methods for computing free energy differences, logarithmic mean-force dynamics (LogMFD) [ Morishita et al., Phys. Rev. E 2012 , 85 , 066702 ] invokes the conservation law in classical mechanics to integrate the MF, which allows us to estimate the free energy profile along the CVs on-the-fly. Here, we present a method called parallel dynamics, which improves the estimation of the MF by employing multiple replicas of the system and is straightforwardly incorporated in LogMFD or a related method. In the parallel dynamics, the MF is evaluated by a nonequilibrium path-ensemble using the multiple replicas based on the Crooks-Jarzynski nonequilibrium work relation. Thanks to the Crooks relation, realizing full-equilibrium states is no longer mandatory for estimating the MF. Additionally, sampling in the hidden subspace orthogonal to the CV space is highly improved with appropriate weights for each metastable state (if any), which is hardly achievable by typical free energy computational methods. We illustrate how to implement parallel dynamics by combining it with LogMFD, which we call logarithmic parallel dynamics (LogPD). Biosystems of alanine dipeptide and adenylate kinase in explicit water are employed as benchmark systems to which LogPD is applied to demonstrate the effect of multiple replicas on the accuracy and efficiency in estimating the free energy profiles using parallel dynamics.

Grid Enabled Geospatial Catalogue Web Service

NASA Technical Reports Server (NTRS)

Chen, Ai-Jun; Di, Li-Ping; Wei, Ya-Xing; Liu, Yang; Bui, Yu-Qi; Hu, Chau-Min; Mehrotra, Piyush

2004-01-01

Geospatial Catalogue Web Service is a vital service for sharing and interoperating volumes of distributed heterogeneous geospatial resources, such as data, services, applications, and their replicas over the web. Based on the Grid technology and the Open Geospatial Consortium (0GC) s Catalogue Service - Web Information Model, this paper proposes a new information model for Geospatial Catalogue Web Service, named as GCWS which can securely provides Grid-based publishing, managing and querying geospatial data and services, and the transparent access to the replica data and related services under the Grid environment. This information model integrates the information model of the Grid Replica Location Service (RLS)/Monitoring & Discovery Service (MDS) with the information model of OGC Catalogue Service (CSW), and refers to the geospatial data metadata standards from IS0 19115, FGDC and NASA EOS Core System and service metadata standards from IS0 191 19 to extend itself for expressing geospatial resources. Using GCWS, any valid geospatial user, who belongs to an authorized Virtual Organization (VO), can securely publish and manage geospatial resources, especially query on-demand data in the virtual community and get back it through the data-related services which provide functions such as subsetting, reformatting, reprojection etc. This work facilitates the geospatial resources sharing and interoperating under the Grid environment, and implements geospatial resources Grid enabled and Grid technologies geospatial enabled. It 2!so makes researcher to focus on science, 2nd not cn issues with computing ability, data locztic, processir,g and management. GCWS also is a key component for workflow-based virtual geospatial data producing.

A study of an adaptive replication framework for orchestrated composite web services.

PubMed

Mohamed, Marwa F; Elyamany, Hany F; Nassar, Hamed M

2013-01-01

Replication is considered one of the most important techniques to improve the Quality of Services (QoS) of published Web Services. It has achieved impressive success in managing resource sharing and usage in order to moderate the energy consumed in IT environments. For a robust and successful replication process, attention should be paid to suitable time as well as the constraints and capabilities in which the process runs. The replication process is time-consuming since outsourcing some new replicas into other hosts is lengthy. Furthermore, nowadays, most of the business processes that might be implemented over the Web are composed of multiple Web services working together in two main styles: Orchestration and Choreography. Accomplishing a replication over such business processes is another challenge due to the complexity and flexibility involved. In this paper, we present an adaptive replication framework for regular and orchestrated composite Web services. The suggested framework includes a number of components for detecting unexpected and unhappy events that might occur when consuming the original published web services including failure or overloading. It also includes a specific replication controller to manage the replication process and select the best host that would encapsulate a new replica. In addition, it includes a component for predicting the incoming load in order to decrease the time needed for outsourcing new replicas, enhancing the performance greatly. A simulation environment has been created to measure the performance of the suggested framework. The results indicate that adaptive replication with prediction scenario is the best option for enhancing the performance of the replication process in an online business environment.

Method to improve passive fit of frameworks on implant-supported prostheses: An in vitro study.

PubMed

Manzella, Carlo; Bignardi, Cristina; Burello, Valerio; Carossa, Stefano; Schierano, Gianmario

2016-07-01

The passivity of the superstructure to the abutments of implant-supported prostheses is necessary for implant-prosthesis success. Improvements are needed in the methods of verifying passivity. The purpose of this in vitro study was to evaluate an inexpensive, easy to make, and user-friendly device to verify the position of the implant abutment replicas of the definitive cast and to avoid framework misfit before fabrication. Eighty stone devices were constructed on a metal base for the in vitro tests. The horizontal, vertical, and angled positions of the implant replicas were created to simulate misfits. The devices were fitted on the abutment replicas, and their ability to identify misfits was evaluated. A statistical analysis was not indicated, because the probability of fracture of the stone devices was 0 or 1. Two mathematical models were built using computer-aided design software (SolidWorks Premium; Dassault Systèmes SolidWorks Corp), and the finite element method was used (Ansys; ANSYS Inc) to simulate the structural behavior of 2 implant configurations (4 and 6 implants). Horizontal misfits of 150 μm, vertical misfits of 50 μm, and angled misfits of 1 degree were detected during the in vitro tests. Different loads and bone quality in the mathematical models did not change stress in the prosthesis configurations on 4 or 6 implants in a relevant way. The fabricated device was easily able to detect the misfits in accordance with the defined parameters. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Pediatric in vitro and in silico models of deposition via oral and nasal inhalation.

PubMed

Carrigy, Nicholas B; Ruzycki, Conor A; Golshahi, Laleh; Finlay, Warren H

2014-06-01

Respiratory tract deposition models provide a useful method for optimizing the design and administration of inhaled pharmaceutical aerosols, and can be useful for estimating exposure risks to inhaled particulate matter. As aerosol must first pass through the extrathoracic region prior to reaching the lungs, deposition in this region plays an important role in both cases. Compared to adults, much less extrathoracic deposition data are available with pediatric subjects. Recently, progress in magnetic resonance imaging and computed tomography scans to develop pediatric extrathoracic airway replicas has facilitated addressing this issue. Indeed, the use of realistic replicas for benchtop inhaler testing is now relatively common during the development and in vitro evaluation of pediatric respiratory drug delivery devices. Recently, in vitro empirical modeling studies using a moderate number of these realistic replicas have related airway geometry, particle size, fluid properties, and flow rate to extrathoracic deposition. Idealized geometries provide a standardized platform for inhaler testing and exposure risk assessment and have been designed to mimic average in vitro deposition in infants and children by replicating representative average geometrical dimensions. In silico mathematical models have used morphometric data and aerosol physics to illustrate the relative importance of different deposition mechanisms on respiratory tract deposition. Computational fluid dynamics simulations allow for the quantification of local deposition patterns and an in-depth examination of aerosol behavior in the respiratory tract. Recent studies have used both in vitro and in silico deposition measurements in realistic pediatric airway geometries to some success. This article reviews the current understanding of pediatric in vitro and in silico deposition modeling via oral and nasal inhalation.

Operator product expansion in Liouville field theory and Seiberg-type transitions in log-correlated random energy models

NASA Astrophysics Data System (ADS)

Cao, Xiangyu; Le Doussal, Pierre; Rosso, Alberto; Santachiara, Raoul

2018-04-01

We study transitions in log-correlated random energy models (logREMs) that are related to the violation of a Seiberg bound in Liouville field theory (LFT): the binding transition and the termination point transition (a.k.a., pre-freezing). By means of LFT-logREM mapping, replica symmetry breaking and traveling-wave equation techniques, we unify both transitions in a two-parameter diagram, which describes the free-energy large deviations of logREMs with a deterministic background log potential, or equivalently, the joint moments of the free energy and Gibbs measure in logREMs without background potential. Under the LFT-logREM mapping, the transitions correspond to the competition of discrete and continuous terms in a four-point correlation function. Our results provide a statistical interpretation of a peculiar nonlocality of the operator product expansion in LFT. The results are rederived by a traveling-wave equation calculation, which shows that the features of LFT responsible for the transitions are reproduced in a simple model of diffusion with absorption. We examine also the problem by a replica symmetry breaking analysis. It complements the previous methods and reveals a rich large deviation structure of the free energy of logREMs with a deterministic background log potential. Many results are verified in the integrable circular logREM, by a replica-Coulomb gas integral approach. The related problem of common length (overlap) distribution is also considered. We provide a traveling-wave equation derivation of the LFT predictions announced in a precedent work.

Effect of sequence and stereochemistry reversal on p53 peptide mimicry.

PubMed

Atzori, Alessio; Baker, Audrey E; Chiu, Mark; Bryce, Richard A; Bonnet, Pascal

2013-01-01

Peptidomimetics effective in modulating protein-protein interactions and resistant to proteolysis have potential in therapeutic applications. An appealing yet underperforming peptidomimetic strategy is to employ D-amino acids and reversed sequences to mimic a lead peptide conformation, either separately or as the combined retro-inverso peptide. In this work, we examine the conformations of inverse, reverse and retro-inverso peptides of p53(15-29) using implicit solvent molecular dynamics simulation and circular dichroism spectroscopy. In order to obtain converged ensembles for the peptides, we find enhanced sampling is required via the replica exchange molecular dynamics method. From these replica exchange simulations, the D-peptide analogues of p53(15-29) result in a predominantly left-handed helical conformation. When the parent sequence is reversed sequence as either the L-peptide and D-peptide, these peptides display a greater helical propensity, feature reflected by NMR and CD studies in TFE/water solvent. The simulations also indicate that, while approximately similar orientations of the side-chains are possible by the peptide analogues, their ability to mimic the parent peptide is severely compromised by backbone orientation (for D-amino acids) and side-chain orientation (for reversed sequences). A retro-inverso peptide is disadvantaged as a mimic in both aspects, and further chemical modification is required to enable this concept to be used fruitfully in peptidomimetic design. The replica exchange molecular simulation approach adopted here, with its ability to provide detailed conformational insights into modified peptides, has potential as a tool to guide structure-based design of new improved peptidomimetics.

Comprehensive MALDI-TOF biotyping of the non-redundant Harvard Pseudomonas aeruginosa PA14 transposon insertion mutant library.

PubMed

Oumeraci, Tonio; Jensen, Vanessa; Talbot, Steven R; Hofmann, Winfried; Kostrzewa, Markus; Schlegelberger, Brigitte; von Neuhoff, Nils; Häussler, Susanne

2015-01-01

Pseudomonas aeruginosa is a gram-negative bacterium that is ubiquitously present in the aerobic biosphere. As an antibiotic-resistant facultative pathogen, it is a major cause of hospital-acquired infections. Its rapid and accurate identification is crucial in clinical and therapeutic environments. In a large-scale MALDI-TOF mass spectrometry-based screen of the Harvard transposon insertion mutant library of P. aeruginosa strain PA14, intact-cell proteome profile spectra of 5547 PA14 transposon mutants exhibiting a plethora of different phenotypes were acquired and analyzed. Of all P. aeruginosa PA14 mutant profiles 99.7% were correctly identified as P. aeruginosa with the Biotyper software on the species level. On the strain level, 99.99% of the profiles were mapped to five different individual P. aeruginosa Biotyper database entries. A principal component analysis-based approach was used to determine the most important discriminatory mass features between these Biotyper groups. Although technical replicas were consistently categorized to specific Biotyper groups in 94.2% of the mutant profiles, biological replicas were not, indicating that the distinct proteotypes are affected by growth conditions. The PA14 mutant profile collection presented here constitutes the largest coherent P. aeruginosa MALDI-TOF spectral dataset publicly available today. Transposon insertions in thousands of different P. aeruginosa genes did not affect species identification from MALDI-TOF mass spectra, clearly demonstrating the robustness of the approach. However, the assignment of the individual spectra to sub-groups proved to be non-consistent in biological replicas, indicating that the differentiation between biotyper groups in this nosocomial pathogen is unassured.

Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models.

PubMed

Fan, Hao; Periole, Xavier; Mark, Alan E

2012-07-01

The efficiency of using a variant of Hamiltonian replica-exchange molecular dynamics (Chaperone H-replica-exchange molecular dynamics [CH-REMD]) for the refinement of protein structural models generated de novo is investigated. In CH-REMD, the interaction between the protein and its environment, specifically, the electrostatic interaction between the protein and the solvating water, is varied leading to cycles of partial unfolding and refolding mimicking some aspects of folding chaperones. In 10 of the 15 cases examined, the CH-REMD approach sampled structures in which the root-mean-square deviation (RMSD) of secondary structure elements (SSE-RMSD) with respect to the experimental structure was more than 1.0 Å lower than the initial de novo model. In 14 of the 15 cases, the improvement was more than 0.5 Å. The ability of three different statistical potentials to identify near-native conformations was also examined. Little correlation between the SSE-RMSD of the sampled structures with respect to the experimental structure and any of the scoring functions tested was found. The most effective scoring function tested was the DFIRE potential. Using the DFIRE potential, the SSE-RMSD of the best scoring structures was on average 0.3 Å lower than the initial model. Overall the work demonstrates that targeted enhanced-sampling techniques such as CH-REMD can lead to the systematic refinement of protein structural models generated de novo but that improved potentials for the identification of near-native structures are still needed. Copyright © 2012 Wiley Periodicals, Inc.

Template-mediated, Hierarchical Engineering of Ordered Mesoporous Films and Powders

NASA Astrophysics Data System (ADS)

Tian, Zheng

Hierarchical control over pore size, pore topology, and meso/mictrostructure as well as material morphology (e.g., powders, monoliths, thin films) is crucial for meeting diverse materials needs among applications spanning next generation catalysts, sensors, batteries, sorbents, etc. The overarching goal of this thesis is to establish fundamental mechanistic insight enabling new strategies for realizing such hierarchical textural control for carbon materials that is not currently achievable with sacrificial pore formation by 'one-pot' surfactant-based 'soft'-templating or multi-step inorganic 'hard-templating. While 'hard'-templating is often tacitly discounted based upon its perceived complexity, it offers potential for overcoming key 'soft'-templating challenges, including bolstering pore stability, accommodating a more versatile palette of replica precursors, realizing ordered/spanning porosity in the case of porous thin films, simplifying formation of bi-continuous pore topologies, and inducing microstructure control within porous replica materials. In this thesis, we establish strategies for hard-templating of hierarchically porous and structured carbon powders and tunable thin films by both multi-step hard-templating and a new 'one-pot' template-replica precursor co-assembly process. We first develop a nominal hard-templating technique to successfully prepare three-dimensionally ordered mesoporous (3DOm) and 3DOm-supported microporous carbon thin films by exploiting our ability to synthesize and assemble size-tunable silica nanoparticles into scalable, colloidal crystalline thin film templates of tunable mono- to multi-layer thickness. This robust thin film template accommodates liquid and/or vapor-phase infiltration, polymerization, and pyrolysis of various carbon sources without pore contraction and/or collapse upon template sacrifice. The result is robust, flexible 3DOm or 3DOm-supported ultra-thin microporous films that can be transferred by stamp techniques to various substrates for low-cost counter-electrodes in dye-sensitized solar cells, as we demonstrate, or as potential high-flux membranes for molecular separations. Inspired by 'one-pot' 'soft'-templating approaches, wherein the pore forming agent and replica precursor are co-assembled, we establish how 'hard'-templating can be carried out in an analogous fashion. Namely, we show how pre-formed silica nanoparticles can be co-assembled from aqueous solutions with a carbon source (glucose), leading to elucidation of a pseudo-phase behavior in which we identify an operating window for synthesis of hierarchically bi-continuous carbon films. Systematic study of the association of carbon precursors with the silica particles in combination with transient coating experiments reveals mechanistic insight into how silica-adsorbed carbon precursor modulates particle assembly and ultimately controls template particle d-spacing. We uncover a critical d-spacing defining the boundary between ordered and disordered mesoporosity within the resulting films. We ultimately extend this thin-film mechanistic insight to realize 'one'-pot, bi-continuous 3DOm carbon powders. Through a combination of X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and high-resolution transmission electron microscopy (HR-TEM), we elucidate novel synthesis-structure relations for template-mediated microstructuring of the 3DOm replica carbons. Attractive properties of the resulting bi-continuous porous carbons for applications, for example, as novel electrodes, include high surface areas, large mesopore volumes, and tunable graphitic content (i.e. >50%) and character. We specifically demonstrate their performance, in thin film form, as counter-electrodes in dye-sensitized solar cells. We also demonstrate how they can be exploited in powder form as high-performance supercapacitor electrodes exhibiting attractive retention and absolute capacitance. We conclude the thesis by demonstrating the versatility of both the thin-film and powder templating processes developed herein, for realizing ordered binary colloidal crystal templates and their bi-modal porous carbon replica films, expanding compositional diversity of the 'one-pot' thin film process beyond carbons to include an example of 3DOm ZrO2 films, and employing the hard-templating process as a strategy for realizing 3DOm carbon-supported nanocarbides.

"Lookalike" Drugs. Specialized Information Service.

ERIC Educational Resources Information Center

Do It Now Foundation, Phoenix, AZ.

The document presents a collection of articles about "lookalike drugs." Article 1 presents readers with a look at "peashooters" (lookalike drugs which are usually replicas of pharmaceutical amphetamines, but increasingly used to describe simulations of cocaine and prescription downers). Lookalikes, although usually legal, are…

Classification of Streptomyces Spore Surfaces into Five Groups

PubMed Central

Dietz, Alma; Mathews, John

1971-01-01

Streptomyces spores surfaces have been classified into five groups, smooth, warty, spiny, hairy, and rugose, by examination of carbon replicas of spores with the transmission electron microscope and by direct examination of spores with the scanning electron microscope. Images PMID:4928607

An Integrated Teaching Module.

ERIC Educational Resources Information Center

Samuel, Marie R.; Seiferth, Berniece B.

This integrated teaching module provides elementary and junior high school teachers with a "hands-on" approach to studying the Anasazi Indian. Emphasis is on creative exploration that focuses on integrating art, music, poetry, writing, geography, dance, history, anthropology, sociology, and archaeology. Replicas of artifacts,…

Knights in White Sneakers.

ERIC Educational Resources Information Center

Raggio, Susan; Zjawin, Dorothy

1982-01-01

A teaching unit to help students explore daily life during the Middle Ages is presented. Techniques for teaching about the medieval social structure, feudal rights and objectives, living arrangements, agricultural practices, and suggestions for building a replica of a medieval village are included. (PP)

48 CFR 2152.215-70 - Contractor records retention.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Contractor chooses to maintain paper documents in electronic format, the electronic version must be an exact replica of the paper document. (End of clause) [70 FR 41155, July 18, 2005] ... MANAGEMENT, FEDERAL EMPLOYEES GROUP LIFE INSURANCE FEDERAL ACQUISITION REGULATION CLAUSES AND FORMS...

48 CFR 2152.215-70 - Contractor records retention.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Contractor chooses to maintain paper documents in electronic format, the electronic version must be an exact replica of the paper document. (End of clause) [70 FR 41155, July 18, 2005] ... MANAGEMENT, FEDERAL EMPLOYEES GROUP LIFE INSURANCE FEDERAL ACQUISITION REGULATION CLAUSES AND FORMS...

48 CFR 2152.215-70 - Contractor records retention.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Contractor chooses to maintain paper documents in electronic format, the electronic version must be an exact replica of the paper document. (End of clause) [70 FR 41155, July 18, 2005] ... MANAGEMENT, FEDERAL EMPLOYEES GROUP LIFE INSURANCE FEDERAL ACQUISITION REGULATION CLAUSES AND FORMS...

48 CFR 2152.215-70 - Contractor records retention.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Contractor chooses to maintain paper documents in electronic format, the electronic version must be an exact replica of the paper document. (End of clause) [70 FR 41155, July 18, 2005] ... MANAGEMENT, FEDERAL EMPLOYEES GROUP LIFE INSURANCE FEDERAL ACQUISITION REGULATION CLAUSES AND FORMS...

A Probabilistic Framework for Constructing Temporal Relations in Replica Exchange Molecular Trajectories.

PubMed

Chattopadhyay, Aditya; Zheng, Min; Waller, Mark Paul; Priyakumar, U Deva

2018-05-23

Knowledge of the structure and dynamics of biomolecules is essential for elucidating the underlying mechanisms of biological processes. Given the stochastic nature of many biological processes, like protein unfolding, it's almost impossible that two independent simulations will generate the exact same sequence of events, which makes direct analysis of simulations difficult. Statistical models like Markov Chains, transition networks etc. help in shedding some light on the mechanistic nature of such processes by predicting long-time dynamics of these systems from short simulations. However, such methods fall short in analyzing trajectories with partial or no temporal information, for example, replica exchange molecular dynamics or Monte Carlo simulations. In this work we propose a probabilistic algorithm, borrowing concepts from graph theory and machine learning, to extract reactive pathways from molecular trajectories in the absence of temporal data. A suitable vector representation was chosen to represent each frame in the macromolecular trajectory (as a series of interaction and conformational energies) and dimensionality reduction was performed using principal component analysis (PCA). The trajectory was then clustered using a density-based clustering algorithm, where each cluster represents a metastable state on the potential energy surface (PES) of the biomolecule under study. A graph was created with these clusters as nodes with the edges learnt using an iterative expectation maximization algorithm. The most reactive path is conceived as the widest path along this graph. We have tested our method on RNA hairpin unfolding trajectory in aqueous urea solution. Our method makes the understanding of the mechanism of unfolding in RNA hairpin molecule more tractable. As this method doesn't rely on temporal data it can be used to analyze trajectories from Monte Carlo sampling techniques and replica exchange molecular dynamics (REMD).

Gamma-ray spectra and doses from the Little Boy replica

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

Moss, C.E.; Lucas, M.C.; Tisinger, E.W.

1984-01-01

Most radiation safety guidelines in the nuclear industry are based on the data concerning the survivors of the nuclear explosions at Hiroshima and Nagasaki. Crucial to determining these guidelines is the radiation from the explosions. We have measured gamma-ray pulse-height distributions from an accurate replica of the Little Boy device used at Hiroshima, operated at low power levels near critical. The device was placed outdoors on a stand 4 m from the ground to minimize environmental effects. The power levels were based on a monitor detector calibrated very carefully in independent experiments. High-resolution pulse-height distributions were acquired with a germaniummore » detector to identify the lines and to obtain line intensities. The 7631 to 7645 keV doublet from neutron capture in the heavy steel case was dominant. Low-resolution pulse-height distributions were acquired with bismuth-germanate detectors. We calculated flux spectra from these distributions using accurately measured detector response functions and efficiency curves. We then calculated dose-rate spectra from the flux spectra using a flux-to-dose-rate conversion procedure. The integral of each dose-rate spectrum gave an integral dose rate. The integral doses at 2 m ranged from 0.46 to 1.03 mrem per 10/sup 13/ fissions. The output of the Little Boy replica can be calculated with Monte Carlo codes. Comparison of our experimental spectra, line intensities, and integral doses can be used to verify these calculations at low power levels and give increased confidence to the calculated values from the explosion at Hiroshima. These calculations then can be used to establish better radiation safety guidelines. 7 references, 7 figures, 2 tables.« less

A Flow Perfusion Bioreactor System for Vocal Fold Tissue Engineering Applications

PubMed Central

Heris, Hossein K.; Thomson, Scott L.; Taher, Rani; Kazemirad, Siavash; Sheibani, Sara; Li-Jessen, Nicole Y.K.; Vali, Hojatollah; Mongeau, Luc

2016-01-01

The human vocal folds (VFs) undergo complex biomechanical stimulation during phonation. The aim of the present study was to develop and validate a phono-mimetic VF flow perfusion bioreactor, which mimics the mechanical microenvironment of the human VFs in vitro. The bioreactor uses airflow-induced self-oscillations, which have been shown to produce mechanical loading and contact forces that are representative of human phonation. The bioreactor consisted of two synthetic VF replicas within a silicone body. A cell-scaffold mixture (CSM) consisting of human VF fibroblasts, hyaluronic acid, gelatin, and a polyethylene glycol cross-linker was injected into cavities within the replicas. Cell culture medium (CCM) was perfused through the scaffold by using a customized secondary flow loop. After the injection, the bioreactor was operated with no stimulation over a 3-day period to allow for cell adaptation. Phonation was subsequently induced by using a variable speed centrifugal blower for 2 h each day over a period of 4 days. A similar bioreactor without biomechanical stimulation was used as the nonphonatory control. The CSM was harvested from both VF replicas 7 days after the injection. The results confirmed that the phono-mimetic bioreactor supports cell viability and extracellular matrix proteins synthesis, as expected. Many scaffold materials were found to degrade because of challenges from phonation-induced biomechanical stimulation as well as due to biochemical reactions with the CCM. The bioreactor concept enables future investigations of the effects of different phonatory characteristics, that is, voice regimes, on the behavior of the human VF cells. It will also help study the long-term functional outcomes of the VF-specific biomaterials before animal and clinical studies. PMID:27537192

Nano-scale zero valent iron transport in a variable aperture dolomite fracture and a glass fracture

NASA Astrophysics Data System (ADS)

Mondal, P.; Sleep, B. E.; Cui, Z.; Zhou, Z.

2014-12-01

Experiments and numerical simulations are being performed to understand the transport behavior of carboxymethyl cellulose polymer stabilized nano-scale zero valent iron (nZVI) in a variable aperture dolomite rock fracture and a variable aperture glass replica of a fractured slate. The rock fracture was prepared by artificially inducing a fracture in a dolomite block along a stylolite, and the glass fracture was prepared by creating molds with melted glass on two opposing sides of a fractured slate rock block. Both of the fractures were 0.28 m in length and 0.21 m in width. Equivalent hydraulic apertures are about 110 microns for the rock fracture and 250 microns for the glass replica fracture. Sodium bromide and lissamine green B (LGB) serve as conservative tracers in the rock fracture and glass replica fracture, respectively. A dark box set-up with a light source and digital camera is being used to visualize the LGB and CMC-nZVI movement in the glass fracture. Experiments are being performed to determine the effects of water specific discharge and CMC concentration on nZVI transport in the fractures. Transmission electron microscopy, dynamic light scattering, and UV-visual spectrophotometry were performed to determine the stability and characteristics of the CMC-nZVI mixture. The transport of bromide, LGB, CMC, and CMC-nZVI in both fractures is being evaluated through analysis of the effluent concentrations. Time-lapse images are also being captured for the glass fracture. Bromide, LGB, and CMC recoveries have exceeded 95% in both fractures. Significant channeling has been observed in the fractures for CMC transport due to viscous effects.

Adaptive multi-GPU Exchange Monte Carlo for the 3D Random Field Ising Model

NASA Astrophysics Data System (ADS)

Navarro, Cristóbal A.; Huang, Wei; Deng, Youjin

2016-08-01

This work presents an adaptive multi-GPU Exchange Monte Carlo approach for the simulation of the 3D Random Field Ising Model (RFIM). The design is based on a two-level parallelization. The first level, spin-level parallelism, maps the parallel computation as optimal 3D thread-blocks that simulate blocks of spins in shared memory with minimal halo surface, assuming a constant block volume. The second level, replica-level parallelism, uses multi-GPU computation to handle the simulation of an ensemble of replicas. CUDA's concurrent kernel execution feature is used in order to fill the occupancy of each GPU with many replicas, providing a performance boost that is more notorious at the smallest values of L. In addition to the two-level parallel design, the work proposes an adaptive multi-GPU approach that dynamically builds a proper temperature set free of exchange bottlenecks. The strategy is based on mid-point insertions at the temperature gaps where the exchange rate is most compromised. The extra work generated by the insertions is balanced across the GPUs independently of where the mid-point insertions were performed. Performance results show that spin-level performance is approximately two orders of magnitude faster than a single-core CPU version and one order of magnitude faster than a parallel multi-core CPU version running on 16-cores. Multi-GPU performance is highly convenient under a weak scaling setting, reaching up to 99 % efficiency as long as the number of GPUs and L increase together. The combination of the adaptive approach with the parallel multi-GPU design has extended our possibilities of simulation to sizes of L = 32 , 64 for a workstation with two GPUs. Sizes beyond L = 64 can eventually be studied using larger multi-GPU systems.

Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field

PubMed Central

Shen, Hujun; Czaplewski, Cezary; Liwo, Adam; Scheraga, Harold A.

2009-01-01

The kinetic-trapping problem in simulating protein folding can be overcome by using a Replica Exchange Method (REM). However, in implementing REM in molecular dynamics simulations, synchronization between processors on parallel computers is required, and communication between processors limits its ability to sample conformational space in a complex system efficiently. To minimize communication between processors during the simulation, a Serial Replica Exchange Method (SREM) has been proposed recently by Hagan et al. (J. Phys. Chem. B 2007, 111, 1416–1423). Here, we report the implementation of this new SREM algorithm with our physics-based united-residue (UNRES) force field. The method has been tested on the protein 1E0L with a temperature-independent UNRES force field and on terminally blocked deca-alanine (Ala10) and 1GAB with the recently introduced temperature-dependent UNRES force field. With the temperature-independent force field, SREM reproduces the results of REM but is more efficient in terms of wall-clock time and scales better on distributed-memory machines. However, exact application of SREM to the temperature-dependent UNRES algorithm requires the determination of a four-dimensional distribution of UNRES energy components instead of a one-dimensional energy distribution for each temperature, which is prohibitively expensive. Hence, we assumed that the temperature dependence of the force field can be ignored for neighboring temperatures. This version of SREM worked for Ala10 which is a simple system but failed to reproduce the thermodynamic results as well as regular REM on the more complex 1GAB protein. Hence, SREM can be applied to the temperature-independent but not to the temperature-dependent UNRES force field. PMID:20011673

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.

PubMed

Paschek, Dietmar; Nymeyer, Hugh; García, Angel E

2007-03-01

We simulate the folding/unfolding equilibrium of the 20-residue miniprotein Trp-cage. We use replica exchange molecular dynamics simulations of the AMBER94 atomic detail model of the protein explicitly solvated by water, starting from a completely unfolded configuration. We employ a total of 40 replicas, covering the temperature range between 280 and 538 K. Individual simulation lengths of 100 ns sum up to a total simulation time of about 4 micros. Without any bias, we observe the folding of the protein into the native state with an unfolding-transition temperature of about 440 K. The native state is characterized by a distribution of root mean square distances (RMSD) from the NMR data that peaks at 1.8A, and is as low as 0.4A. We show that equilibration times of about 40 ns are required to yield convergence. A folded configuration in the entire extended ensemble is found to have a lifetime of about 31 ns. In a clamp-like motion, the Trp-cage opens up during thermal denaturation. In line with fluorescence quenching experiments, the Trp-residue sidechain gets hydrated when the protein opens up, roughly doubling the number of water molecules in the first solvation shell. We find the helical propensity of the helical domain of Trp-cage rather well preserved even at very high temperatures. In the folded state, we can identify states with one and two buried internal water molecules interconnecting parts of the Trp-cage molecule by hydrogen bonds. The loss of hydrogen bonds of these buried water molecules in the folded state with increasing temperature is likely to destabilize the folded state at elevated temperatures.

Long-time atomistic simulations with the Parallel Replica Dynamics method

NASA Astrophysics Data System (ADS)

Perez, Danny

Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

A Flow Perfusion Bioreactor System for Vocal Fold Tissue Engineering Applications.

PubMed

Latifi, Neda; Heris, Hossein K; Thomson, Scott L; Taher, Rani; Kazemirad, Siavash; Sheibani, Sara; Li-Jessen, Nicole Y K; Vali, Hojatollah; Mongeau, Luc

2016-09-01

The human vocal folds (VFs) undergo complex biomechanical stimulation during phonation. The aim of the present study was to develop and validate a phono-mimetic VF flow perfusion bioreactor, which mimics the mechanical microenvironment of the human VFs in vitro. The bioreactor uses airflow-induced self-oscillations, which have been shown to produce mechanical loading and contact forces that are representative of human phonation. The bioreactor consisted of two synthetic VF replicas within a silicone body. A cell-scaffold mixture (CSM) consisting of human VF fibroblasts, hyaluronic acid, gelatin, and a polyethylene glycol cross-linker was injected into cavities within the replicas. Cell culture medium (CCM) was perfused through the scaffold by using a customized secondary flow loop. After the injection, the bioreactor was operated with no stimulation over a 3-day period to allow for cell adaptation. Phonation was subsequently induced by using a variable speed centrifugal blower for 2 h each day over a period of 4 days. A similar bioreactor without biomechanical stimulation was used as the nonphonatory control. The CSM was harvested from both VF replicas 7 days after the injection. The results confirmed that the phono-mimetic bioreactor supports cell viability and extracellular matrix proteins synthesis, as expected. Many scaffold materials were found to degrade because of challenges from phonation-induced biomechanical stimulation as well as due to biochemical reactions with the CCM. The bioreactor concept enables future investigations of the effects of different phonatory characteristics, that is, voice regimes, on the behavior of the human VF cells. It will also help study the long-term functional outcomes of the VF-specific biomaterials before animal and clinical studies.

Nanohybrid vs. fine hybrid composite in Class II cavities: clinical results and margin analysis after four years.

PubMed

Krämer, Norbert; Reinelt, Christian; Richter, Gert; Petschelt, Anselm; Frankenberger, Roland

2009-06-01

This controlled prospective split-mouth study evaluated the clinical behavior of two different resin composites in extended Class II cavities over a period of four years. Thirty patients received 68 direct resin composite restorations (Grandio bonded with Solobond M: n=36, Tetric Ceram bonded with Syntac: n=32) by one dentist in a private practice. All restorations were replacement fillings, 24 cavities (35%) revealed no enamel at the bottom of the proximal box, in 33 cavities (48%) the proximal enamel width was less than 0.5mm. The restorations were examined according to modified USPHS criteria at baseline, and after six months, one, two, and four years. At each recall, impressions were taken for replica preparation. Replicas of 44 select subjects were assessed for marginal quality under a stereo light microscope (SLM) at 130x and 22 replicas were assessed under a scanning electron microscope (SEM) at 200x. Both recall rate and survival rate were 100% after four years of clinical service. No significant difference was found between the restorative materials (p>0.05; Mann-Whitney U-test). Hypersensitivities were significantly reduced over time (p<0.05; Friedman test). A significant deterioration over time was found for the criteria marginal integrity (66% bravo after four years), tooth integrity (15% bravo), filling integrity (73% bravo) and proximal contact (p<0.05; Friedman test). SLM and SEM analysis of restoration margins revealed differences in the amount of perfect margins, in favor of Tetric Ceram (p<0.05). Both materials performed satisfactorily over the four-year observation period. Due to the extension of the restorations, wear was clearly visible after four years of clinical service with 50% bravo ratings.

Disorders of "taste cognition" are associated with insular involvement in patients with Alzheimer's disease and vascular dementia: "memory of food is impaired in dementia and responsible for poor diet".

PubMed

Suto, Teiko; Meguro, Kenichi; Nakatsuka, Masahiro; Kato, Yuriko; Tezuka, Kimihiro; Yamaguchi, Satoshi; Tashiro, Manabu

2014-07-01

In dementia patients, dietary intake problems may occur despite the absence of swallowing problems. We investigated cognitive functions on food and taste in Alzheimer's disease (AD) and vascular dementia (VaD) patients. Participants included 15 healthy controls (HC), 30 AD and 20 VaD patients. Food Cognition Test: Replicas of three popular foods in Japan with no odors were presented visually to each participant, with the instruction to respond with the name of each food. Replicas of food materials were subsequently presented to ask whether they were included in these foods. Taste Cognition Test: Replicas of 12 kinds of foods were presented to describe their expected tastes. The AD/VaD groups exhibited significantly lower scores on Food/Taste Cognition Tests compared with the HC group. These scores correlated inversely with Mini-Mental State Examination (MMSE) scores in the AD group. Decreased dietary intake was observed in 12 of the 50 patients; 8 of the 12 exhibited decreased Taste Cognition Test scores, higher than that of the normal-intake patients. There was no difference in the filter paper taste disc test between HC/AD/VaD groups. To test the hypothesis that the insula is associated with taste cognition, two MMSE-matched AD subgroups (n = 10 vs. 10) underwent positron emission tomography. Glucose metabolism in the right insula was lower in the low taste cognition subgroup. The VaD patients with insular lesions exhibited impaired Taste Cognition Test findings. It is important to consider the cognitive aspect of dietary intake when we care for dementia patients.

Effects of different types of temporary cements on the tensile strength and marginal adaptation of crowns on implants.

PubMed

Akashia, Ana Eliza; Francischone, Carlos Eduardo; Tokutsune, Edson; da Silva, Walter

2002-01-01

The aim of this study was to evaluate the influence of four different types of temporary cements, Tempbond (Kerr), Tempbond NE (Kerr), Improv (Sterioss), and Dycal (Dentsply/Caulk), on the marginal adaptation and tensile strength of prosthetic specimens cemented on replicas of CeraOne abutments. Four test groups were formed: Group 1 (G-1), Tempbond (Kerr); Group 2 (G-2), Tempbond NE (Kerr); Group 3 (G-3), Improv (Sterioss); Group 4 (G-4), Dycal (Dentsply/Caulk). For the specimens, gold cylinders (DCB 160, Nobel Biocare) adapted to stainless steel replicas of CeraOne abutments (Nobel Biocare) were utilized. The replicas on a stainless steel base were made in a special machine for implant components. The cement thicknesses for each luting agent were measured using a Measurement Comparative Microscope (Mitutoyo). The readings obtained before cementation were used as the controls (G-0). Following each group's cementation, the specimens were submitted to tensile strength tests with a Universal Testing Machine (Kratus). The results of the marginal adaptation test as reflected by cement thicknesses were: G-0 = 11.7 microm, G-1 = 35.7 microm (+/- 8.8), G-2 = 41.7 microm (+/- 9.0), G-3 = 32.6 microm (+/- 9.7) and G-4 = 38.2 microm (+/- 6.7). The tensile strength tests yielded the following values: G-1 = 58.5 N (+/- 14.8), G-2 = 51 N (+/- 8.2), G-3 = 61.8 N (+/- 17.1) and G-4 = 71.8 N (+/- 9.3). The four temporary cements tested all provided similar marginal adaptation. G-4 (Dycal) showed a higher tensile strength than G-2 (Tempbond NE).

Accuracy of implant impressions without impression copings: a three-dimensional analysis.

PubMed

Kwon, Joo-Hyun; Son, Yong-Ha; Han, Chong-Hyun; Kim, Sunjai

2011-06-01

Implant impressions without impression copings can be used for cement-retained implant restorations. A comparison of the accuracy of implant impressions with and without impression copings is needed. The purpose of this study was to evaluate and compare the dimensional accuracy of implant definitive casts that are fabricated by implant impressions with and without impression copings. An acrylic resin maxillary model was fabricated, and 3 implant replicas were secured in the right second premolar, first, and second molars. Two impression techniques were used to fabricate definitive casts (n=10). For the coping group (Group C), open tray impression copings were used for the final impressions. For the no-coping group (Group NC), cementable abutments were connected to the implant replicas, and final impressions were made assuming the abutments were prepared teeth. Computerized calculation of the centroids and long axes of the implant or stone abutment replicas was performed. The Mann-Whitney U test analyzed the amount of linear and rotational distortion between groups (α =.05). At the first molar site, Group NC showed significantly greater linear distortion along the Y-axis, with a small difference between the groups (Group C, 7.8 ± 7.4 μm; Group NC, 19.5 ± 12.2). At the second molar site, increased distortion was noted in Group NC for every linear and rotational variable, except for linear distortion along the Z-axis. Implant impression with open tray impression copings produced more accurate definitive casts than those fabricated without impression copings, especially those with greater inter-abutment distance. Copyright © 2011 The Editorial Council of the Journal of Prosthetic Dentistry. Published by Mosby, Inc. All rights reserved.

Grid computing enhances standards-compatible geospatial catalogue service

NASA Astrophysics Data System (ADS)

Chen, Aijun; Di, Liping; Bai, Yuqi; Wei, Yaxing; Liu, Yang

2010-04-01

A catalogue service facilitates sharing, discovery, retrieval, management of, and access to large volumes of distributed geospatial resources, for example data, services, applications, and their replicas on the Internet. Grid computing provides an infrastructure for effective use of computing, storage, and other resources available online. The Open Geospatial Consortium has proposed a catalogue service specification and a series of profiles for promoting the interoperability of geospatial resources. By referring to the profile of the catalogue service for Web, an innovative information model of a catalogue service is proposed to offer Grid-enabled registry, management, retrieval of and access to geospatial resources and their replicas. This information model extends the e-business registry information model by adopting several geospatial data and service metadata standards—the International Organization for Standardization (ISO)'s 19115/19119 standards and the US Federal Geographic Data Committee (FGDC) and US National Aeronautics and Space Administration (NASA) metadata standards for describing and indexing geospatial resources. In order to select the optimal geospatial resources and their replicas managed by the Grid, the Grid data management service and information service from the Globus Toolkits are closely integrated with the extended catalogue information model. Based on this new model, a catalogue service is implemented first as a Web service. Then, the catalogue service is further developed as a Grid service conforming to Grid service specifications. The catalogue service can be deployed in both the Web and Grid environments and accessed by standard Web services or authorized Grid services, respectively. The catalogue service has been implemented at the George Mason University/Center for Spatial Information Science and Systems (GMU/CSISS), managing more than 17 TB of geospatial data and geospatial Grid services. This service makes it easy to share and interoperate geospatial resources by using Grid technology and extends Grid technology into the geoscience communities.

HUMAN ALVEOLAR AND PERITONEAL MACROPHAGES MEDIATE FUNGISTASIS INDEPENDENTLY OF L-ARGININE OXIDATION TO NITRITE OR NITRATE

EPA Science Inventory

Human alveolar macrophages (HAM) from 28 normal volunteers were found to inhibit replication of Cryptoccous neoformans. onditions under which fungistasis occurred were different than those required for mouse peritoneal macrophage-mediated fungi stasis. nhibition of fungal replica...

Neighborhood Preservation.

ERIC Educational Resources Information Center

Benin, Shirley

1984-01-01

Because of concern about the preservation of the historic character of Stamford (Connecticut), children in a pilot program at an elementary school learned about neighborhood history, sketched houses, researched houses which had been torn down and drew and constructed replicas of them, and learned about renovation and period interior design. (IS)

Growth in liquid or solid media.

PubMed

Elbing, K L; Brent, R

2001-05-01

This appendix presents basic procedures for growing overnight (and larger) cultures, monitoring growth, and titering and isolating bacterial cultures by serial dilution. In addition, protocols are provided for isolating single colonies by streaking and spreading a plate. Replica plating and strain storage/retrieval is also detailed.

Benchtop Nanoscale Patterning Using Soft Lithography

ERIC Educational Resources Information Center

Meenakshi, Viswanathan; Babayan, Yelizaveta; Odom, Teri W.

2007-01-01

This paper outlines several benchtop nanoscale patterning experiments that can be incorporated into undergraduate laboratories or advanced high school chemistry curricula. The experiments, supplemented by an online video lab manual, are based on soft lithographic techniques such as replica molding, micro-molding in capillaries, and micro-contact…

Replica and extreme-value analysis of the Jarzynski free-energy estimator

NASA Astrophysics Data System (ADS)

Palassini, Matteo; Ritort, Felix

2008-03-01

We analyze the Jarzynski estimator of free-energy differences from nonequilibrium work measurements. By a simple mapping onto Derrida's Random Energy Model, we obtain a scaling limit for the expectation of the bias of the estimator. We then derive analytical approximations in three different regimes of the scaling parameter x = log(N)/W, where N is the number of measurements and W the mean dissipated work. Our approach is valid for a generic distribution of the dissipated work, and is based on a replica symmetry breaking scheme for x >> 1, the asymptotic theory of extreme value statistics for x << 1, and a direct approach for x near one. The combination of the three analytic approximations describes well Monte Carlo data for the expectation value of the estimator, for a wide range of values of N, from N=1 to large N, and for different work distributions. Based on these results, we introduce improved free-energy estimators and discuss the application to the analysis of experimental data.

Behavioural responses of dogs to asymmetrical tail wagging of a robotic dog replica.

PubMed

Artelle, K A; Dumoulin, L K; Reimchen, T E

2011-03-01

Recent evidence suggests that bilateral asymmetry in the amplitude of tail wagging of domestic dogs (Canis familiaris) is associated with approach (right wag) versus withdrawal (left wag) motivation and may be the by-product of hemispheric dominance. We consider whether such asymmetry in motion of the tail, a crucial appendage in intra-specific communication in all canids, provides visual information to a conspecific leading to differential behaviour. To evaluate this, we experimentally investigated the approach behaviour of free-ranging dogs to the asymmetric tail wagging of a life-size robotic dog replica. Our data, involving 452 separate interactions, showed a significantly greater proportion of dogs approaching the model continuously without stopping when the tail wagged to the left, compared with a right wag, which was more likely to yield stops. While the results indicate that laterality of a wagging tail provides behavioural information to conspecifics, the responses are not readily integrated into the predicted behaviour based on hemispheric dominance.

Ontological Constraints in Children's Inductive Inferences: Evidence From a Comparison of Inferences Within Animals and Vehicles.

PubMed

Tarlowski, Andrzej

2018-01-01

There is a lively debate concerning the role of conceptual and perceptual information in young children's inductive inferences. While most studies focus on the role of basic level categories in induction the present research contributes to the debate by asking whether children's inductions are guided by ontological constraints. Two studies use a novel inductive paradigm to test whether young children have an expectation that all animals share internal commonalities that do not extend to perceptually similar inanimates. The results show that children make category-consistent responses when asked to project an internal feature from an animal to either a dissimilar animal or a similar toy replica. However, the children do not have a universal preference for category-consistent responses in an analogous task involving vehicles and vehicle toy replicas. The results also show the role of context and individual factors in inferences. Children's early reliance on ontological commitments in induction cannot be explained by perceptual similarity or by children's sensitivity to the authenticity of objects.

Precipitation behavior in austenitic and ferritic steels during fast neutron irradiation and thermal aging*1

NASA Astrophysics Data System (ADS)

Kawanishi, H.; Hajima, R.; Sekimura, N.; Arai, Y.; Ishino, S.

1988-07-01

Precipitation behavior has been studied using a carbon extraction replica technique in Ti-modified Type 316 stainless steels (JPCA-2) and 9Cr-2Mo ferritic/martensitic steels (JFMS) irradiated to 8.1 × 10 24 n/m 2 at 873 and 673 K, respectively, in the experimental fast breeder reactor JOYO. Precipitate identification and compositional analysis were carried out on extracted replicas. The results were compared to those from the as-received steel and a control which had been given the same thermal as-treatment as the specimens received during irradiations. Carbides, Ti-sulphides and phosphides were precipitated in JPCA-2. Precipitate observed in JFMS included carbides, Laves-phases and phosphides. The precipitates in both steels were concluded to be stable under irradiation except for MC and M 6C in JPCA-2. Small MC particles were found precipitated in JPCA-2 during both irradiation and aging. Irradiation proved to promote the precipitation of M 6C in JPCA-2.

Parallel replica dynamics method for bistable stochastic reaction networks: Simulation and sensitivity analysis

NASA Astrophysics Data System (ADS)

Wang, Ting; Plecháč, Petr

2017-12-01

Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed.

Quantum structural fluctuation in para-hydrogen clusters revealed by the variational path integral method

NASA Astrophysics Data System (ADS)

Miura, Shinichi

2018-03-01

In this paper, the ground state of para-hydrogen clusters for size regime N ≤ 40 has been studied by our variational path integral molecular dynamics method. Long molecular dynamics calculations have been performed to accurately evaluate ground state properties. The chemical potential of the hydrogen molecule is found to have a zigzag size dependence, indicating the magic number stability for the clusters of the size N = 13, 26, 29, 34, and 39. One-body density of the hydrogen molecule is demonstrated to have a structured profile, not a melted one. The observed magic number stability is examined using the inherent structure analysis. We also have developed a novel method combining our variational path integral hybrid Monte Carlo method with the replica exchange technique. We introduce replicas of the original system bridging from the structured to the melted cluster, which is realized by scaling the potential energy of the system. Using the enhanced sampling method, the clusters are demonstrated to have the structured density profile in the ground state.

Phase diagram of matrix compressed sensing

NASA Astrophysics Data System (ADS)

Schülke, Christophe; Schniter, Philip; Zdeborová, Lenka

2016-12-01

In the problem of matrix compressed sensing, we aim to recover a low-rank matrix from a few noisy linear measurements. In this contribution, we analyze the asymptotic performance of a Bayes-optimal inference procedure for a model where the matrix to be recovered is a product of random matrices. The results that we obtain using the replica method describe the state evolution of the Parametric Bilinear Generalized Approximate Message Passing (P-BiG-AMP) algorithm, recently introduced in J. T. Parker and P. Schniter [IEEE J. Select. Top. Signal Process. 10, 795 (2016), 10.1109/JSTSP.2016.2539123]. We show the existence of two different types of phase transition and their implications for the solvability of the problem, and we compare the results of our theoretical analysis to the numerical performance reached by P-BiG-AMP. Remarkably, the asymptotic replica equations for matrix compressed sensing are the same as those for a related but formally different problem of matrix factorization.

Disk storage management for LHCb based on Data Popularity estimator

NASA Astrophysics Data System (ADS)

Hushchyn, Mikhail; Charpentier, Philippe; Ustyuzhanin, Andrey

2015-12-01

This paper presents an algorithm providing recommendations for optimizing the LHCb data storage. The LHCb data storage system is a hybrid system. All datasets are kept as archives on magnetic tapes. The most popular datasets are kept on disks. The algorithm takes the dataset usage history and metadata (size, type, configuration etc.) to generate a recommendation report. This article presents how we use machine learning algorithms to predict future data popularity. Using these predictions it is possible to estimate which datasets should be removed from disk. We use regression algorithms and time series analysis to find the optimal number of replicas for datasets that are kept on disk. Based on the data popularity and the number of replicas optimization, the algorithm minimizes a loss function to find the optimal data distribution. The loss function represents all requirements for data distribution in the data storage system. We demonstrate how our algorithm helps to save disk space and to reduce waiting times for jobs using this data.

Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

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

Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn

2015-03-28

The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much lessmore » computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.« less

Quantum Effects in Inverse Opal Structures

NASA Astrophysics Data System (ADS)

Bleiweiss, Michael; Datta, Timir; Lungu, Anca; Yin, Ming; Iqbal, Zafar; Palm, Eric; Brandt, Bruce

2002-03-01

Properties of bismuth inverse opals and carbon opal replicas were studied. The bismuth nanostructures were fabricated by pressure infiltration into porous artificial opal, while the carbon opal replicas were created via CVD. These structures form a regular three-dimensional network in which the bismuth and carbon regions percolate in all directions between the close packed spheres of SiO_2. The sizes of the conducting regions are of the order of tens of nanometers. Static susceptibility of the bismuth inverse opal showed clear deHaas-vanAlphen oscillations. Transport measurements, including Hall, were done using standard ac four and six probe techniques in fields up to 17 T* and temperatures between 4.2 and 200 K. Observations of Shubnikov-deHaas oscillations in magnetoresistance, one-dimensional weak localization, quantum Hall and other effects will be discussed. *Performed at the National High Magnetic Field Lab (NHMFL) FSU, Tallahassee, FL. This work was partially supported by grants from DARPA-nanothermoelectrics, NASA-EPSCOR and the USC nanocenter.

Conformational free energies of methyl-α-L-iduronic and methyl-β-D-glucuronic acids in water

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Sagui, Celeste

2010-03-01

We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a nonequilibrium umbrella sampling method, in this case, the recently developed adaptively biased molecular dynamics method, to compute an approximate free energy for the slow modes of the solute in explicit solvent. This approximate free energy is then used to set up a Hamiltonian replica exchange scheme that samples both from biased and unbiased distributions. The final accurate free energy is recovered via the weighted histogram analysis technique applied to all the replicas, and equilibrium properties of the solute are computed from the unbiased trajectory. We illustrate the approach by applying it to the study of the puckering landscapes of the methyl glycosides of α-L-iduronic acid and its C5 epimer β-D-glucuronic acid in water. Big savings in computational resources are gained in comparison to the standard parallel tempering method.

Replicas of the Santa Maria, Nina, Pinta sail by OV-105 on KSC LC Pad 39B

NASA Image and Video Library

1992-05-06

S92-39074 (6 May 1992) --- The centuries-old technology that built Christopher Columbus' three sailing ships passes within a half mile of the 20th-Century Space Shuttle Endeavour, in background, awaiting liftoff on Launch Pad 39B. The replicas of the Santa Maria, Nina, and Pinta wind-powered ships, managed by the Spain '92 Foundation, are on a tour to ports around the Gulf of Mexico and up the Atlantic Coast of the United States. Endeavour is set to lift off on its maiden voyage, STS-49, on May 7, 1992. Video footage of the two types of exploration vessels will be used by NASA for a variety of productions, including the annual Von Braun Exploration forum sponsored by NASA's Marshall Space Flight Center (MSFC), Huntsville, Alabama, in October, 1992. This year's theme is Exploration and the Evolution of Nations. 1992 is the 500th anniversary of Columbus' voyage to the New World.

Chaotic carrier pulse position modulation communication system and method

DOEpatents

Abarbanel, Henry D. I.; Larson, Lawrence E.; Rulkov, Nikolai F.; Sushchik, Mikhail M.; Tsimring, Lev S.; Volkovskii, Alexander R.

2001-01-01

A chaotic carrier pulse position modulation communication system and method is disclosed. The system includes a transmitter and receiver having matched chaotic pulse regenerators. The chaotic pulse regenerator in the receiver produces a synchronized replica of a chaotic pulse train generated by the regenerator in the transmitter. The pulse train from the transmitter can therefore act as a carrier signal. Data is encoded by the transmitter through selectively altering the interpulse timing between pulses in the chaotic pulse train. The altered pulse train is transmitted as a pulse signal. The receiver can detect whether a particular interpulse interval in the pulse signal has been altered by reference to the synchronized replica it generates, and can therefore detect the data transmitted by the receiver. Preferably, the receiver predicts the earliest moment in time it can expect a next pulse after observation of at least two consecutive pulses. It then decodes the pulse signal beginning at a short time before expected arrival of a pulse.

Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water.

PubMed

Babin, Volodymyr; Sagui, Celeste

2010-03-14

We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a nonequilibrium umbrella sampling method, in this case, the recently developed adaptively biased molecular dynamics method, to compute an approximate free energy for the slow modes of the solute in explicit solvent. This approximate free energy is then used to set up a Hamiltonian replica exchange scheme that samples both from biased and unbiased distributions. The final accurate free energy is recovered via the weighted histogram analysis technique applied to all the replicas, and equilibrium properties of the solute are computed from the unbiased trajectory. We illustrate the approach by applying it to the study of the puckering landscapes of the methyl glycosides of alpha-L-iduronic acid and its C5 epimer beta-D-glucuronic acid in water. Big savings in computational resources are gained in comparison to the standard parallel tempering method.

Fog collecting biomimetic surfaces: Influence of microstructure and wettability.

PubMed

Azad, M A K; Ellerbrok, D; Barthlott, W; Koch, K

2015-01-19

We analyzed the fog collection efficiency of three different sets of samples: replica (with and without microstructures), copper wire (smooth and microgrooved) and polyolefin mesh (hydrophilic, superhydrophilic and hydrophobic). The collection efficiency of the samples was compared in each set separately to investigate the influence of microstructures and/or the wettability of the surfaces on fog collection. Based on the controlled experimental conditions chosen here large differences in the efficiency were found. We found that microstructured plant replica samples collected 2-3 times higher amounts of water than that of unstructured (smooth) samples. Copper wire samples showed similar results. Moreover, microgrooved wires had a faster dripping of water droplets than that of smooth wires. The superhydrophilic mesh tested here was proved more efficient than any other mesh samples with different wettability. The amount of collected fog by superhydrophilic mesh was about 5 times higher than that of hydrophilic (untreated) mesh and was about 2 times higher than that of hydrophobic mesh.

Ontological Constraints in Children's Inductive Inferences: Evidence From a Comparison of Inferences Within Animals and Vehicles

PubMed Central

Tarlowski, Andrzej

2018-01-01

There is a lively debate concerning the role of conceptual and perceptual information in young children's inductive inferences. While most studies focus on the role of basic level categories in induction the present research contributes to the debate by asking whether children's inductions are guided by ontological constraints. Two studies use a novel inductive paradigm to test whether young children have an expectation that all animals share internal commonalities that do not extend to perceptually similar inanimates. The results show that children make category-consistent responses when asked to project an internal feature from an animal to either a dissimilar animal or a similar toy replica. However, the children do not have a universal preference for category-consistent responses in an analogous task involving vehicles and vehicle toy replicas. The results also show the role of context and individual factors in inferences. Children's early reliance on ontological commitments in induction cannot be explained by perceptual similarity or by children's sensitivity to the authenticity of objects. PMID:29760669

Quantum structural fluctuation in para-hydrogen clusters revealed by the variational path integral method.

PubMed

Miura, Shinichi

2018-03-14

In this paper, the ground state of para-hydrogen clusters for size regime N ≤ 40 has been studied by our variational path integral molecular dynamics method. Long molecular dynamics calculations have been performed to accurately evaluate ground state properties. The chemical potential of the hydrogen molecule is found to have a zigzag size dependence, indicating the magic number stability for the clusters of the size N = 13, 26, 29, 34, and 39. One-body density of the hydrogen molecule is demonstrated to have a structured profile, not a melted one. The observed magic number stability is examined using the inherent structure analysis. We also have developed a novel method combining our variational path integral hybrid Monte Carlo method with the replica exchange technique. We introduce replicas of the original system bridging from the structured to the melted cluster, which is realized by scaling the potential energy of the system. Using the enhanced sampling method, the clusters are demonstrated to have the structured density profile in the ground state.

Community detection for fluorescent lifetime microscopy image segmentation

NASA Astrophysics Data System (ADS)

Hu, Dandan; Sarder, Pinaki; Ronhovde, Peter; Achilefu, Samuel; Nussinov, Zohar

2014-03-01

Multiresolution community detection (CD) method has been suggested in a recent work as an efficient method for performing unsupervised segmentation of fluorescence lifetime (FLT) images of live cell images containing fluorescent molecular probes.1 In the current paper, we further explore this method in FLT images of ex vivo tissue slices. The image processing problem is framed as identifying clusters with respective average FLTs against a background or "solvent" in FLT imaging microscopy (FLIM) images derived using NIR fluorescent dyes. We have identified significant multiresolution structures using replica correlations in these images, where such correlations are manifested by information theoretic overlaps of the independent solutions ("replicas") attained using the multiresolution CD method from different starting points. In this paper, our method is found to be more efficient than a current state-of-the-art image segmentation method based on mixture of Gaussian distributions. It offers more than 1:25 times diversity based on Shannon index than the latter method, in selecting clusters with distinct average FLTs in NIR FLIM images.

The glassy random laser: replica symmetry breaking in the intensity fluctuations of emission spectra

PubMed Central

Antenucci, Fabrizio; Crisanti, Andrea; Leuzzi, Luca

2015-01-01

The behavior of a newly introduced overlap parameter, measuring the correlation between intensity fluctuations of waves in random media, is analyzed in different physical regimes, with varying amount of disorder and non-linearity. This order parameter allows to identify the laser transition in random media and describes its possible glassy nature in terms of emission spectra data, the only data so far accessible in random laser measurements. The theoretical analysis is performed in terms of the complex spherical spin-glass model, a statistical mechanical model describing the onset and the behavior of random lasers in open cavities. Replica Symmetry Breaking theory allows to discern different kinds of randomness in the high pumping regime, including the most complex and intriguing glassy randomness. The outcome of the theoretical study is, eventually, compared to recent intensity fluctuation overlap measurements demonstrating the validity of the theory and providing a straightforward interpretation of qualitatively different spectral behaviors in different random lasers. PMID:26616194

A SIMPLE FREEZE-FRACTURE REPLICATION METHOD FOR ELECTRON MICROSCOPY

PubMed Central

Bullivant, Stanley; Ames, Adelbert

1966-01-01

A simple method to achieve results similar to the freeze-etching technique of Moor et al. (1961) is described. The frozen tissue is cut under liquid nitrogen with a razor blade outside the evaporator rather than inside with a cooled microtome. The conditions of the experiment do not favor sublimation, and it is proposed that the structure of the replica be explained by local faults in the cleavage plane which leaves structures, such as membranes, standing above the ice. Micrographs of replicas of glycerol-protected frozen small intestine of mouse prepared by the method are presented and the structural details they show are discussed. The problem of vapor-deposited contamination is discussed. It is concluded that this is a practical method for obtaining electron micrographs that are relatively free of artifact, and that further improvements may be expected from the use of rapidly frozen fresh tissue and a clean vacuum system, possibly of the ion-pumped type. PMID:5962938

Advances in thermographic signal reconstruction

NASA Astrophysics Data System (ADS)

Shepard, Steven M.; Frendberg Beemer, Maria

2015-05-01

Since its introduction in 2001, the Thermographic Signal Reconstruction (TSR) method has emerged as one of the most widely used methods for enhancement and analysis of thermographic sequences, with applications extending beyond industrial NDT into biomedical research, art restoration and botany. The basic TSR process, in which a noise reduced replica of each pixel time history is created, yields improvement over unprocessed image data that is sufficient for many applications. However, examination of the resulting logarithmic time derivatives of each TSR pixel replica provides significant insight into the physical mechanisms underlying the active thermography process. The deterministic and invariant properties of the derivatives have enabled the successful implementation of automated defect recognition and measurement systems. Unlike most approaches to analysis of thermography data, TSR does not depend on flawbackground contrast, so that it can also be applied to characterization and measurement of thermal properties of flaw-free samples. We present a summary of recent advances in TSR, a review of the underlying theory and examples of its implementation.

Towards an optimal flow: Density-of-states-informed replica-exchange simulations

DOE PAGES

Vogel, Thomas; Perez, Danny

2015-11-05

Here we learn that replica exchange (RE) is one of the most popular enhanced-sampling simulations technique in use today. Despite widespread successes, RE simulations can sometimes fail to converge in practical amounts of time, e.g., when sampling around phase transitions, or when a few hard-to-find configurations dominate the statistical averages. We introduce a generalized RE scheme, density-of-states-informed RE, that addresses some of these challenges. The key feature of our approach is to inform the simulation with readily available, but commonly unused, information on the density of states of the system as the RE simulation proceeds. This enables two improvements, namely,more » the introduction of resampling moves that actively move the system towards equilibrium and the continual adaptation of the optimal temperature set. As a consequence of these two innovations, we show that the configuration flow in temperature space is optimized and that the overall convergence of RE simulations can be dramatically accelerated.« less

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

PubMed

Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

2015-06-09

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Effect of osmolytes on the thermal stability of proteins: replica exchange simulations of Trp-cage in urea and betaine solutions.

PubMed

Adamczak, Beata; Kogut, Mateusz; Czub, Jacek

2018-04-25

Although osmolytes are known to modulate the folding equilibrium, the molecular mechanism of their effect on thermal denaturation of proteins is still poorly understood. Here, we simulated the thermal denaturation of a small model protein (Trp-cage) in the presence of denaturing (urea) and stabilizing (betaine) osmolytes, using the all-atom replica exchange molecular dynamics simulations. We found that urea destabilizes Trp-cage by enthalpically-driven association with the protein, acting synergistically with temperature to induce unfolding. In contrast, betaine is sterically excluded from the protein surface thereby exerting entropic depletion forces that contribute to the stabilization of the native state. In fact, we find that while at low temperatures betaine slightly increases the folding free energy of Trp-cage by promoting another near-native conformation, it protects the protein against temperature-induced denaturation. This, in turn, can be attributed to enhanced exclusion of betaine at higher temperatures that arises from less attractive interactions with the protein surface.

Rontgen's Discovery of X Rays

ERIC Educational Resources Information Center

Thumm, Walter

1975-01-01

Relates the story of Wilhelm Conrad Rontgen and presents one view of the extent to which the discovery of the x-ray was an accident. Reconstructs the sequence of events that led to the discovery and includes photographs of the lab where he worked and replicas of apparatus used. (GS)

Challenging the Context: Perception, Polity, and Power.

ERIC Educational Resources Information Center

Hartfield, Ronne

1994-01-01

"Contextual areas" employ models, replicas, artwork, art materials, tools, interpretive panels, and interactive computer installations to help visitors explore the historical and cultural context of 6 of 12 works of art at the "Art Inside Out" exhibition in the Kraft General Foods Education Center of the Art Institute of Chicago. (MDH)

34 CFR 3.3 - Authority to affix seal.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 34 Education 1 2012-07-01 2012-07-01 false Authority to affix seal. 3.3 Section 3.3 Education Office of the Secretary, Department of Education OFFICIAL SEAL § 3.3 Authority to affix seal. The Secretary and the Secretary's designees are authorized to affix the Official Seal, replicas, reproductions...

34 CFR 3.3 - Authority to affix seal.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 34 Education 1 2014-07-01 2014-07-01 false Authority to affix seal. 3.3 Section 3.3 Education Office of the Secretary, Department of Education OFFICIAL SEAL § 3.3 Authority to affix seal. The Secretary and the Secretary's designees are authorized to affix the Official Seal, replicas, reproductions...

34 CFR 3.3 - Authority to affix seal.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 34 Education 1 2013-07-01 2013-07-01 false Authority to affix seal. 3.3 Section 3.3 Education Office of the Secretary, Department of Education OFFICIAL SEAL § 3.3 Authority to affix seal. The Secretary and the Secretary's designees are authorized to affix the Official Seal, replicas, reproductions...

Constructing a Celestial Calendar Wheel.

ERIC Educational Resources Information Center

Cousineau, Sarah M.

1999-01-01

Explains how to create a paper replica of the Bighorn Medicine Wheel, an ancient timepiece thought to have been constructed by the Lakota Indians around 1700 A.D. The Bighorn Wheel uses four key seasonal stars as well as the solstice sunrise and sunset to mark the passage of time through the summer. (WRM)

34 CFR 3.3 - Authority to affix seal.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 34 Education 1 2011-07-01 2011-07-01 false Authority to affix seal. 3.3 Section 3.3 Education Office of the Secretary, Department of Education OFFICIAL SEAL § 3.3 Authority to affix seal. The Secretary and the Secretary's designees are authorized to affix the Official Seal, replicas, reproductions...

34 CFR 3.3 - Authority to affix seal.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 34 Education 1 2010-07-01 2010-07-01 false Authority to affix seal. 3.3 Section 3.3 Education Office of the Secretary, Department of Education OFFICIAL SEAL § 3.3 Authority to affix seal. The Secretary and the Secretary's designees are authorized to affix the Official Seal, replicas, reproductions...

76 FR 21944 - Petition for Waiver of Compliance

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-19

... which a replica constructed in 1979, from the same blueprints and tooling is owned and operated by the National Park Service at Promontory Summit, Utah. The Leviathan is constructed to educate the public... Safety Appliance Standards (Sec. 231.15 (b) and (d), Steam locomotives used in road service-- Pilot sill...

Getting Shocks: Teaching Secondary School Physics through History.

ERIC Educational Resources Information Center

Heering, Peter

2000-01-01

Uses several replicas of experimental set-ups that were originally used in electrostatic research in teaching electrostatics through history on secondary school level. Makes visible the change of the style of electrostatic experimentation that took place at the end of the 18th century. (Contains 25 references.) (ASK)

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

Hacke, P.; Terwilliger, K.; Koch, S.

Three crystalline silicon module designs were distributed in five replicas each to five laboratories for testing according to the IEC 62804 (Committee Draft) system voltage durability qualification test for crystalline silicon photovoltaic (PV) modules. The stress tests were performed in environmental chambers at 60 degrees C, 85% relative humidity, 96 h, and with module nameplate system voltage applied.

Phylogenetic Systematics of Schacontia Dyar with a description of eight new species (Lepidoptera: Crambidae)

USDA-ARS?s Scientific Manuscript database

The Neotropical genus Schacontia Dyar (1914) is reviewed and revised to include twelve species. Schacontia replica Dyar, 1914 new synonymy and S. pfeifferi Amsel, 1956 new synonymy are synonymized with S. chanesalis (Druce, 1899) and eight new species are described: Schacontia umbra new species, S. ...

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

Saakyan, D.B.

The variant of the Kirkpatrick-Sherrington model generalized by Derrida for the case of arbitrary spin is considered. When the number of simultaneously interacting neighbors tends to infinity, a solution to the model is obtained not only by reduction to the random-energy model but also by means of the replica method with the Parisi ansatz.

2013 Inaugural Parade

NASA Image and Video Library

2013-01-21

A replica of NASA's Curiosity Rover and members of the Mars Science Laboratory (MSL) science team pass the Presidential viewing stand and President Barack Obama during the inaugural parade honoring Obama, Monday Jan. 21, 2013, in Washington. Obama was sworn-in as the nation's 44th President earlier in the day. Photo Credit: (NASA/Bill Ingalls)

34 CFR 3.4 - Use of the seal.

Code of Federal Regulations, 2013 CFR

2013-07-01

... plaques; (4) For electronic media, motion picture film, video tape and other audiovisual media prepared by...) On electronic media, motion picture film, video tape, and other audiovisual media prepared by or for... seal, replica, reproduction or embossing seal is punishable under 18 U.S.C. 506. (g) Any person using...

34 CFR 3.4 - Use of the seal.

Code of Federal Regulations, 2011 CFR

2011-07-01

... plaques; (4) For electronic media, motion picture film, video tape and other audiovisual media prepared by...) On electronic media, motion picture film, video tape, and other audiovisual media prepared by or for... seal, replica, reproduction or embossing seal is punishable under 18 U.S.C. 506. (g) Any person using...

34 CFR 3.4 - Use of the seal.

Code of Federal Regulations, 2012 CFR

2012-07-01

... plaques; (4) For electronic media, motion picture film, video tape and other audiovisual media prepared by...) On electronic media, motion picture film, video tape, and other audiovisual media prepared by or for... seal, replica, reproduction or embossing seal is punishable under 18 U.S.C. 506. (g) Any person using...

34 CFR 3.4 - Use of the seal.

Code of Federal Regulations, 2010 CFR

2010-07-01

... plaques; (4) For electronic media, motion picture film, video tape and other audiovisual media prepared by...) On electronic media, motion picture film, video tape, and other audiovisual media prepared by or for... seal, replica, reproduction or embossing seal is punishable under 18 U.S.C. 506. (g) Any person using...

34 CFR 3.4 - Use of the seal.

Code of Federal Regulations, 2014 CFR

2014-07-01

... plaques; (4) For electronic media, motion picture film, video tape and other audiovisual media prepared by...) On electronic media, motion picture film, video tape, and other audiovisual media prepared by or for... seal, replica, reproduction or embossing seal is punishable under 18 U.S.C. 506. (g) Any person using...

Leaf Histology--Two Modern Methods.

ERIC Educational Resources Information Center

Freeman, H. E.

1984-01-01

Two methods for examining leaf structure are presented; both methods involve use of "superglue." The first method uses the glue to form a thin, permanent, direct replica of a leaf surface on a microscope slide. The second method uses the glue to examine the three-dimensional structure of spongy mesophyll. (JN)

36 CFR 1200.1 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 1200.1 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION GENERAL RULES... means a display of the form and content of the official seal made on a die so that the seal can be... content. Replica or reproduction means a copy of an official seal or NARA logo displaying the form and...

Audio-Visual Speech Perception Is Special

ERIC Educational Resources Information Center

Tuomainen, J.; Andersen, T.S.; Tiippana, K.; Sams, M.

2005-01-01

In face-to-face conversation speech is perceived by ear and eye. We studied the prerequisites of audio-visual speech perception by using perceptually ambiguous sine wave replicas of natural speech as auditory stimuli. When the subjects were not aware that the auditory stimuli were speech, they showed only negligible integration of auditory and…

28 CFR 803.2 - Authority to affix seal.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 28 Judicial Administration 2 2011-07-01 2011-07-01 false Authority to affix seal. 803.2 Section... COLUMBIA AGENCY SEAL § 803.2 Authority to affix seal. The Director of CSOSA or PSA (as appropriate) and the Director's designees are authorized to affix the Agency seal (including replicas and reproductions) to...

A Wheelchair User with Visual and Intellectual Disabilities Managing Simple Orientation Technology for Indoor Travel

ERIC Educational Resources Information Center

Lancioni, Giulio E.; O'Reilly, Mark F.; Singh, Nirbhay N.; Sigafoos, Jeff; Campodonico, Francesca; Oliva, Doretta

2009-01-01

Persons with profound visual impairments and other disabilities, such as neuromotor and intellectual disabilities, may encounter serious orientation and mobility problems even in familiar indoor environments, such as their homes. Teaching these persons to develop maps of their daily environment, using miniature replicas of the areas or some…

Development of a gastrointestinal tract microscale cell culture analog to predict drug transport

USDA-ARS?s Scientific Manuscript database

Microscale cell culture analogs (uCCAs) are used to study the metabolism and toxicity of a chemical or drug. These in vitro devices are physical replicas of physiologically based pharmacokinetic models that combine microfabrication and cell culture. The goal of this project is to add an independent ...

Third-Graders Learn about Fractions Using Virtual Manipulatives: A Classroom Study

ERIC Educational Resources Information Center

Reimer, Kelly; Moyer, Patricia S.

2005-01-01

With recent advances in computer technology, it is no surprise that the manipulation of objects in mathematics classrooms now includes the manipulation of objects on the computer screen. These objects, referred to as "virtual manipulatives," are essentially replicas of physical manipulatives placed on the World Wide Web in the form of computer…

Hudson River School

ERIC Educational Resources Information Center

McCloskey, Patrick J.

2004-01-01

In this article, the author features the "Clearwater," a full-size working replica of a 19th century Hudson River cargo sloop. The "Clearwater" has been serving New York state students as a link to both local history and the environment, helping them to learn lessons about the history of the Hudson River and the environment,…

Electrophysiological Evidence for a Multisensory Speech-Specific Mode of Perception

ERIC Educational Resources Information Center

Stekelenburg, Jeroen J.; Vroomen, Jean

2012-01-01

We investigated whether the interpretation of auditory stimuli as speech or non-speech affects audiovisual (AV) speech integration at the neural level. Perceptually ambiguous sine-wave replicas (SWS) of natural speech were presented to listeners who were either in "speech mode" or "non-speech mode". At the behavioral level, incongruent lipread…

A School That Captures the Globe.

ERIC Educational Resources Information Center

Walters, Jane

1993-01-01

To teach geography by osmosis, a Memphis high school has evolved into a replica of the world, with each wing a continent and each room a country. Students participate in an annual international celebration showcasing national flags, native dress, and traditional dances, customs, and food. Fund-raising and other learning activities are described.…

A Laboratory Exercise Illustrating the Sensitivity and Specificity of Western Blot Analysis

ERIC Educational Resources Information Center

Chang, Ming-Mei; Lovett, Janice

2011-01-01

Western blot analysis, commonly known as "Western blotting," is a standard tool in every laboratory where proteins are analyzed. It involves the separation of polypeptides in polyacrylamide gels followed by the electrophoretic transfer of the separated polypeptides onto a nitrocellulose or polyvinylidene fluoride membrane. A replica of the…

Assessment of mild steel damage characteristics by physical methods

NASA Astrophysics Data System (ADS)

Botvina, L. R.; Soldatenkov, A. P.; Levin, V. P.; Tyutin, M. R.; Demina, Yu. A.; Petersen, T. B.; Dubov, A. A.; Semashko, N. A.

2016-01-01

The deformation and fracture localization characteristics are estimated by the methods of replicas, acoustic emission, metal magnetic memory, ultrasonic attenuation, microhardness, and electrical resistance. The relation between the estimated physical parameters on the one hand and the plastic zone size and the microcrack concentration in this zone, on the other, is considered.

10 CFR 1002.12 - Use of replicas, reproductions, and embossing seals.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., certificates, medals, and plaques. (5) Motion picture film, video tape and other audiovisual media prepared by...) Motion picture film, video tape, and other audiovisual media prepared by or for DOE and attributed... with this part shall be subject to the provisions of 18 U.S.C. 1017, providing penalties for the...

10 CFR 1002.12 - Use of replicas, reproductions, and embossing seals.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., certificates, medals, and plaques. (5) Motion picture film, video tape and other audiovisual media prepared by...) Motion picture film, video tape, and other audiovisual media prepared by or for DOE and attributed... with this part shall be subject to the provisions of 18 U.S.C. 1017, providing penalties for the...

10 CFR 1002.12 - Use of replicas, reproductions, and embossing seals.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., certificates, medals, and plaques. (5) Motion picture film, video tape and other audiovisual media prepared by...) Motion picture film, video tape, and other audiovisual media prepared by or for DOE and attributed... with this part shall be subject to the provisions of 18 U.S.C. 1017, providing penalties for the...

10 CFR 1002.12 - Use of replicas, reproductions, and embossing seals.

Code of Federal Regulations, 2013 CFR

2013-01-01

..., certificates, medals, and plaques. (5) Motion picture film, video tape and other audiovisual media prepared by...) Motion picture film, video tape, and other audiovisual media prepared by or for DOE and attributed... with this part shall be subject to the provisions of 18 U.S.C. 1017, providing penalties for the...

10 CFR 1002.12 - Use of replicas, reproductions, and embossing seals.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., certificates, medals, and plaques. (5) Motion picture film, video tape and other audiovisual media prepared by...) Motion picture film, video tape, and other audiovisual media prepared by or for DOE and attributed... with this part shall be subject to the provisions of 18 U.S.C. 1017, providing penalties for the...

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

Creutz, Michael

Using the Sigma model to explore the lowest order pseudo-scalar spectrum with SU(3) breaking, this talk considers an additional exact "taste" symmetry to mimic species doubling. Rooting replicas of a valid approach such as Wilson fermions reproduces the desired physical spectrum. In contrast, extra symmetries of the rooted staggered approach leave spurious states and a flavor dependent taste multiplicity.

The Mediated Museum: Computer-Based Technology and Museum Infrastructure.

ERIC Educational Resources Information Center

Sterman, Nanette T.; Allen, Brockenbrough S.

1991-01-01

Describes the use of computer-based tools and techniques in museums. The integration of realia with media-based advice and interpretation is described, electronic replicas of ancient Greek vases in the J. Paul Getty Museum are explained, examples of mediated exhibits are presented, and the use of hypermedia is discussed. (five references) (LRW)

Specific functions of the Rep and Rep' proteins of porcine circovirus during copy-release and rolling-circle DNA replication

USDA-ARS?s Scientific Manuscript database

The roles of two porcine circovirus replication initiator proteins, Rep and Rep', in generating copy-release and rolling-circle DNA replication intermediates were determined. Rep uses the supercoiled closed-circular genome (ccc) to initiate leading-strand synthesis (identical to copy-release replica...

Effects of moiré lattice structure on electronic properties of graphene

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

Huang, Lunan; Wu, Yun; Hershberger, M. T.

Here, we study structural and electronic properties of graphene grown on silicone carbide (SiC) substrate using a scanning tunneling microscope, spot-profile-analysis low-energy electron diffraction, and angle-resolved photoemission spectroscopy. We find several new replicas of Dirac cones in the Brillouin zone. Their locations can be understood in terms of a combination of basis vectors linked to SiC 6 × 6 and graphene 6√3×6√3 reconstruction. Therefore, these new features originate from the moiré caused by the lattice mismatch between SiC and graphene. More specifically, Dirac cone replicas are caused by underlying weak modulation of the ionic potential by the substrate that ismore » then experienced by the electrons in the graphene. We also demonstrate that this effect is equally strong in single- and trilayer graphene; therefore, the additional Dirac cones are intrinsic features rather than the result of photoelectron diffraction. These new features in the electronic structure are very important for the interpretation of recent transport measurements and can assist in tuning the properties of graphene for practical applications.« less

Efficient parallel implementations of QM/MM-REMD (quantum mechanical/molecular mechanics-replica-exchange MD) and umbrella sampling: isomerization of H2O2 in aqueous solution.

PubMed

Fedorov, Dmitri G; Sugita, Yuji; Choi, Cheol Ho

2013-07-03

An efficient parallel implementation of QM/MM-based replica-exchange molecular dynamics (REMD) as well as umbrella samplings techniques was proposed by adopting the generalized distributed data interface (GDDI). Parallelization speed-up of 40.5 on 48 cores was achieved, making our QM/MM-MD engine a robust tool for studying complex chemical dynamics in solution. They were comparatively used to study the torsional isomerization of hydrogen peroxide in aqueous solution. All results by QM/MM-REMD and QM/MM umbrella sampling techniques yielded nearly identical potentials of mean force (PMFs) regardless of the particular QM theories for solute, showing that the overall dynamics are mainly determined by solvation. Although the entropic penalty of solvent rearrangements exists in cisoid conformers, it was found that both strong intermolecular hydrogen bonding and dipole-dipole interactions preferentially stabilize them in solution, reducing the torsional free-energy barrier at 0° by about 3 kcal/mol as compared to that in gas phase.

Statistical mechanics of a single particle in a multiscale random potential: Parisi landscapes in finite-dimensional Euclidean spaces

NASA Astrophysics Data System (ADS)

Fyodorov, Yan V.; Bouchaud, Jean-Philippe

2008-08-01

We construct an N-dimensional Gaussian landscape with multiscale, translation invariant, logarithmic correlations and investigate the statistical mechanics of a single particle in this environment. In the limit of high dimension N → ∞ the free energy of the system and overlap function are calculated exactly using the replica trick and Parisi's hierarchical ansatz. In the thermodynamic limit, we recover the most general version of the Derrida's generalized random energy model (GREM). The low-temperature behaviour depends essentially on the spectrum of length scales involved in the construction of the landscape. If the latter consists of K discrete values, the system is characterized by a K-step replica symmetry breaking solution. We argue that our construction is in fact valid in any finite spatial dimensions N >= 1. We discuss the implications of our results for the singularity spectrum describing multifractality of the associated Boltzmann-Gibbs measure. Finally we discuss several generalizations and open problems, such as the dynamics in such a landscape and the construction of a generalized multifractal random walk.

Topological terms, AdS2 n gravity, and renormalized entanglement entropy of holographic CFTs

NASA Astrophysics Data System (ADS)

Anastasiou, Giorgos; Araya, Ignacio J.; Olea, Rodrigo

2018-05-01

We extend our topological renormalization scheme for entanglement entropy to holographic CFTs of arbitrary odd dimensions in the context of the AdS /CFT correspondence. The procedure consists in adding the Chern form as a boundary term to the area functional of the Ryu-Takayanagi minimal surface. The renormalized entanglement entropy thus obtained can be rewritten in terms of the Euler characteristic and the AdS curvature of the minimal surface. This prescription considers the use of the replica trick to express the renormalized entanglement entropy in terms of the renormalized gravitational action evaluated on the conically singular replica manifold extended to the bulk. This renormalized action is obtained in turn by adding the Chern form as the counterterm at the boundary of the 2 n -dimensional asymptotically AdS bulk manifold. We explicitly show that, up to next-to-leading order in the holographic radial coordinate, the addition of this boundary term cancels the divergent part of the entanglement entropy. We discuss possible applications of the method for studying CFT parameters like central charges.

Generalized ensemble method applied to study systems with strong first order transitions

DOE PAGES

Malolepsza, E.; Kim, J.; Keyes, T.

2015-09-28

At strong first-order phase transitions, the entropy versus energy or, at constant pressure, enthalpy, exhibits convex behavior, and the statistical temperature curve correspondingly exhibits an S-loop or back-bending. In the canonical and isothermal-isobaric ensembles, with temperature as the control variable, the probability density functions become bimodal with peaks localized outside of the S-loop region. Inside, states are unstable, and as a result simulation of equilibrium phase coexistence becomes impossible. To overcome this problem, a method was proposed by Kim, Keyes and Straub, where optimally designed generalized ensemble sampling was combined with replica exchange, and denoted generalized replica exchange method (gREM).more » This new technique uses parametrized effective sampling weights that lead to a unimodal energy distribution, transforming unstable states into stable ones. In the present study, the gREM, originally developed as a Monte Carlo algorithm, was implemented to work with molecular dynamics in an isobaric ensemble and coded into LAMMPS, a highly optimized open source molecular simulation package. Lastly, the method is illustrated in a study of the very strong solid/liquid transition in water.« less

Origin of two time-scale regimes in potentiometric titration of metal oxides. A replica kinetic Monte Carlo study.

PubMed

Zarzycki, Piotr; Rosso, Kevin M

2009-06-16

Replica kinetic Monte Carlo simulations were used to study the characteristic time scales of potentiometric titration of the metal oxides and (oxy)hydroxides. The effect of surface heterogeneity and surface transformation on the titration kinetics were also examined. Two characteristic relaxation times are often observed experimentally, with the trailing slower part attributed to surface nonuniformity, porosity, polymerization, amorphization, and other dynamic surface processes induced by unbalanced surface charge. However, our simulations show that these two characteristic relaxation times are intrinsic to the proton-binding reaction for energetically homogeneous surfaces, and therefore surface heterogeneity or transformation does not necessarily need to be invoked. However, all such second-order surface processes are found to intensify the separation and distinction of the two kinetic regimes. The effect of surface energetic-topographic nonuniformity, as well dynamic surface transformation, interface roughening/smoothing were described in a statistical fashion. Furthermore, our simulations show that a shift in the point-of-zero charge is expected from increased titration speed, and the pH-dependence of the titration measurement error is in excellent agreement with experimental studies.

Isolation of a spontaneous CHO amino acid transport mutant by a combination of tritium suicide and replica plating

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

Dantzig, A.H.; Slayman, C.W.; Adelberg, E.A.

A spontaneous transport mutant of Chinese hamster ovary cells, CHY-1, was isolated by a combination of (/sup 3/H)proline suicide and replica plating. The mutant took up less tritium than the parent, resulting in a lower killing rate during storage. Transport by four separate amino acid transport systems (A, ASC, L, Ly+) was examined. The CHY-1 mutant exhibited normal uptake via the ASC, L, and Ly+ systems. By contrast, uptake of the most specific substrate of the A system, 2-(methylamino)-isobutyric acid, was significantly reduced at low, but not high, concentrations, due to a 3.5-fold increase in Km and a 1.5-fold increasemore » in Vmax. Taken together, these data suggest that the CHY-1 mutation may be in the structural gene coding for the A transport protein. The tritium suicide procedure is discussed, and general equations are derived to predict the maximum storage time for the survival of one mutant cell and the optimum size of the cell population for maximum mutant enrichment.« less

On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry

NASA Astrophysics Data System (ADS)

Müller, Fränze; Fischer, Lutz; Chen, Zhuo Angel; Auchynnikava, Tania; Rappsilber, Juri

2018-02-01

Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between multiple cross-linking reactions using bis[sulfosuccinimidyl] suberate (BS3)-cross-linked human serum albumin (HSA) and evaluated how reproducible cross-linked peptides can be identified and quantified by LC-MS analysis. To make QCLMS accessible to a broader research community, we developed a workflow that integrates the established software tools MaxQuant for spectra preprocessing, Xi for cross-linked peptide identification, and finally Skyline for quantification (MS1 filtering). Out of the 221 unique residue pairs identified in our sample, 124 were subsequently quantified across 10 analyses with coefficient of variation (CV) values of 14% (injection replica) and 32% (reaction replica). Thus our results demonstrate that the reproducibility of QCLMS is in line with the reproducibility of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides.

Morpho peleides butterfly wing imprints as structural colour stamp.

PubMed

Zobl, Sigrid; Salvenmoser, Willi; Schwerte, Thorsten; Gebeshuber, Ille C; Schreiner, Manfred

2016-02-02

This study presents the replication of a color-causing nanostructure based on the upper laminae of numerous cover scales of Morpho peleides butterfly wings and obtained solely by imprinting their upper-wing surfaces. Our results indicate that a simple casting technique using a novel integrated release agent can obtain a large positive replica using negative imprints via Polyvinylsiloxane. The developed method is low-tech and high-yield and is thus substantially easier and less expensive than previous methods. The microstructures were investigated with light microscopy, the nanostructures with both scanning and transmission electron microscopy, and the reflections with UV visible spectrometry. The influence of the release agent and the quality of the master stamp were determined by comparing measurements of the cover-scale sizes and their chromaticity values obtained by their images and with their positive imprints. The master stamp provided multiple positive replicas up to 3 cm(2) in just 1 h with structural coloration effects visible to the naked eye. Thus, the developed method proves the accuracy of the replicated nanostructure and its potential industrial application as a color-producing nanostamp.

Using a Replica of Leeuwenhoek's Microscope to Teach the History of Science and to Motivate Students to Discover the Vision and the Contributions of the First Microscopists

PubMed Central

Loreto, Elgion L.S.; Rocha, João B.T.

2009-01-01

The history of science should be incorporated into science teaching as a means of improving learning and also to increase the students' understanding about the nature of science. In biology education, the history of microscopy deserves a special place. The discovery of this instrument not only opened a new and fantastic microworld but also led to the development of one unifying principle of biological sciences (i.e., cell theory). The microscopes of Leeuwenhoek and Hooke opened windows into the microworld of living organisms. In the present work, the knowledge of these themes was analyzed in a group of students beginning an undergraduate biology course. Our data suggest that the history of microscopy is poorly treated at the secondary school level. We propose a didactic activity using a replica of Leeuwenhoek's microscope made with Plexiglas and a lens obtained from a key chain laser pointer or from a broken CD drive. The proposed activity motivated students to learn about microscopy and helped them to appreciate scientific knowledge from a historical perspective. PMID:19952102

Using a replica of Leeuwenhoek's microscope to teach the history of science and to motivate students to discover the vision and the contributions of the first microscopists.

PubMed

Sepel, Lenira M N; Loreto, Elgion L S; Rocha, João B T

2009-01-01

The history of science should be incorporated into science teaching as a means of improving learning and also to increase the students' understanding about the nature of science. In biology education, the history of microscopy deserves a special place. The discovery of this instrument not only opened a new and fantastic microworld but also led to the development of one unifying principle of biological sciences (i.e., cell theory). The microscopes of Leeuwenhoek and Hooke opened windows into the microworld of living organisms. In the present work, the knowledge of these themes was analyzed in a group of students beginning an undergraduate biology course. Our data suggest that the history of microscopy is poorly treated at the secondary school level. We propose a didactic activity using a replica of Leeuwenhoek's microscope made with Plexiglas and a lens obtained from a key chain laser pointer or from a broken CD drive. The proposed activity motivated students to learn about microscopy and helped them to appreciate scientific knowledge from a historical perspective.

Metainference: A Bayesian inference method for heterogeneous systems.

PubMed

Bonomi, Massimiliano; Camilloni, Carlo; Cavalli, Andrea; Vendruscolo, Michele

2016-01-01

Modeling a complex system is almost invariably a challenging task. The incorporation of experimental observations can be used to improve the quality of a model and thus to obtain better predictions about the behavior of the corresponding system. This approach, however, is affected by a variety of different errors, especially when a system simultaneously populates an ensemble of different states and experimental data are measured as averages over such states. To address this problem, we present a Bayesian inference method, called "metainference," that is able to deal with errors in experimental measurements and with experimental measurements averaged over multiple states. To achieve this goal, metainference models a finite sample of the distribution of models using a replica approach, in the spirit of the replica-averaging modeling based on the maximum entropy principle. To illustrate the method, we present its application to a heterogeneous model system and to the determination of an ensemble of structures corresponding to the thermal fluctuations of a protein molecule. Metainference thus provides an approach to modeling complex systems with heterogeneous components and interconverting between different states by taking into account all possible sources of errors.

Comprehensive quantification of signal-to-noise ratio and g-factor for image-based and k-space-based parallel imaging reconstructions.

PubMed

Robson, Philip M; Grant, Aaron K; Madhuranthakam, Ananth J; Lattanzi, Riccardo; Sodickson, Daniel K; McKenzie, Charles A

2008-10-01

Parallel imaging reconstructions result in spatially varying noise amplification characterized by the g-factor, precluding conventional measurements of noise from the final image. A simple Monte Carlo based method is proposed for all linear image reconstruction algorithms, which allows measurement of signal-to-noise ratio and g-factor and is demonstrated for SENSE and GRAPPA reconstructions for accelerated acquisitions that have not previously been amenable to such assessment. Only a simple "prescan" measurement of noise amplitude and correlation in the phased-array receiver, and a single accelerated image acquisition are required, allowing robust assessment of signal-to-noise ratio and g-factor. The "pseudo multiple replica" method has been rigorously validated in phantoms and in vivo, showing excellent agreement with true multiple replica and analytical methods. This method is universally applicable to the parallel imaging reconstruction techniques used in clinical applications and will allow pixel-by-pixel image noise measurements for all parallel imaging strategies, allowing quantitative comparison between arbitrary k-space trajectories, image reconstruction, or noise conditioning techniques. (c) 2008 Wiley-Liss, Inc.

Out-of-equilibrium protocol for Rényi entropies via the Jarzynski equality.

PubMed

Alba, Vincenzo

2017-06-01

In recent years entanglement measures, such as the von Neumann and the Rényi entropies, provided a unique opportunity to access elusive features of quantum many-body systems. However, extracting entanglement properties analytically, experimentally, or in numerical simulations can be a formidable task. Here, by combining the replica trick and the Jarzynski equality we devise an alternative effective out-of-equilibrium protocol for measuring the equilibrium Rényi entropies. The key idea is to perform a quench in the geometry of the replicas. The Rényi entropies are obtained as the exponential average of the work performed during the quench. We illustrate an application of the method in classical Monte Carlo simulations, although it could be useful in different contexts, such as in quantum Monte Carlo, or experimentally in cold-atom systems. The method is most effective in the quasistatic regime, i.e., for a slow quench. As a benchmark, we compute the Rényi entropies in the Ising universality class in 1+1 dimensions. We find perfect agreement with the well-known conformal field theory predictions.

Unifying model for random matrix theory in arbitrary space dimensions

NASA Astrophysics Data System (ADS)

Cicuta, Giovanni M.; Krausser, Johannes; Milkus, Rico; Zaccone, Alessio

2018-03-01

A sparse random block matrix model suggested by the Hessian matrix used in the study of elastic vibrational modes of amorphous solids is presented and analyzed. By evaluating some moments, benchmarked against numerics, differences in the eigenvalue spectrum of this model in different limits of space dimension d , and for arbitrary values of the lattice coordination number Z , are shown and discussed. As a function of these two parameters (and their ratio Z /d ), the most studied models in random matrix theory (Erdos-Renyi graphs, effective medium, and replicas) can be reproduced in the various limits of block dimensionality d . Remarkably, the Marchenko-Pastur spectral density (which is recovered by replica calculations for the Laplacian matrix) is reproduced exactly in the limit of infinite size of the blocks, or d →∞ , which clarifies the physical meaning of space dimension in these models. We feel that the approximate results for d =3 provided by our method may have many potential applications in the future, from the vibrational spectrum of glasses and elastic networks to wave localization, disordered conductors, random resistor networks, and random walks.

Statistical mechanical analysis of linear programming relaxation for combinatorial optimization problems

NASA Astrophysics Data System (ADS)

Takabe, Satoshi; Hukushima, Koji

2016-05-01

Typical behavior of the linear programming (LP) problem is studied as a relaxation of the minimum vertex cover (min-VC), a type of integer programming (IP) problem. A lattice-gas model on the Erdös-Rényi random graphs of α -uniform hyperedges is proposed to express both the LP and IP problems of the min-VC in the common statistical mechanical model with a one-parameter family. Statistical mechanical analyses reveal for α =2 that the LP optimal solution is typically equal to that given by the IP below the critical average degree c =e in the thermodynamic limit. The critical threshold for good accuracy of the relaxation extends the mathematical result c =1 and coincides with the replica symmetry-breaking threshold of the IP. The LP relaxation for the minimum hitting sets with α ≥3 , minimum vertex covers on α -uniform random graphs, is also studied. Analytic and numerical results strongly suggest that the LP relaxation fails to estimate optimal values above the critical average degree c =e /(α -1 ) where the replica symmetry is broken.

KENNEDY SPACE CENTER, FLA. - A 20-foot by 15-foot replica of the STS-107 logo has been installed above the “A” on the A tower in the transfer aisle of the Vehicle Assembly Building. The debris from the orbiter Columbia, lost in a tragic accident on its return to Earth from the STS-107 mission, is permanently stored in the tower. A dedication ceremony Jan. 29, 2004, unveiled a plaque being installed in the storage area in honor of “Columbia, the crew of STS-107, and their loved ones.”

NASA Image and Video Library

2004-01-29

KENNEDY SPACE CENTER, FLA. - A 20-foot by 15-foot replica of the STS-107 logo has been installed above the “A” on the A tower in the transfer aisle of the Vehicle Assembly Building. The debris from the orbiter Columbia, lost in a tragic accident on its return to Earth from the STS-107 mission, is permanently stored in the tower. A dedication ceremony Jan. 29, 2004, unveiled a plaque being installed in the storage area in honor of “Columbia, the crew of STS-107, and their loved ones.”

KENNEDY SPACE CENTER, FLA. - Workers install a 20-foot by 15-foot replica of the STS-107 logo above the “A” on the A tower in the transfer aisle of the Vehicle Assembly Building. The debris from the orbiter Columbia, lost in a tragic accident on its return to Earth from the STS-107 mission, is permanently stored in the tower. A dedication ceremony Jan. 29, 2004, revealed a plaque being installed in the storage area in honor of “Columbia, the crew of STS-107, and their loved ones.”

NASA Image and Video Library

2004-01-29

KENNEDY SPACE CENTER, FLA. - Workers install a 20-foot by 15-foot replica of the STS-107 logo above the “A” on the A tower in the transfer aisle of the Vehicle Assembly Building. The debris from the orbiter Columbia, lost in a tragic accident on its return to Earth from the STS-107 mission, is permanently stored in the tower. A dedication ceremony Jan. 29, 2004, revealed a plaque being installed in the storage area in honor of “Columbia, the crew of STS-107, and their loved ones.”

Efficient Processing of Data for Locating Lightning Strikes

NASA Technical Reports Server (NTRS)

Medelius, Pedro J.; Starr, Stan

2003-01-01

Two algorithms have been devised to increase the efficiency of processing of data in lightning detection and ranging (LDAR) systems so as to enable the accurate location of lightning strikes in real time. In LDAR, the location of a lightning strike is calculated by solving equations for the differences among the times of arrival (DTOAs) of the lightning signals at multiple antennas as functions of the locations of the antennas and the speed of light. The most difficult part of the problem is computing the DTOAs from digitized versions of the signals received by the various antennas. One way (a time-domain approach) to determine the DTOAs is to compute cross-correlations among variously differentially delayed replicas of the digitized signals and to select, as the DTOAs, those differential delays that yield the maximum correlations. Another way (a frequency-domain approach) to determine the DTOAs involves the computation of cross-correlations among Fourier transforms of variously differentially phased replicas of the digitized signals, along with utilization of the relationship among phase difference, time delay, and frequency.

Effects of moiré lattice structure on electronic properties of graphene

NASA Astrophysics Data System (ADS)

Huang, Lunan; Wu, Yun; Hershberger, M. T.; Mou, Daixiang; Schrunk, Benjamin; Tringides, Michael C.; Hupalo, Myron; Kaminski, Adam

2017-07-01

We study structural and electronic properties of graphene grown on silicone carbide (SiC) substrate using a scanning tunneling microscope, spot-profile-analysis low-energy electron diffraction, and angle-resolved photoemission spectroscopy. We find several new replicas of Dirac cones in the Brillouin zone. Their locations can be understood in terms of a combination of basis vectors linked to SiC 6 × 6 and graphene 6 √{3 }×6 √{3 } reconstruction. Therefore, these new features originate from the moiré caused by the lattice mismatch between SiC and graphene. More specifically, Dirac cone replicas are caused by underlying weak modulation of the ionic potential by the substrate that is then experienced by the electrons in the graphene. We also demonstrate that this effect is equally strong in single- and trilayer graphene; therefore, the additional Dirac cones are intrinsic features rather than the result of photoelectron diffraction. These new features in the electronic structure are very important for the interpretation of recent transport measurements and can assist in tuning the properties of graphene for practical applications.

Classification of electronically generated phantom targets by an Atlantic bottlenose dolphin (Tursiops truncatus).

PubMed

Aubauer, R; Au, W W; Nachtigall, P E; Pawloski, D A; DeLong, C M

2000-05-01

Animal behavior experiments require not only stimulus control of the animal's behavior, but also precise control of the stimulus itself. In discrimination experiments with real target presentation, the complex interdependence between the physical dimensions and the backscattering process of an object make it difficult to extract and control relevant echo parameters separately. In other phantom-echo experiments, the echoes were relatively simple and could only simulate certain properties of targets. The echo-simulation method utilized in this paper can be used to transform any animal echolocation sound into phantom echoes of high fidelity and complexity. The developed phantom-echo system is implemented on a digital signal-processing board and gives an experimenter fully programmable control over the echo-generating process and the echo structure itself. In this experiment, the capability of a dolphin to discriminate between acoustically simulated phantom replicas of targets and their real equivalents was tested. Phantom replicas were presented in a probe technique during a materials discrimination experiment. The animal accepted the phantom echoes and classified them in the same manner as it classified real targets.

Popularity Prediction Tool for ATLAS Distributed Data Management

NASA Astrophysics Data System (ADS)

Beermann, T.; Maettig, P.; Stewart, G.; Lassnig, M.; Garonne, V.; Barisits, M.; Vigne, R.; Serfon, C.; Goossens, L.; Nairz, A.; Molfetas, A.; Atlas Collaboration

2014-06-01

This paper describes a popularity prediction tool for data-intensive data management systems, such as ATLAS distributed data management (DDM). It is fed by the DDM popularity system, which produces historical reports about ATLAS data usage, providing information about files, datasets, users and sites where data was accessed. The tool described in this contribution uses this historical information to make a prediction about the future popularity of data. It finds trends in the usage of data using a set of neural networks and a set of input parameters and predicts the number of accesses in the near term future. This information can then be used in a second step to improve the distribution of replicas at sites, taking into account the cost of creating new replicas (bandwidth and load on the storage system) compared to gain of having new ones (faster access of data for analysis). To evaluate the benefit of the redistribution a grid simulator is introduced that is able replay real workload on different data distributions. This article describes the popularity prediction method and the simulator that is used to evaluate the redistribution.

Parylene C coating for high-performance replica molding.

PubMed

Heyries, Kevin A; Hansen, Carl L

2011-12-07

This paper presents an improvement to the soft lithography fabrication process that uses chemical vapor deposition of poly(chloro-p-xylylene) (parylene C) to protect microfabricated masters and to improve the release of polymer devices following replica molding. Chemical vapor deposition creates nanometre thick conformal coatings of parylene C on silicon wafers having arrays of 30 μm high SU8 pillars with densities ranging from 278 to 10,040 features per mm(2) and aspect ratios (height : width) from 1 : 1 to 6 : 1. A single coating of parylene C was sufficient to permanently promote poly(dimethyl)siloxane (PDMS) mold release and to protect masters for an indefinite number of molding cycles. We also show that the improved release properties of parylene treated masters allow for fabrication with hard polymers, such as poly(urethane), that would otherwise not be compatible with SU8 on silicon masters. Parylene C provides a robust and high performance mold release coating for soft lithography microfabrication that extends the life of microfabricated masters and improves the achievable density and aspect ratio of replicated features.

Statistical mechanical analysis of linear programming relaxation for combinatorial optimization problems.

PubMed

Takabe, Satoshi; Hukushima, Koji

2016-05-01

Typical behavior of the linear programming (LP) problem is studied as a relaxation of the minimum vertex cover (min-VC), a type of integer programming (IP) problem. A lattice-gas model on the Erdös-Rényi random graphs of α-uniform hyperedges is proposed to express both the LP and IP problems of the min-VC in the common statistical mechanical model with a one-parameter family. Statistical mechanical analyses reveal for α=2 that the LP optimal solution is typically equal to that given by the IP below the critical average degree c=e in the thermodynamic limit. The critical threshold for good accuracy of the relaxation extends the mathematical result c=1 and coincides with the replica symmetry-breaking threshold of the IP. The LP relaxation for the minimum hitting sets with α≥3, minimum vertex covers on α-uniform random graphs, is also studied. Analytic and numerical results strongly suggest that the LP relaxation fails to estimate optimal values above the critical average degree c=e/(α-1) where the replica symmetry is broken.

Measurements of drag and flow over biofilm

NASA Astrophysics Data System (ADS)

Hartenberger, Joel; Gose, James W.; Perlin, Marc; Ceccio, Steven L.

2017-11-01

Microbial `slime' biofilms detrimentally affect the performance of every day systems from medical devices to large ocean-going vessels. In flow applications, the presence of biofilm typically results in a drag increase and may alter the turbulence in the adjacent boundary layer. Recent studies emphasize the severity of the drag penalty associated with soft biofouling and suggest potential mechanisms underlying the increase; yet, fundamental questions remain-such as the role played by compliance and the contribution of form drag to the overall resistance experienced by a fouled system. Experiments conducted on live biofilm and 3D printed rigid replicas in the Skin-Friction Flow Facility at the University of Michigan seek to examine these factors. The hydrodynamic performance of the biofilms grown on test panels was evaluated through pressure drop measurements as well as conventional and microscale PIV. High-resolution, 3D rigid replicas of select cases were generated via additive manufacturing using surface profiles obtained from a laser scanning system. Drag and flow measurements will be presented along with details of the growth process and the surface profile characterization method.

Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

NASA Astrophysics Data System (ADS)

De Simone, Alfonso; Derreumaux, Philippe

2010-04-01

The self-assembly of proteins and peptides into amyloid fibrils is connected to over 40 pathological conditions including neurodegenerative diseases and systemic amyloidosis. Diffusible, low molecular weight protein and peptide oligomers that form in the early steps of aggregation appear to be the harmful cytotoxic species in the molecular etiology of these diseases. So far, the structural characterization of these oligomers has remained elusive owing to their transient and dynamic features. We here address, by means of full atomistic replica exchange molecular dynamics simulations, the energy landscape of heptamers of the amyloidogenic peptide NHVTLSQ from the beta-2 microglobulin protein. The simulations totaling 5 μs show that low molecular weight oligomers in explicit solvent consist of β-barrels in equilibrium with amorphous states and fibril-like assemblies. The results, also accounting for the influence of the pH on the conformational properties, provide a strong evidence of the formation of transient β-barrel assemblies in the early aggregation steps of amyloid-forming systems. Our findings are discussed in terms of oligomers cytotoxicity.

Dual-Templated Cobalt Oxide for Photochemical Water Oxidation.

PubMed

Deng, Xiaohui; Bongard, Hans-Josef; Chan, Candace K; Tüysüz, Harun

2016-02-19

Mesoporous Co3 O4 was prepared using a dual templating approach whereby mesopores inside SiO2 nanospheres, as well as the void spaces between the nanospheres, were used as templates. The effect of calcination temperature on the crystallinity, morphology, and textural parameters of the Co3 O4 replica was investigated. The catalytic activity of Co3 O4 for photochemical water oxidation in a [Ru(bpy)3 ](2+) [S2 O8 ](2-) system was evaluated. The Co3 O4 replica calcined at the lowest temperature (150 °C) exhibited the best performance as a result of the unique nanostructure and high surface area arising from the dual templating. The performance of Co3 O4 with highest surface area was further examined in electrochemical water oxidation. Superior activity over high temperature counterpart and decent stability was observed. Furthermore, CoO with identical morphology was prepared from Co3 O4 using an ethanol reduction method and a higher turnover-frequency number for photochemical water oxidation was obtained. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Anomalously Fast Diffusion of Targeted Carbon Nanotubes in Cellular Spheroids.

PubMed

Wang, Yichun; Bahng, Joong Hwan; Che, Quantong; Han, Jishu; Kotov, Nicholas A

2015-08-25

Understanding transport of carbon nanotubes (CNTs) and other nanocarriers within tissues is essential for biomedical imaging and drug delivery using these carriers. Compared to traditional cell cultures in animal studies, three-dimensional tissue replicas approach the complexity of the actual organs and enable high temporal and spatial resolution of the carrier permeation. We investigated diffusional transport of CNTs in highly uniform spheroids of hepatocellular carcinoma and found that apparent diffusion coefficients of CNTs in these tissue replicas are anomalously high and comparable to diffusion rates of similarly charged molecules with molecular weights 10000× lower. Moreover, diffusivity of CNTs in tissues is enhanced after functionalization with transforming growth factor β1. This unexpected trend contradicts predictions of the Stokes-Einstein equation and previously obtained empirical dependences of diffusivity on molecular mass for permeants in gas, liquid, solid or gel. It is attributed to the planar diffusion (gliding) of CNTs along cellular membranes reducing effective dimensionality of diffusional space. These findings indicate that nanotubes and potentially similar nanostructures are capable of fast and deep permeation into the tissue, which is often difficult to realize with anticancer agents.

Digital Earth reloaded - Beyond the next generation

NASA Astrophysics Data System (ADS)

Ehlers, M.; Woodgate, P.; Annoni, A.; Schade, S.

2014-02-01

Digital replicas (or 'mirror worlds') of complex entities and systems are now routine in many fields such as aerospace engineering; archaeology; medicine; or even fashion design. The Digital Earth (DE) concept as a digital replica of the entire planet occurs in Al Gore's 1992 book Earth in the Balance and was popularized in his speech at the California Science Center in January 1998. It played a pivotal role in stimulating the development of a first generation of virtual globes, typified by Google Earth that achieved many elements of this vision. Almost 15 years after Al Gore's speech, the concept of DE needs to be re-evaluated in the light of the many scientific and technical developments in the fields of information technology, data infrastructures, citizen?s participation, and earth observation that have taken place since. This paper intends to look beyond the next generation predominantly based on the developments of fields outside the spatial sciences, where concepts, software, and hardware with strong relationships to DE are being developed without referring to this term. It also presents a number of guiding criteria for future DE developments.

Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.

PubMed

Olson, Mark A; Lee, Michael S

2014-01-01

A central problem of computational structural biology is the refinement of modeled protein structures taken from either comparative modeling or knowledge-based methods. Simulations are commonly used to achieve higher resolution of the structures at the all-atom level, yet methodologies that consistently yield accurate results remain elusive. In this work, we provide an assessment of an adaptive temperature-based replica exchange simulation method where the temperature clients dynamically walk in temperature space to enrich their population and exchanges near steep energetic barriers. This approach is compared to earlier work of applying the conventional method of static temperature clients to refine a dataset of conformational decoys. Our results show that, while an adaptive method has many theoretical advantages over a static distribution of client temperatures, only limited improvement was gained from this strategy in excursions of the downhill refinement regime leading to an increase in the fraction of native contacts. To illustrate the sampling differences between the two simulation methods, energy landscapes are presented along with their temperature client profiles.

On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome

PubMed Central

Olson, Mark A.

2017-01-01

Intrinsically disordered proteins that populate the so-called “Dark Proteome” offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP. An assessment is provided of the accuracy of two generalized Born solvent models (GBMV2 and GBSW2) using the CHARMM force field and applied with temperature-based replica exchange dynamics to calculate the disorder propensity of the peptide and its probability density of states in a continuum solvent. A further comparison is presented of applying an explicit/implicit solvent hybrid replica exchange simulation of the peptide to determine the effect of modeling water interactions at the all-atom resolution. PMID:28197405

On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome.

PubMed

Olson, Mark A

2017-01-01

Intrinsically disordered proteins that populate the so-called "Dark Proteome" offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP. An assessment is provided of the accuracy of two generalized Born solvent models (GBMV2 and GBSW2) using the CHARMM force field and applied with temperature-based replica exchange dynamics to calculate the disorder propensity of the peptide and its probability density of states in a continuum solvent. A further comparison is presented of applying an explicit/implicit solvent hybrid replica exchange simulation of the peptide to determine the effect of modeling water interactions at the all-atom resolution.

Effects of moiré lattice structure on electronic properties of graphene

DOE PAGES

Huang, Lunan; Wu, Yun; Hershberger, M. T.; ...

2017-07-10

Here, we study structural and electronic properties of graphene grown on silicone carbide (SiC) substrate using a scanning tunneling microscope, spot-profile-analysis low-energy electron diffraction, and angle-resolved photoemission spectroscopy. We find several new replicas of Dirac cones in the Brillouin zone. Their locations can be understood in terms of a combination of basis vectors linked to SiC 6 × 6 and graphene 6√3×6√3 reconstruction. Therefore, these new features originate from the moiré caused by the lattice mismatch between SiC and graphene. More specifically, Dirac cone replicas are caused by underlying weak modulation of the ionic potential by the substrate that ismore » then experienced by the electrons in the graphene. We also demonstrate that this effect is equally strong in single- and trilayer graphene; therefore, the additional Dirac cones are intrinsic features rather than the result of photoelectron diffraction. These new features in the electronic structure are very important for the interpretation of recent transport measurements and can assist in tuning the properties of graphene for practical applications.« less

A LAMMPS implementation of volume-temperature replica exchange molecular dynamics

NASA Astrophysics Data System (ADS)

Liu, Liang-Chun; Kuo, Jer-Lai

2015-04-01

A driver module for executing volume-temperature replica exchange molecular dynamics (VTREMD) was developed for the LAMMPS package. As a patch code, the VTREMD module performs classical molecular dynamics (MD) with Monte Carlo (MC) decisions between MD runs. The goal of inserting the MC step was to increase the breadth of sampled configurational space. In this method, states receive better sampling by making temperature or density swaps with their neighboring states. As an accelerated sampling method, VTREMD is particularly useful to explore states at low temperatures, where systems are easily trapped in local potential wells. As functional examples, TIP4P/Ew and TIP4P/2005 water models were analyzed using VTREMD. The phase diagram in this study covered the deeply supercooled regime, and this test served as a suitable demonstration of the usefulness of VTREMD in overcoming the slow dynamics problem. To facilitate using the current code, attention was also paid on how to optimize the exchange efficiency by using grid allocation. VTREMD was useful for studying systems with rough energy landscapes, such as those with numerous local minima or multiple characteristic time scales.

Generalized ensemble method applied to study systems with strong first order transitions

NASA Astrophysics Data System (ADS)

Małolepsza, E.; Kim, J.; Keyes, T.

2015-09-01

At strong first-order phase transitions, the entropy versus energy or, at constant pressure, enthalpy, exhibits convex behavior, and the statistical temperature curve correspondingly exhibits an S-loop or back-bending. In the canonical and isothermal-isobaric ensembles, with temperature as the control variable, the probability density functions become bimodal with peaks localized outside of the S-loop region. Inside, states are unstable, and as a result simulation of equilibrium phase coexistence becomes impossible. To overcome this problem, a method was proposed by Kim, Keyes and Straub [1], where optimally designed generalized ensemble sampling was combined with replica exchange, and denoted generalized replica exchange method (gREM). This new technique uses parametrized effective sampling weights that lead to a unimodal energy distribution, transforming unstable states into stable ones. In the present study, the gREM, originally developed as a Monte Carlo algorithm, was implemented to work with molecular dynamics in an isobaric ensemble and coded into LAMMPS, a highly optimized open source molecular simulation package. The method is illustrated in a study of the very strong solid/liquid transition in water.

Controlled replication: reduce the capacity occupied by redundant replicas in tiled chip multiprocessors

NASA Astrophysics Data System (ADS)

Li, Hao; Xie, Lunguo

2013-03-01

The design of cache system for Chip Multiprocessor (CMP) face many challenges because future CMPs will have more cores and greater on-chip cache capacity. There are two base design schemes about L2 cache: private scheme in which each L2 slice is treated as a private L2 cache and shared scheme in which all L2 slices are treated as a large L2 cache shared by all cores. Private caches provide the lowest hit latency but reduce the total effective cache capacity. A shared L2 cache increases the effective cache capacity but has long hit latencies when data is on a remote tile. This paper present a new Controlled Replication (CR) policy to reduce the capacities occupied by redundant shared replicas. the new CR policy increases the effective capacity than victim replication scheme and has lower hit latency than shared scheme. We evaluate the various schemes using full-system simulation of parallel applications. Results show that CR reduces the average memory access latency of shared scheme by an average of 13%, providing better overall performance than victim replication and shared schemes.

Fractal dimension of interfaces in Edwards-Anderson spin glasses for up to six space dimensions.

PubMed

Wang, Wenlong; Moore, M A; Katzgraber, Helmut G

2018-03-01

The fractal dimension of domain walls produced by changing the boundary conditions from periodic to antiperiodic in one spatial direction is studied using both the strong-disorder renormalization group algorithm and the greedy algorithm for the Edwards-Anderson Ising spin-glass model for up to six space dimensions. We find that for five or fewer space dimensions, the fractal dimension is lower than the space dimension. This means that interfaces are not space filling, thus implying that replica symmetry breaking is absent in space dimensions fewer than six. However, the fractal dimension approaches the space dimension in six dimensions, indicating that replica symmetry breaking occurs above six dimensions. In two space dimensions, the strong-disorder renormalization group results for the fractal dimension are in good agreement with essentially exact numerical results, but the small difference is significant. We discuss the origin of this close agreement. For the greedy algorithm there is analytical expectation that the fractal dimension is equal to the space dimension in six dimensions and our numerical results are consistent with this expectation.

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

PubMed

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

2010-12-15

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

Multifractality and freezing phenomena in random energy landscapes: An introduction

NASA Astrophysics Data System (ADS)

Fyodorov, Yan V.

2010-10-01

We start our lectures with introducing and discussing the general notion of multifractality spectrum for random measures on lattices, and how it can be probed using moments of that measure. Then we show that the Boltzmann-Gibbs probability distributions generated by logarithmically correlated random potentials provide a simple yet non-trivial example of disorder-induced multifractal measures. The typical values of the multifractality exponents can be extracted from calculating the free energy of the associated Statistical Mechanics problem. To succeed in such a calculation we introduce and discuss in some detail two analytically tractable models for logarithmically correlated potentials. The first model uses a special definition of distances between points in space and is based on the idea of multiplicative cascades which originated in theory of turbulent motion. It is essentially equivalent to statistical mechanics of directed polymers on disordered trees studied long ago by Derrida and Spohn (1988) in Ref. [12]. In this way we introduce the notion of the freezing transition which is identified with an abrupt change in the multifractality spectrum. Second model which allows for explicit analytical evaluation of the free energy is the infinite-dimensional version of the problem which can be solved by employing the replica trick. In particular, the latter version allows one to identify the freezing phenomenon with a mechanism of the replica symmetry breaking (RSB) and to elucidate its physical meaning. The corresponding one-step RSB solution turns out to be marginally stable everywhere in the low-temperature phase. We finish with a short discussion of recent developments and extensions of models with logarithmic correlations, in particular in the context of extreme value statistics. The first appendix summarizes the standard elementary information about Gaussian integrals and related subjects, and introduces the notion of the Gaussian free field characterized by logarithmic correlations. Three other appendices provide the detailed exposition of a few technical details underlying the replica analysis of the model discussed in the lectures.

Monitoring the progression of erosive tooth wear (ETW) using BEWE index in casts and their 3D images: A retrospective longitudinal study.

PubMed

Marro, Francisca; De Lat, Liesa; Martens, Luc; Jacquet, Wolfgang; Bottenberg, Peter

2018-04-13

To determine if the Basic erosive tooth wear index (BEWE index) is able to assess and monitor ETW changes in two consecutive cast models, and detect methodological differences when using the corresponding 3D image replicas. A total of 480 pre-treatment and 2-year post-treatment orthodontic models (n = 240 cast models and n = 240 3D image replicas) from 120 adolescents treated between 2002 and 2013 at the Gent Dental Clinic, Belgium, were scored using the BEWE index. For data analysis only posterior sextants were considered, and inter-method differences were evaluated using Wilcoxon Signed Rank test, Kappa values and Mc Nemar tests (p < 0.05). Correlations between methods were determined using Kendall tau correlation test. Significant changes of ETW were detected between two consecutive models when BEWE index was used to score cast models or their 3D image replicas (p < 0.001). A strong significant correlation (τb: 0.74; p < 0.001) was shown between both methods However, 3D image-BEWE index combination showed a higher probability for detecting initial surface changes, and scored significantly higher than casts (p < 0.001). Incidence and progression of ETW using 3D images was 13.3% (n = 16) and 60.9% (n = 56) respectively, with two subjects developing BEWE = 3 in at least one tooth surface. BEWE index is a suitable tool for the scoring of ETW lesions in 3D images and cast. The combination of both digital 3D records and index, can be used for the monitoring of ETW in a longitudinal approach. The higher sensibility of BEWE index when scoring 3D images might improve the early diagnosis of ETW lesions. The BEWE index combined with digital 3D records of oral conditions might improve the practitioner performance with respect to early diagnosis, monitoring and managing ETW. Copyright © 2018 Elsevier Ltd. All rights reserved.

Replacing Heavily Damaged Teeth by Third Molar Autotransplantation With the Use of Cone-Beam Computed Tomography and Rapid Prototyping.

PubMed

Verweij, Jop P; Anssari Moin, David; Wismeijer, Daniel; van Merkesteyn, J P Richard

2017-09-01

This article describes the autotransplantation of third molars to replace heavily damaged premolars and molars. Specifically, this article reports on the use of preoperative cone-beam computed tomographic planning and 3-dimensional (3D) printed replicas of donor teeth to prepare artificial tooth sockets. In the present case, an 18-year-old patient underwent autotransplantation of 3 third molars to replace 1 premolar and 2 molars that were heavily damaged after trauma. Approximately 1 year after the traumatic incident, autotransplantation with the help of 3D planning and rapid prototyping was performed. The right maxillary third molar replaced the right maxillary first premolar. The 2 mandibular wisdom teeth replaced the left mandibular first and second molars. During the surgical procedure, artificial tooth sockets were prepared with the help of 3D printed donor tooth copies to prevent iatrogenic damage to the actual donor teeth. These replicas of the donor teeth were designed based on the preoperative cone-beam computed tomogram and manufactured with the help of 3D printing techniques. The use of a replica of the donor tooth resulted in a predictable and straightforward procedure, with extra-alveolar times shorter than 2 minutes for all transplantations. The transplanted teeth were placed in infraocclusion and fixed with a suture splint. Postoperative follow-up showed physiologic integration of the transplanted teeth and a successful outcome for all transplants. In conclusion, this technique facilitates a straightforward and predictable procedure for autotransplantation of third molars. The use of printed analogues of the donor teeth decreases the risk of iatrogenic damage and the extra-alveolar time of the transplanted tooth is minimized. This facilitates a successful outcome. Copyright © 2017 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

New force replica exchange method and protein folding pathways probed by force-clamp technique.

PubMed

Kouza, Maksim; Hu, Chin-Kun; Li, Mai Suan

2008-01-28

We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. This new approach was applied to obtain the force-temperature phase diagram and other thermodynamical quantities of the three-domain ubiquitin. Using the C(alpha)-Go model and the Langevin dynamics, we have shown that the refolding pathways of single ubiquitin depend on which terminus is fixed. If the N end is fixed then the folding pathways are different compared to the case when both termini are free, but fixing the C terminal does not change them. Surprisingly, we have found that the anchoring terminal does not affect the pathways of individual secondary structures of three-domain ubiquitin, indicating the important role of the multidomain construction. Therefore, force-clamp experiments, in which one end of a protein is kept fixed, can probe the refolding pathways of a single free-end ubiquitin if one uses either the polyubiquitin or a single domain with the C terminus anchored. However, it is shown that anchoring one end does not affect refolding pathways of the titin domain I27, and the force-clamp spectroscopy is always capable to predict folding sequencing of this protein. We have obtained the reasonable estimate for unfolding barrier of ubiquitin, using the microscopic theory for the dependence of unfolding time on the external force. The linkage between residue Lys48 and the C terminal of ubiquitin is found to have the dramatic effect on the location of the transition state along the end-to-end distance reaction coordinate, but the multidomain construction leaves the transition state almost unchanged. We have found that the maximum force in the force-extension profile from constant velocity force pulling simulations depends on temperature nonlinearly. However, for some narrow temperature interval this dependence becomes linear, as have been observed in recent experiments.

Surface roughness evaluation on mandrels and mirror shells for future X-ray telescopes

NASA Astrophysics Data System (ADS)

Sironi, Giorgia; Spiga, D.

2008-07-01

More X-ray missions that will be operating in near future, like particular SIMBOL-X, e-Rosita, Con-X/HXT, SVOM/XIAO and Polar-X, will be based on focusing optics manufactured by means of the Ni electroforming replication technique. This production method has already been successfully exploited for SAX, XMM and Swift-XRT. Optical surfaces for X-ray reflection have to be as smooth as possible also at high spatial frequencies. Hence it will be crucial to take under control microroughness in order to reduce the scattering effects. A high rms microroughness would cause the degradation of the angular resolution and loss of effective area. Stringent requirements have therefore to be fixed for mirror shells surface roughness depending on the specific energy range investigated, and roughness evolution has to be carefully monitored during the subsequent steps of the mirror-shells realization. This means to study the roughness evolution in the chain mandrel, mirror shells, multilayer deposition and also the degradation of mandrel roughness following iterated replicas. Such a study allows inferring which phases of production are the major responsible of the roughness growth and could help to find solutions optimizing the involved processes. The exposed study is carried out in the context of the technological consolidation related to SIMBOL-X, along with a systematic metrological study of mandrels and mirror shells. To monitor the roughness increase following each replica, a multiinstrumental approach was adopted: microprofiles were analysed by means of their Power Spectral Density (PSD) in the spatial frequency range 1000-0.01 μm. This enables the direct comparison of roughness data taken with instruments characterized by different operative ranges of frequencies, and in particular optical interferometers and Atomic Force Microscopes. The performed analysis allowed us to set realistic specifications on the mandrel roughness to be achieved, and to suggest a limit for the maximum number of a replica a mandrel can undergo before being refurbished.

Torque resistance of impression copings after direct implant impression: An in vitro evaluation of impression materials with and without adhesive.

PubMed

Auroy, Pascal; Nicolas, Emanuel; Bedouin, Yvan

2017-01-01

No data are available on the ability of an impression coping to resist the manual placement of an abutment replica (implant analog) during prosthodontic laboratory procedures after a direct (pick-up) impression. The purpose of this in vitro study was to evaluate the torque resistance of impression copings after a direct impression, that is, the amount of rotational torque sufficient to induce irreversible displacement of impression copings in the impression material bulk once the impression has been made. A reference model with 5 abutment replicas was constructed. Five impression copings were screwed onto the abutment replicas, and standardized impressions were made. A controlled twisting force was applied to each impression coping. A torque tester recorded the torque variation. Three elastomeric impression materials were tested. ANOVA and the Tukey test (α=.05) were performed using an average of 30 measurements per impression material, with and without adhesive. ANOVA and the Tukey test results showed that the adhesive, cohesive, and mechanical bonds between the impression coping and the impression material depended greatly on the type of material and that the average rupture threshold of these bonds was statistically significantly different in pairwise comparisons (P<.05). The curve analysis showed that when the impression materials are used with adhesives, the deformation of the interface is irreversible beyond 5 Ncm of torque. The polyether impression material is the direct impression material that showed the highest breakdown threshold for adhesive bonding when used without an adhesive. The use of an adhesive on impression copings leads to irreversible deformation of the interface at torque stresses well below the adhesive bond threshold of the same materials used without an adhesive. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

An ultrastructural analysis of the epithelial-fiber interface (EFI) in primate lenses.

PubMed

Kuszak, J R; Novak, L A; Brown, H G

1995-11-01

The purpose of this study was to conduct a comprehensive ultrastructural analysis of the epithelial-fiber interface (EFI) in normal adult primate (Macaque nemestrina and fascicularis; 6-9 years old, n = 10) lenses. Scanning electron microscopy (SEM) was used to initially characterize the gross size, shape and three-dimensional organization of central zone (cz) epithelial cells and the anterior ends of elongating fibers beneath these cells. This fiducial information was essential to properly orient lens pieces in freeze fracture specimen carriers for the production of replicas with unambiguously identifiable EFI. Transmission electron microscopy (TEM) of replicas and thin-sectioned material were used to ultrastructurally analyse the cz EFI. TEM thin-sectioned material was also used to ultrastructurally analyse the pregerminative (pgz), germinative (gz) and transitional zone (tz) EFI. Correlative SEM and TEM of cz EFI components revealed that the apical membrane of both epithelial and elongating fiber cells were irregularly polygonal in shape, and aligned in parallel as smooth, concave-convex surfaces. However, whereas epithelial cell apical surfaces had minimal size variation, elongating fibers were larger and considerably variable in size. Quantitative analysis of > 10000 micron2 cz elongating fiber apical surfaces failed to detect any gap junctions defined in freeze fracture replicas as complementary aggregates of transmembrane proteins (connexons) conjoined across a narrowed extracellular space. However, a comparable frequency of vesicular events was noted in this region as quantified previously in adult and embryonic chick lens. Correlative TEM analysis > 1500 linear micrometers of thin-sectioned EFI from this region confirmed the presence of epithelial-epithelial gap junctions, elongating fiber-elongating fiber gap junctions, and an extreme paucity of epithelial-elongating fiber gap junctions. In contrast, TEM analysis of > 1000 linear micrometers of thin-sectioned pgz, gz and tz EFI, confirmed the presence of epithelial-epithelial gap junctions, elongating fiber-elongating fiber gap junctions, numerous epithelial-elongating fiber adherens junctions and a few epithelial-elongating fiber gap junctions. Thus, the results of this and previous quantitative morphological and physiological studies (electronic and dye coupling) demonstrate that there is limited coupling between cz epithelial cells and underlying elongating fibers. Furthermore, the absence of gap junctional plaques in cz EFI freeze-fracture replicas and either pentalaminar or septalaminar profiles in correlative thin-sections, suggests that this limited coupling could be mediated via isolated gap junction channels. However, the results of this and previous quantitative studies further show that a greater degree of coupling exists across the pgz, gz and tz regions of the EFI and that this coupling is likely to be mediated by gap junction plaques. Finally, this and other studies continue to demonstrate that transcytotic processes play a role in lens physiology at the EFI.

Projectile Motion Gets the Hose

ERIC Educational Resources Information Center

Goff, John Eric; Liyanage, Chinthaka

2011-01-01

Students take a weekly quiz in our introductory physics course. During the week in which material focused on projectile motion, we not-so-subtly suggested what problem the students would see on the quiz. The quiz problem was an almost exact replica of a homework problem we worked through in the class preceding the quiz. The goal of the problem is…

Bacterial-based Systems for Expression and Purification of Recombinant Lassa Virus Proteins of Immunological Relevance

DTIC Science & Technology

2008-06-06

sites. Abbreviations include: MBP gene (malE), MBP promoter (Ptac), philamentous phage origin of replication ( M13 ori), bacterial origin of replica...notwithstanding any other provision of law, no person shall be subject to a penalty for failing to comply with a collection of information if it does not display

War and Peace: Toys, Teachers, and Tots.

ERIC Educational Resources Information Center

Dodd, Arleen; And Others

War play is play with a toy that initiates violence or play that involves the imitation of war. War play can involve: (1) the use of toys based on television cartoon shows to imitate the action in the cartoons; (2) play with replicas of war paraphernalia or manipulatives shaped into guns; and (3) dramatic play. The negative effects on children…

Computing Relative Free Energies of Solvation Using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange

DTIC Science & Technology

2010-10-21

paper assess the reversible works needed to alchemi - cally change each molecule to the benzene core reference state. To automate the alchemical...the alchemi - cal free energies or reversible works, the TI procedure split the interval from the real state of the molecule at λ ) 0 to the reference

A Medieval Clock Made out of Simple Materials

ERIC Educational Resources Information Center

Danese, B.; Oss, S.

2008-01-01

A cheap replica of the verge-and-foliot clock has been built from simple materials. It is a didactic tool of great power for physics teaching at every stage of schooling, in particular at university level. An account is given of its construction and its working principles, together with motivated examples of a few activities. (Contains 3 tables…

PEER Reports

Science.gov Websites

our reports. To order b&w hard copies of 2011 PEER Reports and beyond: PEER no longer keeps copies . Reports are individually priced based on the length of the report. If you are interested in a color hard copy of any reports, contact Replica Digital Ink by email. To order b&w hard copies of PEER Reports

Virtual Worlds vs Books and Videos in History Education

ERIC Educational Resources Information Center

Ijaz, Kiran; Bogdanovych, Anton; Trescak, Tomas

2017-01-01

In this paper, we investigate an application of virtual reality and artificial intelligence (AI) as a technological combination that has a potential to improve the learning experience and engage with the modern generation of students. To address this need, we have created a virtual reality replica of one of humanity's first cities, the city of…

Flow Liner Slot Edge Replication Feasibility Study

NASA Technical Reports Server (NTRS)

Newman, John A.; Willard, Scott A.; Smith, Stephen W.; Piascik, Robert S.

2006-01-01

Surface replication has been proposed as a method for crack detection in space shuttle main engine flowliner slots. The results of a feasibility study show that examination of surface replicas with a scanning electron microscope can result in the detection of cracks as small as 0.005 inch, and surface flaws as small as 0.001 inch, for the flowliner material.

Quench studies of ILC cavities

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

Eremeev, Grigory; Geng, Rongli; Palczewski, Ari

2011-07-01

Quench limits accelerating gradient in SRF cavities to a gradient lower than theoretically expected for superconducting niobium. Identification of the quenching site with thermometry and OST, optical inspection, and replica of the culprit is an ongoing effort at Jefferson Lab aimed at better understanding of this limiting phenomenon. In this contribution we present our finding with several SRF cavities that were limited by quench.

How Different Media Affect Adolescents' Views of the Hero: Lessons from Amistad

ERIC Educational Resources Information Center

Friedland, Ellen S.; Phelps, Stephen; del Prado Hill, Pixita

2006-01-01

"Amistad," the story of a group of Mende people illegally brought to the United States from West Africa in 1839, was taught to a group of 90 eighth grade students. To learn about the "Amistad," these eighth graders visited a replica of the ship, read a nonfiction account of the Amistad story, and viewed the Steven Spielberg…

Silicon diatom frustules as nanostructured photoelectrodes.

PubMed

Chandrasekaran, Soundarrajan; Sweetman, Martin J; Kant, Krishna; Skinner, William; Losic, Dusan; Nann, Thomas; Voelcker, Nicolas H

2014-09-18

In the quest for solutions to meeting future energy demands, solar fuels play an important role. A particularly promising example is photocatalysis since even incremental improvements in performance in this process are bound to translate into significant cost benefits. Here, we report that semiconducting and high surface area 3D silicon replicas prepared from abundantly available diatom fossils sustain photocurrents and enable solar energy conversion.

Thin sectioning and surface replication of ice at low temperature.

USGS Publications Warehouse

Daley, M.A.; Kirby, S.H.

1984-01-01

We have developed a new technique for making thin sections and surface replicas of ice at temperatures well below 273d K. The ability to make thin sections without melting sample material is important in textural and microstructural studies of ice deformed at low temperatures because of annealing effects we have observed during conventional section making.-from Author

The Integration of Operations and Intelligence Getting Information to the Warfighter

DTIC Science & Technology

1997-03-01

strike missions in the Negev Desert against highly accurate replicas of the missile sites. On the day of the attack, Syrian airspace was scanned by E-2C...With F-15 and F-16 pilots flying combat air patrols, IAF F-4s armed with SHRIKE anti- radiation missiles, and F-16s loaded with standoff Maverick

Development, Implementation, and Analysis of Desktop-Scale Model Industrial Equipment and a Critical Thinking Rubric for Use in Chemical Engineering Education

ERIC Educational Resources Information Center

Golter, Paul B.

2011-01-01

In order to address some of the challenges facing engineering education, namely the demand that students be better prepared to practice professional as well as technical skills, we have developed an intervention consisting of equipment, assessments and a novel pedagogy. The equipment consists of desktop-scale replicas of common industrial…

Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase

DTIC Science & Technology

2012-08-30

drug resistance to two antiviral drugs, zanamivir and oseltamivir. We augmented molecular dynamics (MD) with Hamiltonian Replica Exchange and...conformations that are virtually identical to WT [10]. Molecular simulations that rigorously model the microscopic structure and thermodynamics PLOS...influenza neuraminidase (NA) that confer drug resistance to two antiviral drugs, zanamivir and oseltamivir. We augmented molecular dynamics (MD) with

Fabrication of cylindrical superhydrophobic microchannels by replicating lotus leaf structures on internal walls

NASA Astrophysics Data System (ADS)

Das, Ajit; Bhaumik, Soubhik Kumar

2018-04-01

Cylindrical superhydrophobic microchannels are fabricated by replicating lotus leaf structures on internal walls. The fabrication process comprises of three steps: the creation of a cylindrical mold of a glass rod (125 µm) with polystyrene films bearing negative imprints of lotus leaf (superhydrophobic) structures; casting polydimethylsiloxane (PDMS, Sylgard 184) over the mold; and solvent-assisted pulling off of the glass rod to leave a positive replica on the inner wall of the PDMS cast. The last crucial step is achieved through selective dissolution of the intermediate negative replica layer in the cylindrical mold without any swelling effect. The high fidelity of the replication process is confirmed through scanning electron microscope (SEM) imaging. The attained superhydrophobicity is assessed by comparing the dynamics of the advancing meniscus in the fabricated microchannels with that over a similarly fabricated smooth microchannel. Contact angle studies of the meniscus reveal a lower capillary effect and drag force experienced by the superhydrophobic microchannel compared to smooth ones. Studies based on velocity lead to a prediction of a drag reduction of 35%. A new avenue is thus opened up for microfabrication and flow analysis of closed superhydrophobic (SH) conduits in lab on chip and microfluidic applications.

Initial Binding of Ions to the Interhelical Loops of Divalent Ion Transporter CorA: Replica Exchange Molecular Dynamics Simulation Study

PubMed Central

Zhang, Tong; Mu, Yuguang

2012-01-01

Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg2+ ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg2+ ions with binding free energy −7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg2+ ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation. PMID:22952795

Gap junctions on hippocampal mossy fiber axons demonstrated by thin-section electron microscopy and freeze–fracture replica immunogold labeling

PubMed Central

Hamzei-Sichani, Farid; Kamasawa, Naomi; Janssen, William G. M.; Yasumura, Thomas; Davidson, Kimberly G. V.; Hof, Patrick R.; Wearne, Susan L.; Stewart, Mark G.; Young, Steven R.; Whittington, Miles A.; Rash, John E.; Traub, Roger D.

2007-01-01

Gap junctions have been postulated to exist between the axons of excitatory cortical neurons based on electrophysiological, modeling, and dye-coupling data. Here, we provide ultrastructural evidence for axoaxonic gap junctions in dentate granule cells. Using combined confocal laser scanning microscopy, thin-section transmission electron microscopy, and grid-mapped freeze–fracture replica immunogold labeling, 10 close appositions revealing axoaxonic gap junctions (≈30–70 nm in diameter) were found between pairs of mossy fiber axons (≈100–200 nm in diameter) in the stratum lucidum of the CA3b field of the rat ventral hippocampus, and one axonal gap junction (≈100 connexons) was found on a mossy fiber axon in the CA3c field of the rat dorsal hippocampus. Immunogold labeling with two sizes of gold beads revealed that connexin36 was present in that axonal gap junction. These ultrastructural data support computer modeling and in vitro electrophysiological data suggesting that axoaxonic gap junctions play an important role in the generation of very fast (>70 Hz) network oscillations and in the hypersynchronous electrical activity of epilepsy. PMID:17640909

Deconvolution of interferometric data using interior point iterative algorithms

NASA Astrophysics Data System (ADS)

Theys, C.; Lantéri, H.; Aime, C.

2016-09-01

We address the problem of deconvolution of astronomical images that could be obtained with future large interferometers in space. The presentation is made in two complementary parts. The first part gives an introduction to the image deconvolution with linear and nonlinear algorithms. The emphasis is made on nonlinear iterative algorithms that verify the constraints of non-negativity and constant flux. The Richardson-Lucy algorithm appears there as a special case for photon counting conditions. More generally, the algorithm published recently by Lanteri et al. (2015) is based on scale invariant divergences without assumption on the statistic model of the data. The two proposed algorithms are interior-point algorithms, the latter being more efficient in terms of speed of calculation. These algorithms are applied to the deconvolution of simulated images corresponding to an interferometric system of 16 diluted telescopes in space. Two non-redundant configurations, one disposed around a circle and the other on an hexagonal lattice, are compared for their effectiveness on a simple astronomical object. The comparison is made in the direct and Fourier spaces. Raw "dirty" images have many artifacts due to replicas of the original object. Linear methods cannot remove these replicas while iterative methods clearly show their efficacy in these examples.

Surface microstructures of daisy florets (Asteraceae) and characterization of their anisotropic wetting.

PubMed

Koch, Kerstin; Bennemann, Michael; Bohn, Holger F; Albach, Dirk C; Barthlott, Wilhelm

2013-09-01

The surface microstructures on ray florets of 62 species were characterized and compared with modern phylogenetic data of species affiliation in Asteraceae to determine sculptural patterns and their occurrence in the tribes of Asteraceae. Their wettability was studied to identify structural-induced droplet adhesion, which can be used for the development of artificial surfaces for water harvesting and passive surface water transport. The wettability was characterized by contact angle (CA) and tilt angle measurements, performed on fresh ray florets and their epoxy resin replica. The CAs on ray florets varied between 104° and 156°, but water droplets did not roll off when surface was tilted at 90°. Elongated cell structures and cuticle folding orientated in the same direction as the cell elongation caused capillary forces, leading to anisotropic wetting, with extension of water droplets along the length axis of epidermis cells. The strongest elongation of the droplets was also supported by a parallel, cell-overlapping cuticle striation. In artificial surfaces made of epoxy replica of ray florets, this effect was enhanced. The distribution of the identified four structural types exhibits a strong phylogenetic signal and allows the inference of an evolutionary trend in the modification of floret epidermal cells.

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

PubMed

Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam

2018-04-30

A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.

Contribution to the study of the vasculature of submandibular and sublingual glands and lymph nodes of rats by corrosion cast technique combined with scanning electron microscopy.

PubMed

Rossi-Schneider, Tíssiana Rachel; Verli, Flaviana Dornela; Yurgel, Liliane Soares; De Souza, Maria Antonieta Lopes; Cherubini, Karen

2008-10-01

The study of anatomical structures in their normal state allows the identification of pathological changes that can occur in them. Angiogenesis and the vasculature have been widely studied, mainly because of their association with the development of neoplasms. One of the methods applied for such purposes is the corrosion cast technique, which provides a copy of the vessels with normal as well as pathological structures. The replica of the vasculature provided by this technique allows the three-dimensional analysis of vessels by means of scanning electron microscopy. The aim of the present study was to demonstrate, by means of corrosion casts, the angioarchitecture of the submandibular and sublingual glands and lymph nodes. Scanning electron microscopy showed that the three structures have distinct vascular patterns. The corrosion cast technique can be employed in the study of the angioarchitecture of the submandibular and sublingual glands and lymph nodes, but requires specific precautions. The removal of the structures en bloc and the handling of the replicas with the aid of a stereoscopic magnifier reduce the risk of fractures. (c) 2008 Wiley-Liss, Inc.

Metainference: A Bayesian inference method for heterogeneous systems

PubMed Central

Bonomi, Massimiliano; Camilloni, Carlo; Cavalli, Andrea; Vendruscolo, Michele

2016-01-01

Modeling a complex system is almost invariably a challenging task. The incorporation of experimental observations can be used to improve the quality of a model and thus to obtain better predictions about the behavior of the corresponding system. This approach, however, is affected by a variety of different errors, especially when a system simultaneously populates an ensemble of different states and experimental data are measured as averages over such states. To address this problem, we present a Bayesian inference method, called “metainference,” that is able to deal with errors in experimental measurements and with experimental measurements averaged over multiple states. To achieve this goal, metainference models a finite sample of the distribution of models using a replica approach, in the spirit of the replica-averaging modeling based on the maximum entropy principle. To illustrate the method, we present its application to a heterogeneous model system and to the determination of an ensemble of structures corresponding to the thermal fluctuations of a protein molecule. Metainference thus provides an approach to modeling complex systems with heterogeneous components and interconverting between different states by taking into account all possible sources of errors. PMID:26844300

Effect of cross sectional geometry on PDMS micro peristaltic pump performance: comparison of SU-8 replica molding vs. micro injection molding.

PubMed

Graf, Neil J; Bowser, Michael T

2013-10-07

Two different fabrication methods were employed to fabricate micropumps with different cross-sectional channel geometries. The first was to fabricate rectangular cross-sectional microchannel geometries using the well known fabrication method of replica molding (REM). The second, and far less utilized fabrication technique, was to create microchannel molds using an in-house fabricated handheld micro injection molding apparatus. The injection mold apparatus was designed for use with elastomeric room temperature vulcanization (RTV) polymers, as opposed to most other injection molding machines, which are designed for use with thermoplastic polymers. The injection mold's bottom plate was used as a microchannel molding template. The molding template was created by threading a small-diameter wire (150 μm or less) through the injection mold's bottom plate, with subsequent adhesion and smoothing of a thin piece of aluminum foil over the wire-raised injection mold template. When molded against, the template produced a rounded/Gaussian-shaped PDMS microchannel. The design of the injection mold will be presented, along with a direct comparison for micropump performance metrics such as flow rate, valving characteristics, and maximum backpressures attainable for each of the respective micropump channel geometries.

Experiments with Coler magnetic current apparatus

NASA Astrophysics Data System (ADS)

Ludwig, T.

Experiments with a replica of the famous Coler "Magnetstromapparat" (magnetic current apparatus) were conducted. The replica was built at the same institute at the Technical University of Berlin where the original was tested by Prof. Kloss in 1925. The details of the setup will be presented in this paper. The investigation of the Coler device was done with modern methods. The output was measured with a digital multi meter (DMM) and a digital storage oscilloscope (DSO). The results of the measurements will be presented. Did Coler convert vacuum fluctuations via magnetic, electric and acoustic resonance into electricity? There is a strong connection between magnetism and quantum field radiation energy. The magnetic moment of the electron is in part an energy exchange with the radiation field. The energy output of the Coler apparatus is measured. Furthermore the dynamics of the ferromagnetic magnets that Coler reported as the working principle of his device was investigated with magnetic force microscopy (MFM) and the spectroscopy mode of an atomic force microscope (AFM). The magnetic and acoustic resonance was investigated with magnetic force microscopy (MFM). The connection between ZPE and magnetism will be discussed as well as the perspective of using magnetic systems as a means to convert vacuum fluctuations into usable electricity.